Opened 8 years ago

Closed 6 years ago

Last modified 6 years ago

#10508 closed enhancement (fixed)

Update ATLAS to stable version 3.10.1

Reported by: vbraun Owned by: tbd
Priority: major Milestone: sage-5.10
Component: packages: standard Keywords: ATLAS spkg
Cc: dimpase, fbissey, leif, kcrisman Merged in: sage-5.10.beta5
Authors: Volker Braun, Jeroen Demeyer, Jean-Pierre Flori Reviewers: Benjamin Jones, Karl-Dieter Crisman, Dmitrii Pasechnik, Georg Weber, François Bissey, John Palmieri, Volker Braun
Report Upstream: Reported upstream. No feedback yet. Work issues:
Branch: Commit:
Dependencies: #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415, #14344, #14465, #12832, #14617 Stopgaps:

Description (last modified by jdemeyer)

The new atlas release now builds netlib lapack itself, so the lapack tarball is now included in the ATLAS spkg.

  • Updated to newest upstream source, various patches are no longer required
  • SAGE_ATLAS_LIB=path now searches in path/libatlas.so instead of path/lib/libatlas.so so it works for people with atlas in /lib64, too.
  • Threading is now enabled by default
  • Flush before os.system (#13210)

Upstream has made some attempt at changing the layout of the shared libraries, which is now different from the static libraries. The atlas spkg contains a stub autoconf/libtools project that unpacks the static libraries and repacks them into equivalent shared libraries.

By default, ATLAS will now try twice to get timings and fail immediately if throttling is enabled. If auto-tuning fails build with SAGE_ATLAS_ARCH=fast, and if that fails with SAGE_ATLAS_ARCH=base. On x86, the fast and base targets are the new ATLAS generic targets x86SSE3 and x86SSE2/x86x87.

There is an upstream problem where compilation sometimes crashes during xextract because of a buffer overflow due to small fixed-sized buffers for filenames.

Updated spkg:

  1. http://boxen.math.washington.edu/home/jpflori/spkg/atlas-3.10.1.p0.spkg.

Apply

  1. 10508_root.patch to the SAGE_ROOT repository
  2. trac_10508_doctest.rebased.patch and trac_10508_update_atlas_docs.rebased.patch to the Sage repository.
  3. 10508_scripts.patch to local/bin.

Remove the lapack and blas packages.

Attachments (13)

trac_10508_update_atlas_docs.patch (5.0 KB) - added by vbraun 7 years ago.
Initial patch
trac_10508_doctest.patch (1.9 KB) - added by vbraun 6 years ago.
Updated patch
atlas-3.10.0.p1.ARMv7.native.log (11.6 KB) - added by Snark 6 years ago.
Log of compilation of atlas-3.10.0.p1 with SAGE_ATLAS_ARCH=ARMv7 on a native box
atlas-3.10.0.p1.ARMv7.qemu.log (12.7 KB) - added by Snark 6 years ago.
Log of compilation of atlas-3.10.0.p1 with SAGE_ATLAS_ARCH=ARMv7 in a qemu vm
atlas-3.10.0.p1.ARMv7.NEON.native.log (11.3 KB) - added by Snark 6 years ago.
Log of compilation of atlas-3.10.0.p1 with SAGE_ATLAS_ARCH=ARMv7,NEON on a real box
cvxopt-1.1.5.p1.diff (2.2 KB) - added by jpflori 6 years ago.
Rebased spkg diff, for review only.
trac_10508_doctest.rebased.patch (1.6 KB) - added by kini 6 years ago.
apply to $SAGE_ROOT/devel/sage
10508_root.patch (3.2 KB) - added by jdemeyer 6 years ago.
10508_scripts.patch (382 bytes) - added by jdemeyer 6 years ago.
compilers.patch (1.5 KB) - added by jpflori 6 years ago.
Use FC instead of sage_fortran and preserve compiler options.
trac_10508_update_atlas_docs.rebased.patch (4.5 KB) - added by jpflori 6 years ago.
thread.patch (4.8 KB) - added by jpflori 6 years ago.
Use leif's fix.
atlas-3.10.1.p0.diff (74.2 KB) - added by jdemeyer 6 years ago.
spkg diff 3.8.4.p1 -> 3.10.1.p0, except for the removal of old patches

Download all attachments as: .zip

Change History (550)

comment:1 Changed 8 years ago by vbraun

Note that you cannot just use sage -f atlas-3.9.32.spkg to update atlas only. Many other spkgs use blas/lapack and must be rebuilt. The easiest way is to do a separate Sage installation...

The cvxopt spkg needs to be updated to link correctly with this atlas release, see #10509.

comment:2 Changed 8 years ago by dimpase

  • Cc dimpase added

comment:3 Changed 8 years ago by dimpase

  • Status changed from new to needs_info

Does it mean that LAPACK spkg can be removed, too?

comment:4 Changed 8 years ago by vbraun

Yes, the lapack spkg can be removed.

I'm still trying to debug some issues with linbox...

comment:5 Changed 8 years ago by fbissey

  • Cc fbissey added

BLAS can also be removed if we go with this. f2c which was used before we got ATLAS to provide cblas by f2c-ing the BLAS package should also be removed (I think it listed in scipy's dependency only).

comment:6 follow-up: Changed 8 years ago by dimpase

on 32-bit x86 Linux (Debian squeeze) I get the following, when trying to install the spkg (applied the patches to a pristine Sage 4.6.1.alpha3):

...
make -j1 libatlas.so libptf77blas.so libf77blas.so \
                libptcblas.so libcblas.so liblapack.so
make[3]: Entering directory `/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/lib'
ld -melf_i386 -shared -soname /usr/local/src/sage/sage-4.6.1.alpha3/local/lib/libatlas.so -o libatlas.so \
           -rpath-link /usr/local/src/sage/sage-4.6.1.alpha3/local/lib \
           --whole-archive libatlas.a --no-whole-archive -lc -lm
make[3]: *** No rule to make target `libptf77blas.a', needed by `libptf77blas.so'.  Stop.
make[3]: Leaving directory `/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/at
las-3.9.32/ATLAS-build/lib'
make[2]: *** [ptshared] Error 2
make[2]: Leaving directory `/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/at
las-3.9.32/ATLAS-build/lib'
Configuration:
    SAGE_LOCAL: /usr/local/src/sage/sage-4.6.1.alpha3/local
    linker_Solaris?: False
    PPC?: False
    SPKG_DIR: /usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32
    linker_GNU?: True
    ld: GNU
    system: Linux
    Darwin?: False
    machine: i686
    fortran: gfortran
    Solaris?: False
    fortran_g95?: False
    bits: 32bit
    CYGWIN?: False
    SPARC?: False
    fortran_GNU?: True
    FreeBSD?: False
    32bit?: True
    Linux?: True
    64bit?: False
    Intel?: False
    processor: 

comment:7 in reply to: ↑ 6 Changed 8 years ago by dimpase

Replying to dimpase:

on 32-bit x86 Linux (Debian squeeze) I get the following, when trying to install the spkg (applied the patches to a pristine Sage 4.6.1.alpha3):

complete install.log is here: http://boxen.math.washington.edu/home/dima/tmp/install-alt3.9.log.gz

comment:8 follow-up: Changed 8 years ago by vbraun

Hi Dima,

I think the problem is

make[6]: Entering directory `/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/tune/sysinfo'
gcc -c -DL2SIZE=4194304 -I/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/include -I/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/../src//include -I/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/../src//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_CoreDuo -DATL_CPUMHZ=800 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632  -fomit-frame-pointer -O3 -mfpmath=387 -fPIC -m32 /usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/../src//tune/sysinfo/findNT.c
gcc -DL2SIZE=4194304 -I/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/include -I/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/../src//include -I/usr/local/src/sage/sage-4.6.1.alpha3/spkg/build/atlas-3.9.32/ATLAS-build/../src//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_CoreDuo -DATL_CPUMHZ=800 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632  -fomit-frame-pointer -O3 -mfpmath=387 -fPIC -m32 -o xfindNT findNT.o ATL_walltime.o -lm
/usr/lib/crt1.o: In function `_start':
(.text+0x18): undefined reference to `main'
collect2: ld returned 1 exit status
make[6]: *** [xfindNT] Error 1

This fails because ATL_NCPU is not set. Do you have a single-core processor? I guess the threaded libraries are not built in that case.

comment:9 in reply to: ↑ 8 ; follow-up: Changed 8 years ago by dimpase

Replying to vbraun:

This fails because ATL_NCPU is not set. Do you have a single-core processor? I guess the threaded libraries are not built in that case.

yes, it's single-core. An old Pentium M. (Atlas 3.8 spkg does not build on it, at all)

comment:10 follow-up: Changed 8 years ago by vbraun

I changed the spkg-install to make only single-threaded shared libraries if necessary. Should work now.

For simplicity, I made spkgs for cvxopts and sage_scripts. So you need to add

http://www.stp.dias.ie/~vbraun/Sage/spkg/atlas-3.9.32.spkg http://www.stp.dias.ie/~vbraun/Sage/spkg/cvxopt-1.1.3.p0.spkg http://www.stp.dias.ie/~vbraun/Sage/spkg/sage_scripts-4.6.1.alpha3.p0.spkg

to $SAGE_ROOT/spkg/standard and then

  • replace spkg/install with the attached version (Note that sage_scripts overwrites this file during installation, aargh)
  • replace spkg/standard/deps with the attached version.

I'm still having doctest errors with linbox...

comment:11 in reply to: ↑ 10 Changed 8 years ago by dimpase

Replying to vbraun:

I changed the spkg-install to make only single-threaded shared libraries if necessary. Should work now.

It builds OK, but then testlong gives quite a bit of failures:

The following tests failed:
        sage -t  -long -force_lib "devel/sage/doc/en/bordeaux_2008/elliptic_curves.rst"
        sage -t  -long -force_lib "devel/sage/sage/modular/modsym/space.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/modsym/tests.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/modsym/subspace.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/modsym/ambient.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/modform/space.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/modform/element.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/modform/ambient.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/hecke/submodule.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/abvar/abvar.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/abvar/torsion_subgroup.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/abvar/cuspidal_subgroup.py"
        sage -t  -long -force_lib "devel/sage/sage/modular/abvar/finite_subgroup.py"
        sage -t  -long -force_lib "devel/sage/sage/matrix/matrix_integer_dense.pyx"
        sage -t  -long -force_lib "devel/sage/sage/matrix/matrix_integer_dense_hnf.py"
        sage -t  -long -force_lib "devel/sage/sage/rings/qqbar.py"
        sage -t  -long -force_lib "devel/sage/sage/finance/time_series.pyx"
        sage -t  -long -force_lib "devel/sage/sage/schemes/elliptic_curves/padic_lseries.py"
        sage -t  -long -force_lib "devel/sage/sage/schemes/elliptic_curves/ell_modular_symbols.py"
        sage -t  -long -force_lib "devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py"
        sage -t  -long -force_lib "devel/sage/sage/schemes/elliptic_curves/sha_tate.py"
Total time for all tests: 30045.4 seconds

I do not know how many of them are Atlas related, though. The log is here: http://boxen.math.washington.edu/home/dima/tmp/testlong-atl3.9.log

comment:12 follow-up: Changed 8 years ago by fbissey

A lot of it is probably related. Was this a build from scratch? linbox calls seem to be particularly affected, there are a lot of failures in that path: sage.matrix.matrix_integer_dense.Matrix_integer_dense._charpoly_linbox stuff going through: sage.matrix.matrix_rational_dense.Matrix_rational_dense.right_kernel is also affected and that smells like atlas at work too.

I must say we have observed a number of failures related to ATLAS-3.9.23 in sage-on-gentoo: https://github.com/cschwan/sage-on-gentoo/issues#issue/3 you have failure there too but not due to iml/ATLAS as far as I can see. https://github.com/cschwan/sage-on-gentoo/issues#issue/6 more subtle. I see you have the failure with devel/sage/sage/finance/time_series.pyx you may want to look the comment I wrote about it in the section "known test failures for Sage on Gentoo": https://github.com/cschwan/sage-on-gentoo/wiki/Known-test-failures note that sage-on-gentoo can use (c)blas-reference, ATLAS or gsl-cblas or some combinations - in fact amd and intel libraries could in principle be used but no one I know has tried. http://www.gentoo.org/proj/en/science/blas-lapack.xml

Not sure about the SIGFPE, it could come from a result rounded to 0 or the like.

comment:13 in reply to: ↑ 12 Changed 8 years ago by dimpase

Replying to fbissey:

A lot of it is probably related. Was this a build from scratch?

yes, it's a build from scratch, on the same machine (old Pentium M) as already discussed above.

linbox calls seem to be particularly affected, there are a lot of failures in that path:

I wonder if these are Atlas bugs, or Linbox bugs...

One should try an OSX build.

comment:14 follow-up: Changed 8 years ago by fbissey

why OS X in particular? I could do that but not before the 5th of January, when my university reopens. Ok I could do it before that but I'll enjoy the break a little bit more :)

comment:15 in reply to: ↑ 14 ; follow-up: Changed 8 years ago by dimpase

Replying to fbissey:

why OS X in particular? I could do that but not before the 5th of January, when my university reopens. Ok I could do it before that but I'll enjoy the break a little bit more :)

Or does OSX remain disabled for Atlas, i.e. it's not built?

comment:16 in reply to: ↑ 15 Changed 8 years ago by fbissey

Replying to dimpase:

Replying to fbissey:

why OS X in particular? I could do that but not before the 5th of January, when my university reopens. Ok I could do it before that but I'll enjoy the break a little bit more :)

Or does OSX remain disabled for Atlas, i.e. it's not built?

I had forgotten about that. I checked the spkg and ATLAS is not built on cygwin and OS X. So it makes sense.

comment:17 follow-up: Changed 8 years ago by vbraun

I get the same doctest errors. Most of them are linbox related. The SIGFPE is from converting a NAN into a GMP integer, but I haven't gotten to the root of the NAN yet. In trying to debug this I've noticed that there are a bunch of valgrind warnings in the linbox code path we are using. I've asked some more specific questions on the linbox-use mailinglist:

https://groups.google.com/d/topic/linbox-use/N3QNNOQuTAc/discussion

But so far no final conclusion.

comment:18 in reply to: ↑ 9 ; follow-up: Changed 8 years ago by fbissey

Replying to dimpase:

Replying to vbraun:

This fails because ATL_NCPU is not set. Do you have a single-core processor? I guess the threaded libraries are not built in that case.

yes, it's single-core. An old Pentium M. (Atlas 3.8 spkg does not build on it, at all)

I notice you say it is a Pentium M, yet ATLAS is compiling things with the assumption that it is a coreduo: -DATL_ARCH_CoreDuo -DATL_CPUMHZ=800 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632 I am guessing the speed is right but the rest is not. Was your successful build using these parameters? I had in one instance a non-working ATLAS because the cpu type was misdetected (wanted to use sse3 when it didn't have them). The build was curiously successful but the library was unusable.

comment:19 in reply to: ↑ 18 Changed 8 years ago by dimpase

Replying to fbissey:

Replying to dimpase:

Replying to vbraun:

This fails because ATL_NCPU is not set. Do you have a single-core processor? I guess the threaded libraries are not built in that case.

yes, it's single-core. An old Pentium M. (Atlas 3.8 spkg does not build on it, at all)

I notice you say it is a Pentium M, yet ATLAS is compiling things with the assumption that it is a coreduo: -DATL_ARCH_CoreDuo -DATL_CPUMHZ=800 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632 I am guessing the speed is right but the rest is not. Was your successful build using these parameters? I had in one instance a non-working ATLAS because the cpu type was misdetected (wanted to use sse3 when it didn't have them). The build was curiously successful but the library was unusable.

The processor is Pentium M Banias 1.1GHz, http://ark.intel.com/Product.aspx?id=27600 (according to GotoBlas? installation procedure :-))

The Atlas built is not totally useless, it works for many doctests. By the way, 3.8 also thinks it's a CoreDuo?. And it works. I saw somewhere a note that it's OK.

comment:20 in reply to: ↑ 17 Changed 8 years ago by fbissey

Replying to vbraun:

I get the same doctest errors. Most of them are linbox related. The SIGFPE is from converting a NAN into a GMP integer, but I haven't gotten to the root of the NAN yet. In trying to debug this I've noticed that there are a bunch of valgrind warnings in the linbox code path we are using. I've asked some more specific questions on the linbox-use mailinglist:

https://groups.google.com/d/topic/linbox-use/N3QNNOQuTAc/discussion

But so far no final conclusion.

Converting a NAN into a GMP integer is exactly what was happening in https://github.com/cschwan/sage-on-gentoo/issues/3 and it didn't happen when using gslcblas. I will do a full build of sage-on-gentoo with 3.9.40 (or 41) and see if I can see anything.

comment:21 Changed 8 years ago by fbissey

Yuck, still got problems leading to linbox, I got the ones leading to iml too. Note that using another cblas like gslcblas/openblas/reference(netlib) all these problems disappear which seem to indicate that there is something going on in ATLAS itself or that all the others gets it wrong (I realise that on a stock sage you may have trouble compiling iml with anything else than ATLAS, it requires some patching to the configure script to be able to do so).

comment:23 Changed 8 years ago by fbissey

I have 3.9.41 now, the only difference was it compiled faster because there was tuning for my cpu. But we could investigate 3.8.4. Thanks for pointing it is out, some of us (me at least) didn't think it would ever happen. We may have a stable ATLAS supporting newer CPUs at last, and it looks like I could test it quickly.

comment:24 Changed 8 years ago by fbissey

OK 3.8.4 doesn't suffer from any of the drawbacks that are apparent in 3.9.23+.

The big drawback is that it doesn't build lapack nicely on its own, provided we point to the sources like the latest 3.9.xx do. That means spkg-install would need a little bit more work.

Opinions?

comment:25 Changed 8 years ago by vbraun

Can we keep this ticket focused on the development version of atlas and discuss the stable ATLAS on #10226? I updated the spkg on the latter ticket to the new stable ATLAS release.

comment:26 Changed 8 years ago by fbissey

Sure. My current opinion and that's something I am pushing to sage-on-gentoo users is to avoid ATLAS 3.9.xx for the time being. It is possible that ATLAS-3.9.xx is doing something permissible that iml and linbox are not ready to catch. My line of thought is that I remember that some algorithm in iml takes the inverse of a result returned by cblas. If the result is 0 instead of a small value we may have our NaN, more likely some result from ATLAS is a NaN.

comment:27 Changed 8 years ago by leif

  • Cc leif added

Note that you can copy updated spkgs into spkg/standard/ and then do

env SAGE_UPGRADING=yes make build

to rebuild all dependent packages.

(We should perhaps add make targets for that to the top-level Makefile and document them in the Developer's Guide, as this is currently just a side-effect of the effort to make upgrading work.)

If you at the same time need to apply patches to the Sage library, things get a bit more complicated, as e.g. Sage switches to the main branch before reinstalling the Sage library package. One safe way is to first apply the patches, create a new sage-x.y.z-whatever spkg (with devel/sage/spkg-dist) and replace the one in spkg/standard/ with that one (or at least make sure newest_version will pick up the right one).

Note that the extension modules' dependencies in module_list.py are currently far from complete. #8664 adds some in a generic way by adding them automatically in setup.py, i.e. lets modules also depend on the headers of the libraries they use (which [only] works if the headers' mtimes get modified / updated during installation of their corresponding libraries). The dumb alternative is to run sage -ba-force after an "upgrade" process.

comment:28 follow-up: Changed 7 years ago by leif

Ping.

comment:29 in reply to: ↑ 28 Changed 7 years ago by dimpase

Replying to leif:

Ping.

just fired up my vintage MacOSX 32-bit Powerbbok PPC... Will know more in, like, 12 hours...

comment:30 follow-up: Changed 7 years ago by fbissey

Several issues:

  • atlas is now at version 3.9.49 (last I checked)
  • I have reports of it failling to build on some old opterons
  • @dimpase: do you need atlas on OS X ppc? Don't you use vectorize like the other OS X?
  • I haven't checked but I am quite sure from other reports that cblas_dgem{m,v} is still buggy (someone posted that R built against that Atlas lapack was giving them trouble and R upstream pointed the finger to Atlas).

comment:31 in reply to: ↑ 30 Changed 7 years ago by dimpase

Replying to fbissey:

Several issues:

  • atlas is now at version 3.9.49 (last I checked)
  • I have reports of it failling to build on some old opterons

so what? I have a 5-year old 32-bit Intel laptop on which the sage-current Atlas does not build.

  • @dimpase: do you need atlas on OS X ppc? Don't you use vectorize like the other OS X?

indeed. But that's for #10509. Oops, was posting on the wrong ticket...

comment:32 Changed 7 years ago by kcrisman

With respect to comment:33:ticket:12011, should this be closed as a dup of #12011?

comment:33 Changed 7 years ago by dimpase

  • Status changed from needs_info to needs_review

propose to close this one and refer to #12011 the the continuation of the upgrade work.

comment:34 Changed 7 years ago by vbraun

  • Milestone changed from sage-5.0 to sage-duplicate/invalid/wontfix
  • Status changed from needs_review to positive_review

I would say #12011 is a duplicate of my ticket but oh well ;-)

comment:35 Changed 7 years ago by jdemeyer

  • Authors set to Volker Braun
  • Description modified (diff)
  • Milestone changed from sage-duplicate/invalid/wontfix to sage-5.0
  • Status changed from positive_review to needs_work
  • Summary changed from Update ATLAS to version 3.9.32 to Update ATLAS to version 3.9.x

Seems like #12011 isn't a duplicate after all...

comment:36 Changed 7 years ago by vbraun

  • Description modified (diff)

comment:37 Changed 7 years ago by vbraun

  • Description modified (diff)

comment:38 Changed 7 years ago by jdemeyer

  • Milestone changed from sage-5.1 to sage-5.3

Obviously, the patches to spkg/install and spkg/standard/deps must be rebased.

comment:39 Changed 7 years ago by jdemeyer

It makes a lot more sense to me to put the LAPACK tarball at the top level of the spkg instead of in patches/.

patches/ATLAS-lib/autom4te.cache should be removed.

comment:40 Changed 7 years ago by jdemeyer

I don't like using assert for control flow, because that's not what it's meant for.

Why not replace those by (see #13210)

if rc != 0:
    print "Error: foo"
    sys.exit(rc)

comment:41 Changed 7 years ago by jdemeyer

There is something wrong with the history in SPKG.txt (atlas-3.8.4 is completely missing and there is atlas-3.9.68 for #12011 which never got merged)

comment:42 follow-up: Changed 7 years ago by vbraun

I don't have any strong opinion on where to put the lapack tarball, except that our convention of only allowing a single src/ directory is shortsighted.

Note that I'm not using assertions for control flow, i.e. I'm not using

  try:
    <command>
  except AssertionError:
    <alternative>

Note that you could theoretically also catch the SystemExit exception, so sys.exit() isn't different from assert in that regard. I'm only using assertions to ensure the following contract holds: spkg-install completes successfully only if the relevant atlas configure/make completed with rc==0

I'll replace the asserts by something that returns rc as exit code, though.

comment:43 Changed 7 years ago by vbraun

  • Description modified (diff)

comment:44 in reply to: ↑ 42 Changed 7 years ago by jdemeyer

Replying to vbraun:

I'm only using assertions to ensure the following contract holds: spkg-install completes successfully only if the relevant atlas configure/make completed with rc==0

I think (IMHO but I might be wrong) that assertions should be used only in a situation where an assertion being false indicates a bug in the program. If rc != 0 in spkg-install, that is an ordinary error condition, not a bug in the spkg-install script.

comment:45 follow-up: Changed 7 years ago by jdemeyer

Starting from sage-5.1, I get one doctest failure:

File "/release/merger/sage-5.1-atlas/devel/sage-main/sage/rings/polynomial/polynomial_element.pyx", line 1039:
    sage: parent(poly)([ 0.0 if abs(c)<=1e-14 else c for c in poly.coeffs() ])
Expected:
    1.0
Got:
    1.02140518266e-14*x^2 + 1.0

comment:46 in reply to: ↑ 45 Changed 7 years ago by dimpase

Replying to jdemeyer:

Starting from sage-5.1, I get one doctest failure:

     sage: parent(poly)([ 0.0 if abs(c)<=1e-14 else c for c in poly.coeffs() ])

it's most probably not at Atlas problem, but rather that 1e-14 (any solid rationale behind this choice? I guess not.) needs to be adjusted.

comment:47 Changed 7 years ago by benjaminfjones

  • Reviewers set to Benjamin Jones

Testing in sage-5.1.rc1 on x86_64 debian Linux:

$ uname -a
Linux sage 2.6.32 #1 SMP Fri Sep 2 21:08:57 CDT 2011 x86_64 GNU/Linux

$ head -18 /proc/cpuinfo 
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 44
model name      : Intel(R) Xeon(R) CPU           X5690  @ 3.47GHz
stepping        : 2
cpu MHz         : 3465.790
cache size      : 12288 KB
fpu             : yes
fpu_exception   : yes
cpuid level     : 11
wp              : yes
flags           : fpu de tsc msr pae cx8 sep cmov pat clflush mmx fxsr sse sse2 ss ht syscall nx lm constant_tsc rep_good aperfmperf pni pclmulqdq ssse3 cx16 sse4_1 sse4_2 popcnt aes hypervisor lahf_lm ida arat
bogomips        : 6931.58
clflush size    : 64
cache_alignment : 64
address sizes   : 40 bits physical, 48 bits virtual
power management:

BEFORE new ATLAS spkg

sage -t  "devel/sage-main/sage/modular/modsym/ambient.py"   
         [11.6 s]

sage -t  "devel/sage-main/sage/modular/hecke/ambient_module.py"
         [4.2 s]

sage -t  "devel/sage-main/sage/modular/hecke/hecke_operator.py"
         [3.0 s]

AFTER new spkg

  1. untar'd fresh sage-5.1.rc1
  2. replaced atlas-3.8.4.p1.spkg with atlas-3.9.85.spkg
  3. make build

SPKG build log: http://sage.math.washington.edu/home/bjones/atlas-3.9.85.log

Build atlas-3.9.85

real    11m18.595s
user    11m15.906s
sys     2m56.099s
Successfully installed atlas-3.9.85

Tests

sage -t  "devel/sage-main/sage/modular/modsym/ambient.py"   
         [11.6 s]

sage -t  "devel/sage-main/sage/modular/hecke/ambient_module.py"
         [4.2 s]

sage -t  "devel/sage-main/sage/modular/hecke/hecke_operator.py"
         [3.1 s]

All tests

$ make ptestlong
...
All tests passed!
Total time for all tests: 1282.1 seconds

comment:48 Changed 7 years ago by fbissey

3.10.0 has just been released a few hours ago. Do we try to go for it? Like Jeroen remarked there may be tolerance issues depending on the hardware. I know I have one when using openblas instead of ATLAS.

comment:49 Changed 7 years ago by vbraun

  • Description modified (diff)
  • Status changed from needs_work to needs_review
  • Summary changed from Update ATLAS to version 3.9.x to Update ATLAS to stable version 3.10

comment:50 follow-up: Changed 7 years ago by vbraun

The new spkg will attempt to build on OSX if SAGE_ATLAS_ARCH is set. Untested, but a start.

I also am planning to allow SAGE_ATLAS_LIB=system and use ldconfig -p to get the system atlas, if available. Though perhaps we should do that in a later version. This spkg seems to fix some build issues that people reported on the sage mailinglists so it might be good to get it in sooner rather than later.

comment:51 in reply to: ↑ 50 Changed 7 years ago by jdemeyer

Replying to vbraun:

so it might be good to get it in sooner rather than later.

+1, let's not worry now about changing the working of SAGE_ATLAS_LIB.

comment:52 Changed 7 years ago by jdemeyer

  • Dependencies set to sage-5.2.beta0

comment:53 Changed 7 years ago by jdemeyer

  • Description modified (diff)

comment:54 Changed 7 years ago by jdemeyer

  • Description modified (diff)

comment:55 Changed 7 years ago by jdemeyer

In spkg-install, I find it confusing that you have a function build() which calls configure() and make_atlas().

I would get rid of build() and simply call configure() and make_atlas() directly.

comment:56 Changed 7 years ago by jdemeyer

  • Status changed from needs_review to needs_work

About SAGE_FAT_BINARY: at one point you are checking

os.environ.has_key('SAGE_FAT_BINARY')

and at another you are checking

os.environ.get('SAGE_FAT_BINARY', 'no') == 'yes' and conf['Intel?']

I think the correct check is

os.environ.get('SAGE_FAT_BINARY', 'no') == 'yes'

"SAGE_FAT_BINARY" has evolved to mean "build a generic binary on any processor", so it's not Intel specific anymore. Just call configure_base().

Last edited 7 years ago by jdemeyer (previous) (diff)

comment:57 Changed 7 years ago by jdemeyer

Somebody needs to review 10508_doctest.patch

comment:58 Changed 7 years ago by jdemeyer

Detail: in system_with_flush(), your print command should not have a space after "Running". The space is automatically added by print.

comment:59 Changed 7 years ago by vbraun

Updated spkg to remove the space and make the SAGE_FAT_BINARY check uniform.

I'm fine with the doctests patch...

comment:60 Changed 7 years ago by vbraun

I'm always calling build() except in one place where I want to allow configure() to fail (because throttling is enabled).

comment:61 Changed 7 years ago by jdemeyer

Is this expected? Compare the build time on arando (Ubuntu 12.04 i386):

real    104m44.021s
user    97m25.753s
sys     1m18.157s
Successfully installed atlas-3.8.4.p1
real    259m50.222s
user    233m21.879s
sys     7m38.405s
Successfully installed atlas-3.10.0

comment:62 Changed 7 years ago by vbraun

  • Status changed from needs_work to needs_review

I've noticed before that the build time for the "generic" binary is rather long. Its not entirely generic, it is still doing timing for cache edges. But the result will be a working library, it won't probe funky asm implementations that other CPUs might not support. I'll ask on the ATLAS mailinglist for clarification.

comment:63 follow-up: Changed 7 years ago by jdemeyer

Timing on x86_64 with SAGE_FAT_BINARY=yes on sage.math:

real    139m50.733s
user    134m30.710s
sys     7m12.390s
Successfully installed atlas-3.8.4.p1
real    350m5.662s
user    330m23.460s
sys     22m1.010s
Successfully installed atlas-3.10.0

Why does the new ATLAS take so much longer to build than the old one?

comment:64 in reply to: ↑ 63 ; follow-up: Changed 7 years ago by leif

Replying to jdemeyer:

Timing on x86_64 with SAGE_FAT_BINARY=yes on sage.math:

real    139m50.733s
user    134m30.710s
sys     7m12.390s
Successfully installed atlas-3.8.4.p1
real    350m5.662s
user    330m23.460s
sys     22m1.010s
Successfully installed atlas-3.10.0

Why does the new ATLAS take so much longer to build than the old one?

I can beat that:

Finished installing shared ATLAS library.

real	821m14.881s
user	739m58.560s
sys	58m23.440s
Successfully installed atlas-3.10.0

(That's with sage -f ... on an otherwise idle machine, an AMD Fusion E-450 running Ubuntu 10.04.4 LTS x86_64.)

It took far more time than building all of Sage [in parallel, on that dual-core CPU], including the old ATLAS spkg. I currently have no figures for a separate ATLAS 3.8.4 build, but the timings from previous parallel Sage builds on that machine vary between

real	214m52.096s
user	175m5.390s
sys	9m56.210s
Successfully installed atlas-3.8.4.p1

and

real	256m32.949s
user	217m30.760s
sys	10m31.050s
Successfully installed atlas-3.8.4.p1

(The LAPACK and BLAS spkg build times in these builds are a few minutes and less than one minute [wall time], respectively.)

I was actually hoping ATLAS 3.9.x / 3.10 meanwhile "knows" these AMD CPUs and therefore builds at least a bit faster...

comment:65 Changed 7 years ago by leif

FWIW, ptestlong passed (after rebuilding all dependent packages) with Sage 5.2.beta0 (without applying the doctest patch).

comment:66 Changed 7 years ago by fbissey

We have noticed the building time increase in Gentoo as well. At 3.9.82 I think. Apparently they have changed how they detect the compiler and that's what causing the spike. But it seem fixed in 3.10.0 unless we are carrying a specific patch in Gentoo

     Fri Jun 29 13:42:08 2012 >>> sci-libs/atlas-3.9.80
       merge time: 8 minutes and 4 seconds.

     Wed Jul  4 14:56:21 2012 >>> sci-libs/atlas-3.9.82
       merge time: 3 hours, 54 minutes and 30 seconds.

     Wed Jul 11 11:11:23 2012 >>> sci-libs/atlas-3.10.0
       merge time: 8 minutes and 34 seconds.

comment:67 Changed 7 years ago by vbraun

If I set SAGE_ATLAS_ARCH=Corei2,AVX,SSE3,SSE2,SSE1 then I can also compile atlas-3.10.0 in about 10 minutes. The issue is only with the "generic" archdefs, which seem to be not sufficiently specialzied. I've raised this issue on the ATLAS mailinglist.

comment:68 Changed 7 years ago by vbraun

The updated atlas spkg also installs a script atlas-config in $SAGE_LOCAL/bin which can be used to compute new architectural defaults. I need somebody on Linux i386 to first install the new spkg and then run

SAGE_FAT_BINARY=yes atlas-config --archdef

to grind out the archdefs for the i386 "generic" target. I'm currently doing this for x86_64, but I don't have a i386 machine. This will use sudo to turn off CPU throttling so you need to be a sudoer.

[vbraun@volker-desktop sage-5.2.beta1]$ ./local/bin/atlas-config --help
usage: atlas-config [-h] [--unthrottle PID] [--archdef]

(Re-)Build ATLAS (http://math-atlas.sourceforge.net) according to the
SAGE_ATLAS_ARCH environment variable

optional arguments:
  -h, --help        show this help message and exit
  --unthrottle PID  switch CPU throttling off until PID finishes
  --archdef         build archdef tarball and save it to the current directory

comment:69 follow-up: Changed 7 years ago by vbraun

I've updated the spkg with new 64-bit generic archdefs, this now builds in about 10 mins.

comment:70 in reply to: ↑ 69 Changed 7 years ago by leif

Replying to vbraun:

I've updated the spkg with new 64-bit generic archdefs, this now builds in about 10 mins.

md5sum?

I incidentally just downloaded some new version (163f090f18bb8616e93617677a644cd8) and triggered a full build from scratch.

comment:71 Changed 7 years ago by vbraun

The newest version is 8a16c9d39add1c6c3f37e13986e2a3cc and thats whats linked in the ticket.

comment:72 Changed 7 years ago by vbraun

The new version d33e9114156d8373fa61f957b379e029 changes the "fast" 64-bit archdef to P4E64SSE3.

It turns out that there are no 64-bit generic archdefs, which might have been one reason for why ATLAS was slow to compile. The SPKG uses the existing 32-bit archdefs or the 64-bit one that I made. On x86 the spkg should produce a working ATLAS library within 10-30 mins, and only go through the tuning process if either

  • CPU throttling is disabled (scaling_governor=performance, needs root), or
  • SAGE_ATLAS_ARCH is explicitly set to something different from "base" / "fast".

comment:73 follow-up: Changed 7 years ago by vbraun

PS: Surprisingly enough, the new ATLAS spkg actually compiled on OSX (bsd.math)! If you want to try yourself just set SAGE_ATLAS_ARCH="base" to force building on OSX.

comment:74 in reply to: ↑ 73 Changed 7 years ago by benjaminfjones

Replying to vbraun:

PS: Surprisingly enough, the new ATLAS spkg actually compiled on OSX (bsd.math)! If you want to try yourself just set SAGE_ATLAS_ARCH="base" to force building on OSX.

Very cool. I just got ATLAS to build on my OS X 10.6.8 machine setting SAGE_ATLAS_ARCH=Corei2. Running long tests now.

comment:75 follow-up: Changed 7 years ago by benjaminfjones

Update: ATLAS-3.10.0 built successfully on my OS X 10.6.8 machine with SAGE_ATLAS_ARCH=Corei2, the build took approx. 16 mins. The build log is at http://sage.math.washington.edu/home/bjones/atlas-3.10.0.log. Sage passes all make ptestlong tests. The spkg looks very good to me. I'd give this a positive review, but maybe it should be tested by a few other reviewers on other platforms first.

comment:76 in reply to: ↑ 75 Changed 7 years ago by dimpase

Replying to benjaminfjones:

Update: ATLAS-3.10.0 built successfully on my OS X 10.6.8 machine with SAGE_ATLAS_ARCH=Corei2, the build took approx. 16 mins. The build log is at http://sage.math.washington.edu/home/bjones/atlas-3.10.0.log. Sage passes all make ptestlong tests. The spkg looks very good to me. I'd give this a positive review, but maybe it should be tested by a few other reviewers on other platforms first.

I've built it successfully on OS X 10.6.8 (with Core2 Duo) and setting SAGE_ATLAS_ARCH="base".

comment:77 Changed 7 years ago by leif

Well, there's at least room for nitpicking (a couple of typos and some inconsistencies as well as superfluous code in spkg-install and probably configuration.py, don't recall)... I'll maybe take a look at it again tomorrow, and probably provide a patch (provided Volker doesn't plan to make further major changes to these files).


How about also installing a user script for convenience to save the built ATLAS libraries to another place (for later use with SAGE_ATLAS_LIB)?

Regarding the mentioned excessive tuning times, I also wonder whether we should use something like SAGE_ATLAS_ARCH=fast (or base) by default, i.e., only do self-tuning if the user explicitly asks for it in some way. I guess the Sage Installation Guide needs to get updated anyway w.r.t. ATLAS and environment variables.

comment:78 Changed 7 years ago by leif

The root repo patch should get rebased for Sage 5.2.rc0.

comment:79 Changed 7 years ago by jhpalmieri

On hawk (OpenSolaris):

DONE configure                                                                                     
Finished configuring ATLAS.                                                                        
Running make -j1                                                                                   
make[2]: Entering directory `/export/home/palmieri/testing/ATLAS/sage-5.2.rc0/spkg/build/atlas-3.1\
0.0/ATLAS-build'                                                                                   
make[2]: warning: -jN forced in submake: disabling jobserver mode.                                 
make -j1 -f Make.top build                                                                         
make[3]: Entering directory `/export/home/palmieri/testing/ATLAS/sage-5.2.rc0/spkg/build/atlas-3.1\
0.0/ATLAS-build'                                                                                   
Make.top:1: Make.inc: No such file or directory                                                    
Make.top:325: warning: overriding commands for target `/AtlasTest'                                 
Make.top:76: warning: ignoring old commands for target `/AtlasTest'                                
make[3]: *** No rule to make target `Make.inc'.  Stop.                                             
make[3]: Leaving directory `/export/home/palmieri/testing/ATLAS/sage-5.2.rc0/spkg/build/atlas-3.10\
.0/ATLAS-build'                                                                                    
make[2]: *** [build] Error 2                                                                       
make[2]: Leaving directory `/export/home/palmieri/testing/ATLAS/sage-5.2.rc0/spkg/build/atlas-3.10\
.0/ATLAS-build'                                                                                    
------------------------------------------------------------                                       
  File "./spkg-install", line 478, in <module>                                                     
    assert_success(rc, bad='Failed to build ATLAS.', good='Finished building ATLAS core.')         
  File "./spkg-install", line 74, in assert_success                                                
    traceback.print_stack(file=sys.stdout)                                                         
------------------------------------------------------------                                       
Error:  Failed to build ATLAS.                                                                     
                                                                                                   
real    4m10.778s                                                                                  
user    0m7.766s                                                                                   
sys     0m8.391s                                                                                   
Successfully installed atlas-3.10.0                                                                
Deleting temporary build directory                                                                 
/export/home/palmieri/testing/ATLAS/sage-5.2.rc0/spkg/build/atlas-3.10.0                           
Finished installing atlas-3.10.0.spkg 

I don't know why it's not building, but it shouldn't exit saying "Successfully installed atlas-3.10.0". I added a print statement, and "rc" is 512. The documentation for sys.exit says that for the argument, "Most systems require it to be in the range 0-127, and produce undefined results otherwise." We could instead do this:

  • spkg-install

    diff --git a/spkg-install b/spkg-install
    a b def assert_success(rc, good=None, bad=No 
    7474    traceback.print_stack(file=sys.stdout)
    7575    print '-'*60
    7676    if bad is not None:
    77         print 'Error: ', bad
    78     sys.exit(rc)
     77        sys.exit('Error: %s' % bad)
     78    sys.exit(1)
    7979
    8080######################################################################
    8181### Skip building ATLAS on specific systems

comment:80 Changed 7 years ago by jhpalmieri

  • Status changed from needs_review to needs_work

comment:81 follow-up: Changed 7 years ago by leif

On Ubuntu 10.04.4 LTS x86_64 (AMD E-450), with Sage 5.2.rc0 and SAGE_ATLAS_ARCH=fast I get:

...

Building using specific architecture.
Fast configuration on Intel x86_64 compatible CPUs.
Running configure with arch = P4E64SSE3, isa extensions ('SSE3', 'SSE2', 'SSE1'), archdef dir None
Traceback (most recent call last):
  File "./spkg-install", line 454, in <module>
    rc = build()
  File "./spkg-install", line 447, in build
    rc = configure(arch, isa_ext, archdef_dir)
  File "./spkg-install", line 315, in configure
    cmd += ' -A '+str(ATLAS_MACHTYPE.index(arch))
ValueError: tuple.index(x): x not in tuple

real    0m0.701s
user    0m0.090s
sys     0m0.060s
************************************************************************
Error installing package atlas-3.10.0
************************************************************************

comment:82 Changed 7 years ago by fbissey

Built successfully on power7. A few oddities in the log but I don't think they are important

make -j1 atlas_run atldir=/hpc/scratch/frb15/sandbox/sage-5.1.beta5/spkg/build/atlas-3.10.0/ATLAS-build exe=xprobe_comp redir=config1.out \
                args="-v 0 -o atlconf.txt -O 1 -A 7 -Si nof77 0 -V 6  -Fa ic '-fPIC' -C sm 'gcc' -Fa sm '-fPIC' -C dm 'gcc' -Fa dm '-fPIC' 
-C sk 'gcc' -Fa sk '-fPIC' -C dk 'gcc' -Fa dk '-fPIC' -C xc 'gcc' -Fa xc '-fPIC' -Fa gc '-fPIC' -C if 'sage_fortran' -Fa if '-fPIC' -b 64 -
d b /hpc/scratch/frb15/sandbox/sage-5.1.beta5/spkg/build/atlas-3.10.0/ATLAS-build"
make[1]: Entering directory `/hpc/scratch/frb15/sandbox/sage-5.1.beta5/spkg/build/atlas-3.10.0/ATLAS-build'
cd /hpc/scratch/frb15/sandbox/sage-5.1.beta5/spkg/build/atlas-3.10.0/ATLAS-build ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 7 -Si nof77 0 
-V 6  -Fa ic '-fPIC' -C sm 'gcc' -Fa sm '-fPIC' -C dm 'gcc' -Fa dm '-fPIC' -C sk 'gcc' -Fa sk '-fPIC' -C dk 'gcc' -Fa dk '-fPIC' -C xc 'gcc
' -Fa xc '-fPIC' -Fa gc '-fPIC' -C if 'sage_fortran' -Fa if '-fPIC' -b 64 -d b /hpc/scratch/frb15/sandbox/sage-5.1.beta5/spkg/build/atlas-3
.10.0/ATLAS-build > config1.out
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
sh: -c: line 0: unexpected EOF while looking for matching ``'
sh: -c: line 1: syntax error: unexpected end of file
probe_f2c.o: In function `ATL_tmpnam':
/hpc/scratch/frb15/sandbox/sage-5.1.beta5/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/include/atlas_sys.h:224: warning: the use of `
tmpnam' is dangerous, better use `mkstemp'

I noticed that libcblas.so is using rpath

ldd -r local/lib/libcblas.so.2.1.0 
        linux-vdso64.so.1 =>  (0x0000040000000000)
        libatlas.so.2 => /hpc/scratch/frb15/sandbox/sage-5.1.beta5/local/lib/libatlas.so.2 (0x0000040000060000)
        libpthread.so.0 => /lib64/power7/libpthread.so.0 (0x00000400008a0000)
        libm.so.6 => /lib64/power7/libm.so.6 (0x00000400008e0000)
        libc.so.6 => /lib64/power7/libc.so.6 (0x00000400009c0000)
        /lib64/ld64.so.1 (0x0000000024560000)

And that's from outside the sage shell. However for f77blas and presumably lapack, libgfortran is not rpath-ed (I am using sage gcc's spkg in this case).

That is important info if you want to put atlas libraries in another location.

I will run a few tests shortly.

comment:83 Changed 7 years ago by benjaminfjones

Volker, do you still need architecture defaults for i386? I have access to an old laptop with a Centrino M processor that reports being i386 / i686 in uname -a and in /proc/cpuinfo:

cpu family 6
cpu model 13
Intel Pentium M

I haven't ever built Sage on it, I imagine it would take several years, but I'm willing to give it a try.

comment:84 follow-up: Changed 7 years ago by vbraun

  • John, I'm against changing the exit codes, we report whatever the sub-process spat out. So even if its >127, thats just what we were handed so clearly its a supported exit code.

I don't have an account on hawk, but in any case that should not stop us from shipping an updated ATLAS that fixes build issues on modern hard/software. We can always clean up second-tier platforms later. But do post the whole log, the error is likely further up.

  • Leif, are you working on a patch? In configure_fast(), we should set
    arch = 'P4E'
    
    instead of P4E64SSE3 is added later. This is what causes your build failure.
  • Francois: the weird messages are normal. The rpaths are set by libtools and are what libtools likes to set. As long as we set LD_LIBRARY_PATH this doesn't matter except when we distribute the binaries. This needs to be fixed some day in all shared libs but not on this ticket.
  • Benjamin: no I don't need 32-bit archdefs, this should be covered by what ATLAS already ships with. The atlas spkg should build relatively quickly now except for the cases in 72

comment:85 in reply to: ↑ 84 Changed 7 years ago by jhpalmieri

Replying to vbraun:

  • John, I'm against changing the exit codes, we report whatever the sub-process spat out. So even if its >127, thats just what we were handed so clearly its a supported exit code.

But after sys.exit(512), Python has return code of zero, on sage.math, OS X, and OpenSolaris. So sage-spkg thinks the spkg installed correctly, which it clearly didn't. From the documentation for os.system, it looks to me that its output should be divided by 512 to get a return code suitable for sys.exit, but I'm not sure about that. However you want to fix it, it has to be changed: it's not acceptable for the compilation to fail but for spkg-install to have a return code of zero.

I don't have an account on hawk, but in any case that should not stop us from shipping an updated ATLAS that fixes build issues on modern hard/software. We can always clean up second-tier platforms later. But do post the whole log, the error is likely further up.

The log is posted at http://sage.math.washington.edu/home/palmieri/misc/atlas-3.10.0.log.

comment:86 Changed 7 years ago by jdemeyer

Something along the following lines should be used to handle rc, see http://docs.python.org/library/os.html

if os.WIFEXITED(rc):
    rc = os.WEXITSTATUS(rc)
elif os.WIFSIGNALED(rc):
    rc = 128 + os.WTERMSIG(rc)
else:
    raise SystemError("Unknown return value %i for os.system()"%rc)

comment:87 Changed 7 years ago by vbraun

I've investigated and reported the Solaris build issue upstream at https://sourceforge.net/tracker/?func=detail&aid=3545418&group_id=23725&atid=379483

comment:88 Changed 7 years ago by vbraun

The return value is actually the return value of os.system(), which is described in http://docs.python.org/library/os.html#os.wait

To extract the exit status, we should just do sys.exit((rc >> 8) & 0x7f). Leif, are you working on the spkg right now?

comment:89 Changed 7 years ago by vbraun

The workaround for the Solaris build issue is to use the fqn for $CC and sage_fortran

comment:90 Changed 7 years ago by vbraun

Since Leif apparently isn't around I implemented the fqn workaround for the Solaris build and the return status issues. Solaris build is still broken but now at a different place. Updated spkg at the same place, md5sum is 878695a26071cfe73a9977bd8413b748.

comment:91 Changed 7 years ago by jhpalmieri

This version now builds on hawk: log file here.

comment:92 Changed 7 years ago by vbraun

Sounds good! I updated the spkg with yet another SPARC Solaris fix, md5sum is 6dbcf22c920626380f2cba877cca4cb1. Though still doesn't work on mark/skynet, but at least makes it now into the compile phase. In any case SPARC solaris issues shouldn't delay this ticket.

comment:93 in reply to: ↑ 81 ; follow-up: Changed 7 years ago by leif

Replying to leif:

On Ubuntu 10.04.4 LTS x86_64 (AMD E-450), with Sage 5.2.rc0 and SAGE_ATLAS_ARCH=fast I get:

ValueError: tuple.index(x): x not in tuple

Using SAGE_ATLAS_ARCH=base in contrast worked (and ptestlong passed with Sage 5.2.rc0, FWIW):

real    34m12.187s
user    30m3.170s
sys     5m30.850s
Successfully installed atlas-3.10.0

Still not that fast, but approximately within your estimates...

comment:94 in reply to: ↑ 93 ; follow-up: Changed 7 years ago by vbraun

Replying to leif:

real 34m12.187s

Thats pretty good for 18W TDP. I take it compiling all of Sage takes 2+ hours on that machine?

comment:95 in reply to: ↑ 94 ; follow-up: Changed 7 years ago by leif

Replying to vbraun:

Replying to leif:

real 34m12.187s

Thats pretty good for 18W TDP. I take it compiling all of Sage takes 2+ hours on that machine?

Sure. Although ATLAS currently consumes only <= 9W ;-)

Unfortunately ATLAS is built quite late (due to its odd dependency on Sage's Python -- while your script is apparently designed to support Python 2.4 as well), so a fair amount of the time spent building Sage only one core is used (because the remaining packages directly or indirectly depend on ATLAS).

I reinstalled the updated spkg again with SAGE_ATLAS_ARCH=fast:

real    40m20.227s
user    36m26.220s
sys     6m9.500s
Successfully installed atlas-3.10.0

comment:96 follow-up: Changed 7 years ago by jhpalmieri

An update: on hawk, I unpacked a sage-5.2.rc0 tarball, replaced the old ATLAS spkg with this one, and built from scratch. There are a bunch of doctest failures:

The following tests failed:                                                                        
                                                                                                   
        sage -t  --long -force_lib devel/sage/sage/matrix/matrix2.pyx # 12 doctests failed
        sage -t  --long -force_lib devel/sage/sage/misc/functional.py # 1 doctests failed
        sage -t  --long -force_lib devel/sage/sage/finance/time_series.pyx # 6 doctests failed
        sage -t  --long -force_lib devel/sage/sage/numerical/test.py # Killed/crashed
        sage -t  --long -force_lib devel/sage/sage/modular/modform/numerical.py # 3 doctests failed
        sage -t  --long -force_lib devel/sage/sage/numerical/optimize.py # Killed/crashed
        sage -t  --long -force_lib devel/sage/sage/matrix/matrix_double_dense.pyx # 68 doctests failed
        sage -t  --long -force_lib devel/sage/doc/en/a_tour_of_sage/index.rst # Killed/crashed
        sage -t  --long -force_lib devel/sage/doc/en/numerical_sage/cvxopt.rst # Killed/crashed
        sage -t  --long -force_lib devel/sage/doc/fr/a_tour_of_sage/index.rst # Killed/crashed
        sage -t  --long -force_lib devel/sage/doc/tr/a_tour_of_sage/index.rst # Killed/crashed
        sage -t  --long -force_lib devel/sage/sage/combinat/e_one_star.py # Killed/crashed

For example:

File "/export/home/palmieri/testing/ATLAS/sage-5.2.rc0/devel/sage-main/sage/matrix/matrix2.pyx", line 8157:
    sage: (A - M*G).zero_at(10^-12)
Expected:
    [0.0 0.0 0.0]
    [0.0 0.0 0.0]
    [0.0 0.0 0.0]
Got:
    [                                 0.0                                  0.0                                  0.0]
    [  -0.10532733041 + 0.0950573490006*I   0.017805411596 - 0.0512258178986*I -0.0226596712913 + 0.0414519876977*I]
    [  0.100615400305 + 0.0962034401538*I -0.0779990660567 - 0.0543172822202*I   0.057608664751 + 0.0154619373789*I]

and

File "/export/home/palmieri/testing/ATLAS/sage-5.2.rc0/devel/sage-main/sage/misc/functional.py", line 1144:
    sage: norm(M)
Expected:
    10.6903311292
Got:
    10.4323182134

I'll try to build again in case something wrong the first time.

comment:97 in reply to: ↑ 96 Changed 7 years ago by leif

Replying to jhpalmieri:

An update: on hawk, I unpacked a sage-5.2.rc0 tarball, replaced the old ATLAS spkg with this one, and built from scratch. There are a bunch of doctest failures:

Did you apply the root repo patch (to remove the BLAS and LAPACK spkgs)?

comment:98 Changed 7 years ago by jhpalmieri

Oops, no, I forgot. One more time...

comment:99 Changed 7 years ago by jhpalmieri

Now Sage doesn't build on hawk, I guess due to the problems noted on #10509: cvxopt doesn't build, because it says

ld: fatal: library -lblas: not found

I'll skip building cvxopt and continue with the rest of the build.

comment:100 follow-up: Changed 7 years ago by vbraun

I don't think the cvxopt problem is due to #10509. The cvxopt spkg explicitly links against blas, this is bad. From the cvxopt patches/setup.py.patch:

+ libraries = ['m','lapack','gsl','blas','gslcblas','cblas','gfortran','atlas']

this is wrong, it should be f77blas if the Fortran version is actually used or not there at all. Of course all modern systems have a libblas.so somewhere so the linker finds it, notes that it is not used, and proceeds. Except that on Hawk, I guess, there is no system-wide libblas. We should proceed removing blas in this ticket and then fix cvxopt on second-tier platforms later.

comment:101 Changed 7 years ago by jhpalmieri

I meant that linking to blas was noted at #10509 as a possible problem, not that #10509 was causing this issue.

comment:102 Changed 7 years ago by vbraun

You are right, that the patch on #10509 should have been applied to cvxopt a long time ago then it wouldn't break here.

comment:103 in reply to: ↑ 95 ; follow-up: Changed 7 years ago by leif

Replying to leif:

Replying to vbraun:

Replying to leif:

real 34m12.187s

Thats pretty good for 18W TDP. I take it compiling all of Sage takes 2+ hours on that machine?

[...]

I reinstalled the updated spkg again with SAGE_ATLAS_ARCH=fast:

real    40m20.227s
user    36m26.220s
sys     6m9.500s
Successfully installed atlas-3.10.0

ROFL, with SAGE_ATLAS_ARCH="AMD64K10h,SSE3,SSE2,SSE1,3DNow" (which involves self-tuning) it took

real	36m15.153s
user	31m23.290s
sys	5m56.960s
Successfully installed atlas-3.10.0

Also a bit strange is that the timing for ptestlong (all for Sage 5.2.rc0, GCC 4.4.3) was

base < fast < AMD64K10h

(i.e., fastest with SAGE_ATLAS_ARCH=base), although I think at least during the last run the machine was partially loaded with other stuff as well, and clearly ptestlong isn't very appropriate to benchmark ATLAS performance... ;-)

[Not going to use the ATLAS tools for comparison right now, perhaps later...]

comment:104 Changed 7 years ago by leif

P.S.:

Another weird thing are (non-fatal w.r.t. the build) errors like

FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch
FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch
FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch
FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch
FlagCheck.c:1: error: bad value (armv7) for -march= switch
FlagCheck.c:1: error: bad value (armv7) for -mtune= switch
FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch
FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch
FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch
FlagCheck.c:1: error: bad value (ultrasparc) for -mtune= switch
FlagCheck.c:1: error: bad value (970) for -mtune= switch

even if one specifies the architecture (i.e., on x86).

comment:105 Changed 7 years ago by jhpalmieri

On hawk: with the appropriate patches applied, I still get some test failures, but as far as I can tell, they're all due to cvxopt being broken. So it looks pretty good.

comment:106 follow-up: Changed 7 years ago by leif

Is it intentional that static libraries no longer get installed (although built)?

comment:107 Changed 7 years ago by fbissey

On cvxopt I am doing a new spkg in #13160 I'll check what I have done there. My main issue with the current spkg is it is horribly overlinked.

comment:108 in reply to: ↑ 106 ; follow-up: Changed 7 years ago by vbraun

Replying to leif:

Is it intentional that static libraries no longer get installed (although built)?

Upstream really only builds static libraries. But static libraries suck for our purposes. So yet, it is intentional that the static libraries are not installed.

comment:109 in reply to: ↑ 100 Changed 7 years ago by dimpase

Replying to vbraun:

I don't think the cvxopt problem is due to #10509. The cvxopt spkg explicitly links against blas, this is bad. From the cvxopt patches/setup.py.patch:

+ libraries = ['m','lapack','gsl','blas','gslcblas','cblas','gfortran','atlas']

this is wrong, it should be f77blas if the Fortran version is actually used or not there at all. Of course all modern systems have a libblas.so somewhere so the linker finds it, notes that it is not used, and proceeds. Except that on Hawk, I guess, there is no system-wide libblas. We should proceed removing blas in this ticket and then fix cvxopt on second-tier platforms later.

Perhaps this ticket should get #13160 as a dependence. One thing I checked is that it appears to work on OSX 10.6.8, both with native blas/lapack, and with Atlas 3.10 from this ticket. I imagine #13160 can get finalized quickly.

comment:110 in reply to: ↑ 103 Changed 7 years ago by leif

Replying to leif:

[Not going to use the ATLAS tools for comparison right now, perhaps later...]

FWIW, while make time works, make atlvat2.pdf ... (to build ATLAS vs. ATLAS comparison charts) seems to be broken -- for me it always fails with a buffer overflow.

comment:111 in reply to: ↑ 108 Changed 7 years ago by leif

Replying to vbraun:

Replying to leif:

Is it intentional that static libraries no longer get installed (although built)?

Upstream really only builds static libraries. But static libraries suck for our purposes. So yet, it is intentional that the static libraries are not installed.

Well, as long as also the shared libraries are present, they're (usually) preferred over the static ones (i.e., unless one explicitly asks for linking against the latter), so copying these into $SAGE_LOCAL/lib/ IMHO shouldn't hurt. (The static libraries are btw. needed to compare different ATLAS installations; the only way to "keep" them is to reinstall the ATLAS spkg with ./sage -f -s ... or to set SAGE_KEEP_BUILT_SPKGS, and manually copy them.)

Note that previously installed static ATLAS libraries currently don't get removed. Don't know whether that may cause trouble (e.g. with upgrading); see above.

comment:112 Changed 7 years ago by vbraun

Its true that it doesn't hurt to have the static libraries as long as you don't use them. This is like saying that a knife doesn't hurt until you are stabbed with it. True, but why put a sharp blade under the couch pillow in hopes that nobody will sit on it?

It would be nice to have some system to compare different atlas versions and compile runs, but thats definitely for another ticket. Ideally the atlas-config python script could save the atlas libraries in a private directory, for example by setting a special environment variable while building atlas. And then have some way to tabulate the performance of different installs.

comment:113 Changed 7 years ago by vbraun

  • Dependencies changed from sage-5.2.beta0 to #13160
  • Status changed from needs_work to needs_review

I think the only remaining blocker is that it (or rather, cvxopt) doesn't build on hawk. Since I don't have an account, can someone test it (the spkg + patches from this ticket + the cvxopt spkg from #13160)? Everything else in this ticket has been reviewed already, we just have to check that the interaction with cvxopt is fixed on the last "fully supported" platform.

comment:114 Changed 7 years ago by jhpalmieri

Cvxopt still doesn't build. I see the same error when using the ATLAS spkg here or when setting SAGE_ATLAS_LIB=/ATLAS32. Here is the log.

Does the ATLAS spkg here build on skynet/mark (and Solaris on sparc in general)?

comment:115 Changed 7 years ago by fbissey

Why the heck is it not finding gsl? Oh I see the include line is actually wrong. I'll check the spkg but we should continue with cvxopt issues at #13160.

comment:116 Changed 7 years ago by vbraun

John, now that you verified that it works on Hawk is there anything else that prevents you from pressing the positive review button? ;-)

comment:117 Changed 7 years ago by jhpalmieri

I'm testing on a few skynet machines. Should I expect it to work on mark?

comment:118 follow-up: Changed 7 years ago by vbraun

It worked for me on mark (sparc solaris)

comment:119 in reply to: ↑ 118 Changed 7 years ago by jdemeyer

Replying to vbraun:

It worked for me on mark (sparc solaris)

OMG cool, Skynet is back up. I was totally unaware of that!

comment:120 Changed 7 years ago by leif

I'm still not happy with "discarding" the built static libraries; there should at least be some convenient way to save them (other than SAGE_KEEP_BUILT_SPKGS=yes or installing with sage (-i|-f) -s ....)

Another issue is the extremely increased build time on some machines if one doesn't set SAGE_ATLAS_ARCH. Don't know how we could handle that, but it certainly gives rise to a lot of user complaints.

comment:121 Changed 7 years ago by leif

P.S.: W.r.t. the "knife": If you don't want to install static libraries (somewhere), at least previous ones should get removed (or moved somewhere else) upon a successful ATLAS build.

comment:122 follow-up: Changed 7 years ago by vbraun

Now that I added the generic 64-bit archdefs the default build time (without setting SAGE_ATLAS_ARCH) should be moderate on all x86 systems. I.e. less CPU time than building the rest of Sage.

Your suggestions about handling the static libraries are enhancement requests. By itself, its useless to keep a backup of the static libraries somewhere. I agree that one should keep them around and devise a way to benchmark them, but not on this ticket. Also I'm against attempting to delete stuff from previous installs unless it actively conflicts with the new spkg. Which it does not, the damage of statically linking is already done.

comment:123 Changed 7 years ago by jhpalmieri

I'm willing to give this a positive review now. Leif, what about you? Can we defer your issues to a follow-up?

comment:124 in reply to: ↑ 122 ; follow-up: Changed 7 years ago by leif

Replying to vbraun:

Now that I added the generic 64-bit archdefs the default build time (without setting SAGE_ATLAS_ARCH) should be moderate on all x86 systems. I.e. less CPU time than building the rest of Sage.

Ok, hopefully...


Your suggestions about handling the static libraries are enhancement requests. By itself, its useless to keep a backup of the static libraries somewhere. I agree that one should keep them around and devise a way to benchmark them, but not on this ticket.

I'd rather say not installing them [anywhere] is a regression w.r.t. the previous spkg.

Also I'm against attempting to delete stuff from previous installs unless it actively conflicts with the new spkg. Which it does not, the damage of statically linking is already done.

If so, it shouldn't hurt to keep ATLAS installing them either... ;-)

[I'd expect "more damage" when having different .a and .so library versions.]

comment:125 Changed 7 years ago by leif

I'm not wanting to hold up this ticket, but IMHO the Installation Guide should get updated, at least documenting the new atlas-config script.

comment:126 in reply to: ↑ 124 Changed 7 years ago by vbraun

Replying to leif:

I'd rather say not installing them [anywhere] is a regression w.r.t. the previous spkg.

Its a major improvement, not a regression!

If so, it shouldn't hurt to keep ATLAS installing them either... ;-)

As I explained previously, thats not true. We have to change things to make them better. But we can't un-link the static linkage that has happened previously, so when you upgrade from an existing spkg you potentially keep the old code. And there is nothing a new atlas spkg can do about this. If you want to be sure that you don't have cruft statically linked you'll have to do a clean install. This is precisely why it was a bad idea to install static libraries previously.

Changed 7 years ago by vbraun

Initial patch

comment:127 Changed 7 years ago by vbraun

  • Description modified (diff)

I've added documentation to the installation guide for the atlas-config script and updated the environment variables.

comment:128 Changed 7 years ago by jhpalmieri

I note that on OS X, the test suite doesn't run, even if ATLAS is built. This could perhaps be dealt with on a follow-up ticket? Maybe only skip self-tests if

"$UNAME" = "Darwin" -a -z "$SAGE_ATLAS_ARCH"

or something like that?

More seriously, I'm having problems with this on the skynet machine iras. I'm building Sage from scratch, using the spkgs from this ticket and #13160. The ATLAS build started about 15 hours ago, and nothing has been written to the log file for at least 6 hours. I'm going to quit and restart the build...

comment:129 follow-up: Changed 7 years ago by jhpalmieri

On skynet machine iras:

real    2251m2.189s
user    2175m58.212s
sys     16m29.112s

This is not really acceptable. And then:

RHS=74, nrm=184.678650
RHS=75, nrm=248.384750
RHS=76, nrm=291.507111
RHS=77, nrm=337.993896
RHS=78, nrm=335.039612
RHS=79, nrm=477.389954
RHS=80, nrm=334.815796
make[5]: *** [csanity_test] Error 1
make[5]: *** Waiting for unfinished jobs....
make[5]: Leaving directory `/home/palmieri/iras/sage-5.2.10508/spkg/build/atlas-\
3.10.0/ATLAS-build/bin'
make[4]: *** [sanity_test] Error 2
make[4]: Leaving directory `/home/palmieri/iras/sage-5.2.10508/spkg/build/atlas-\
3.10.0/ATLAS-build/bin'
make[3]: *** [sanity_test] Error 2
make[3]: Leaving directory `/home/palmieri/iras/sage-5.2.10508/spkg/build/atlas-\
3.10.0/ATLAS-build'
make[2]: *** [test] Error 2
make[2]: Leaving directory `/home/palmieri/iras/sage-5.2.10508/spkg/build/atlas-\
3.10.0/ATLAS-build'
An error occurred when running the ATLAS self-tests.

comment:130 in reply to: ↑ 129 ; follow-up: Changed 7 years ago by leif

Replying to jhpalmieri:

On skynet machine iras:

real    2251m2.189s
user    2175m58.212s
sys     16m29.112s

Ouch. How long did 3.8.4 take to build, and did you suspend the ECM background jobs? (They're back again...)

Presumably something to report upstream, but perhaps we can tweak it ourselves somehow.

comment:131 follow-ups: Changed 7 years ago by vbraun

Clint Whaley (ATLAS developer) doesn't have access to Itanium any more, so its not surprising that it does a full search. If its too slow for you then get yourself a new computer ;-) I'll have a look at the self-test issue, but it seems that the build/install works. Right?

I'd also like to remind everyone that this ticket, even if it doesn't pass its own testsuite on some dead arch, fixes actual issues with modern CPUs as reported on the mailinglist.

comment:132 Changed 7 years ago by vbraun

  • Report Upstream changed from N/A to Reported upstream. No feedback yet.

comment:133 in reply to: ↑ 131 ; follow-up: Changed 7 years ago by dimpase

Replying to vbraun:

Clint Whaley (ATLAS developer) doesn't have access to Itanium any more, so its not surprising that it does a full search. If its too slow for you then get yourself a new computer ;-) I'll have a look at the self-test issue, but it seems that the build/install works. Right?

Can't one use the current ATLAS spkg on Itaniums instead of the new one? Or there are incompatibility problems?

Itaniums are not a dying breed, at least AFAIK Intels still plans to release a new Itanium chip this year. So just hoping that they'd be gone soon is too optimistic. Should we try getting Clint Whaley access to an Itanium machine?

comment:134 in reply to: ↑ 133 ; follow-up: Changed 7 years ago by vbraun

Replying to dimpase:

Can't one use the current ATLAS spkg on Itaniums instead of the new one? Or there are incompatibility problems?

We can use a preinstalled ATLAS library on the buildbots. Given that this is by far the slowest part of the compile cycle, I think thats reasonable. We even do this officially on OSX where we always use the system-provided BLAS. But perhaps easier would be to update the Itanium archdef so that it doesn't have to tune. I just started a compile on iras, but don't expect the answer too soon ;-)

Itaniums are not a dying breed, at least AFAIK Intels still plans to release a new Itanium chip this year.

Well Intel made some unfortunate (for them) contractual commitments here... But ia64 is certainly not getting much love.

Should we try getting Clint Whaley access to an Itanium machine?

I've asked to that extend on the sage-skynet list.

comment:135 Changed 7 years ago by aginiewicz

It worked on 2 machines I tested, but failed on a PIII machine - it turns out that Atlas 3.10.0 does not work on PIII but the fix is simple - see http://math-atlas.sourceforge.net/errata.html#piiisse2 for confirmation.

I've uploaded spkg containing fix for this to https://github.com/downloads/aginiewicz/spkgs/atlas-3.10.0.spkg

comment:136 in reply to: ↑ 131 Changed 7 years ago by leif

Replying to vbraun:

I'd also like to remind everyone that this ticket, even if it doesn't pass its own testsuite on some dead arch, fixes actual issues with modern CPUs as reported on the mailinglist.

You mean the (reproducible) segfaults on some AVX CPUs? These can be solved by reinstalling the ATLAS spkg (one or two times) -- which doesn't take that long, as these CPUs are fast... ;-)

No, seriously, as a temporary "solution", we could at least put the old ATLAS, BLAS and LAPACK spkgs into the experimental branch, such that (e.g.) Itanium users can still access them (to be installed manually with ./sage -f ... of course).


W.r.t. the "dead archictecture": It's IMHO always good to test on a broad range of platforms, as that might expose real bugs that just incidentally don't show up on the "mainstream" (Intel, AMD, meanwhile perhaps also ARM); if one day GCC does no longer support Itanium, the situation will be different.

comment:137 in reply to: ↑ 134 Changed 7 years ago by leif

Replying to vbraun:

Replying to dimpase:

Can't one use the current ATLAS spkg on Itaniums instead of the new one? Or there are incompatibility problems?

We can use a preinstalled ATLAS library on the buildbots. Given that this is by far the slowest part of the compile cycle, I think thats reasonable.

Therefore I was suggesting to also install some script to easily "save" the ATLAS libs somewhere for later use with SAGE_ATLAS_LIB (orthogonal to the static libraries issue).

comment:138 in reply to: ↑ 130 Changed 7 years ago by jhpalmieri

Replying to leif:

Replying to jhpalmieri:

On skynet machine iras:

real    2251m2.189s
user    2175m58.212s
sys     16m29.112s

Ouch. How long did 3.8.4 take to build, and did you suspend the ECM background jobs? (They're back again...)

real    61m42.034s
user    52m55.672s
sys     1m54.940s

When compiling the new ATLAS spkg, I suspended two of the background processes (that is, I did touch /tmp/iras1 and touch /tmp/iras2). When compiling the previous version, I didn't bother to do this.

Replying to vbraun:

I'd also like to remind everyone that this ticket, even if it doesn't pass its own testsuite on some dead arch, fixes actual issues with modern CPUs as reported on the mailinglist.

I don't feel too strongly about it either way, but I would be a little surprised if Jeroen is willing to merge this if it takes so long to build on iras.

comment:139 Changed 7 years ago by vbraun

Thats quite a speedup. I guess in your earlier test ATLAS failed to use the SAGE_ATLAS_ARCH=fast build because of system load (first attempt), then tried SAGE_ATLAS_ARCH=base which is the old Itanium (not Itanium 2), which then did a full search for timings. Something like that must have happened, the compile is not just 30x faster without background jobs running.

So I guess all problems are solved?

comment:140 Changed 7 years ago by jhpalmieri

Ah, no, I think you misunderstand: it's quite a slow-down. The shorter time (~1 hour) is for 3.8.4 without suspending background processes, the longer time (~37 hours) is for 3.10.0 with two background processes suspended.

comment:141 Changed 7 years ago by jdemeyer

I'm going to test this on the buildbot soon, that should give more information.

comment:142 Changed 7 years ago by jdemeyer

This causes a build failure for cvxopt on OS X 10.4 PPC:

running build_ext
building 'gsl' extension
creating build/temp.macosx-10.4-ppc-2.7
creating build/temp.macosx-10.4-ppc-2.7/C
gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/buildbot/build/sage/moufang-1/moufang_full/build/sage-5.3.beta3/local/include -I/Users/buildbot/build/sage/moufang-1/moufang_full/build/sage-5.3.beta3/local/include/python2.7 -c C/gsl.c -o build/temp.macosx-10.4-ppc-2.7/C/gsl.o
C/gsl.c: In function 'initgsl':
C/gsl.c:198:13: warning: variable 'm' set but not used [-Wunused-but-set-variable]
gcc -bundle -undefined dynamic_lookup -L/Users/buildbot/build/sage/moufang-1/moufang_full/build/sage-5.3.beta3/local/lib build/temp.macosx-10.4-ppc-2.7/C/gsl.o -L/Users/buildbot/build/sage/moufang-1/moufang_full/build/sage-5.3.beta3/local/lib -L/Users/buildbot/build/sage/moufang-1/moufang_full/build/sage-5.3.beta3/local/lib -lm -lgsl -lblas -lgfortran -lm -o build/lib.macosx-10.4-ppc-2.7/cvxopt/gsl.so
/usr/bin/ld: can't locate file for: -lblas
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

comment:143 Changed 7 years ago by jdemeyer

  • Status changed from needs_review to needs_work

Also, ATLAS failed to build on various Buildbot systems: arando (Linux i386), lena (Linux x86_64), cicero (Linux i386), iras (Linux ia64), hawk (OpenSolaris? i386).

I just tried the build once, I will retry them. But in any case, the build is more flaky than the previous version of ATLAS.

comment:144 follow-up: Changed 7 years ago by vbraun

  • Cc kcrisman added

The OSX 10.4 issue is a cvxopt bug. Where is BLAS in the ancient vecLib and why didn't Apple call it libblas? In any case I don't have access to a museum Mac, so somebody else will have to figure that out.

comment:145 Changed 7 years ago by fbissey

Technically if we want to use atlas on OS X a number of spkg including cvxopt needs to be updated. I am not sure I would call it a cvxopt bug because that's part of the configuration we introduced in spkg-install. Before the inclusion of this spkg cvxopt probably would have picked up libblas from the blas spkg. We can fix this in cvxopt of course.

comment:146 Changed 7 years ago by jhpalmieri

I have had no problems building this on hawk (see /export/home/palmieri/testing/ATLAS/sage-5.3.beta2). On iras, as I said above, it built, but it took a long time. I haven't tried the others that you mentioned.

comment:147 Changed 7 years ago by jdemeyer

More buildbot results:

First attempt failed for arando (Linux i386), lena (Linux x86_64), flavius (Linux x86_64), cicero (Linux i386), iras (Linux ia64), hawk (OpenSolaris i386).

Second attempt failed for arando (Linux i386), flavius (Linux x86_64), cicero (Linux i386), iras (Linux ia64), hawk (OpenSolaris i386).

Last edited 7 years ago by jdemeyer (previous) (diff)

comment:148 Changed 7 years ago by jhpalmieri

On the first try, this built successfully for me on iras, lena, and hawk. (I've built it at least twice on iras and hawk, with no failures.) On the other hand, cicero (Linux x86) and flavius (Linux x86_64) both fail to build, with essentially the same error. Log file here. They also both took a long time (about 17 hours for cicero) trying to build the ATLAS spkg. I think we need some new different settings, because the build times for cicero, flavius (almost 19 hours), and iras (34.5 hours this time) are way too long.

comment:149 follow-up: Changed 7 years ago by vbraun

Oh I see, cicero/flavius have only a single CPU core. Talking about a blast from the past! In that case ATLAS doesn't build threaded static libraries, so we can't build threaded shared libraries. They are also so old that ATLAS can't figure out whether CPU throttling is enabled, so the full timings are collected instead of immediately falling back to a pre-defined archdef. Instead of trying to catch this in the ATLAS spkg and potentially not running the tuning in cases where we ought to, I think we should just configure the buildbot to set SAGE_ATLAS_ARCH=base on these ancient machines.

comment:150 Changed 6 years ago by jhpalmieri

I thought one of the purposes of the buildbot was to test that Sage builds "out of the box" on a variety of platforms, so tuning environment variables for use with the buildbot machines doesn't seem like the right solution. But maybe I'm not thinking about the buildbot the right way.

Also, supporting "ancient" machines is important: if we want mathematicians in underdeveloped countries, for example, to be able to use Sage, they may not have access to anything better.

comment:151 Changed 6 years ago by vbraun

Well nobody stops you from tuning ATLAS for a day if you have an ancient computer. Its just annoying on the buildbot if you want to test something else than the ATLAS build. I guess the question is: Do we want, by default, to build a state-of-the-art BLAS library on all computers or only on sufficiently modern ones?

comment:152 in reply to: ↑ 149 ; follow-ups: Changed 6 years ago by jdemeyer

Replying to vbraun:

Oh I see, cicero/flavius have only a single CPU core. Talking about a blast from the past! In that case ATLAS doesn't build threaded static libraries, so we can't build threaded shared libraries.

Is that a bug in ATLAS or a bug in spkg-install? The version of ATLAS currently in Sage doesn't have this problem.

And I'm with John on trying the build "out of the box" on the buildbots as much as possible. And I don't consider single-core machines ancient.

comment:153 in reply to: ↑ 152 Changed 6 years ago by dimpase

Replying to jdemeyer:

And I'm with John on trying the build "out of the box" on the buildbots as much as possible.

well, 37 hours for a single package sounds like buildbot abuse. And I think that the default for slow machines with a single CPUs should be a basic Atlas install, with as little tuning as possible. There should be however be good documentation available on how to improve Atlas performance on a host, by rebuilding the spkg.

And I don't consider single-core machines ancient.

One way or another, single-core machines do not need many features of the new Atlas. Perhaps it's time to think about versioning possibilities: a meta-package Atlas that installs an appropriate for the architecture version?

comment:154 in reply to: ↑ 152 ; follow-up: Changed 6 years ago by vbraun

Replying to jdemeyer:

And I'm with John on trying the build "out of the box" on the buildbots as much as possible.

So if you are fine with waiting 2 days for the slower buildbots to complete then that settles it.

comment:155 Changed 6 years ago by jhpalmieri

Is there some sort of preliminary testing which could be done in spkg-install to try to catch machines which might take many hours to build ATLAS? For those machines, we could set the appropriate environment variable to skip as much tuning as possible, and then for quicker machines, we do more tuning. Something like

if [ -z "$SAGE_ATLAS_ARCH" && machine_is_too_old ]; then
   SAGE_ATLAS_ARCH='skip tuning' # or whatever
fi

(For 'machine_is_too_old', maybe just seeing if it only has one core would be enough.) Then the user can force tuning by setting SAGE_ATLAS_ARCH to something appropriate. I'm not sure this the the right variable, but anyway, I hope you understand the idea. Is this workable?

comment:156 Changed 6 years ago by vbraun

The old machines are slow because they are old and because there are no up-to-date architectural defaults for ancient hardware. None of this can be fixed by a magic environment variable (except pointing SAGE_ATLAS_LIB to the system atlas libraries). Basically, you can't skip tuning sparc just because you have i386 archdefs. There is a lot of assembler code that will be unhappy.

Also, I don't think there is an easy way to know that atlas would take a long time without actually building it. We could just install a reference blas on all non-starte-of-the-art machines (say, less than 4 cores and 2GHz). But this will be a major rewrite of how Sage builds its BLAS libraries.

comment:157 in reply to: ↑ 154 Changed 6 years ago by jdemeyer

Replying to vbraun:

So if you are fine with waiting 2 days for the slower buildbots to complete then that settles it.

It doesn't quite settle it, because the new spkg simply fails to build on some machines.

comment:158 Changed 6 years ago by vbraun

I know, and I will make sure it builds on those machines. What I can't do is make ATLAS build fast on ancient hardware.

comment:159 in reply to: ↑ 152 Changed 6 years ago by jdemeyer

I would like to know the answer to this question: do what extent are these issues upstream issues or issues with Sage? Because the current ATLAS-3.8.4 works fine.

Replying to jdemeyer:

Replying to vbraun:

Oh I see, cicero/flavius have only a single CPU core. Talking about a blast from the past! In that case ATLAS doesn't build threaded static libraries, so we can't build threaded shared libraries.

Is that a bug in ATLAS or a bug in spkg-install? The version of ATLAS currently in Sage doesn't have this problem.

comment:160 Changed 6 years ago by vbraun

The current ATLAS does not work fine for some modern CPUs (search the mailinglist for reports), nor does it have AVX support. Realistically, if you want to have a fast BLAS then you need to track upstream pretty closely since a lot of linear algebra performance boils down to having a good (asm) implementation tuned to your particular hardware.

The build failures that I have seen logs for were just bugs in the Sage buildscript that I'm working on fixing.

comment:161 Changed 6 years ago by vbraun

The updated spkg fixes the issue with single-core processors. Builds fine on cicero.

comment:162 follow-ups: Changed 6 years ago by jhpalmieri

Builds on cicero and flavius. On mark (Solaris), I see a problem building scipy. Could this be related? Log here.

Edit: more info, from the numpy log:

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not found in /home/palmieri/mark/sage-5.3.beta1-ATLAS/local/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
/home/palmieri/mark/sage-5.3.beta1-ATLAS/spkg/build/numpy-1.5.1.p1/src/numpy/distutils/system_info.py:1010: UserWarning:
*********************************************************************
    Lapack library (from ATLAS) is probably incomplete:
      size of /home/palmieri/mark/sage-5.3.beta1-ATLAS/local/lib/liblapack.so is 360k (expected >4000k)

    Follow the instructions in the KNOWN PROBLEMS section of the file
    numpy/INSTALL.txt.
*********************************************************************

If you have an account on skynet, feel free to look around /home/palmieri/mark/sage-5.3.beta1-ATLAS/.

Last edited 6 years ago by jhpalmieri (previous) (diff)

comment:163 follow-up: Changed 6 years ago by fbissey

Yes totally ATLAS related. May you could also post ATLAS's log or at least the end bit of it where it builds lapack.

comment:164 Changed 6 years ago by vbraun

I've added archdefs for Itanium2, now build time is a lot faster:

vbraun@iras:~/opt/iras/sage-5.3.beta0> SAGE_ATLAS_ARCH=fast ./sage -f http://www.stp.dias.ie/~vbraun/Sage/spkg/atlas-3.10.0.spkg
[...]
real    44m44.170s
user    41m47.156s
sys     2m42.456s

Though if you don't specify SAGE_ATLAS_ARCH it will still run, by default, a full tuning. If that fails for any reason it will try SAGE_ATLAS_ARCH=fast next.

comment:165 in reply to: ↑ 163 Changed 6 years ago by jhpalmieri

Replying to fbissey:

Yes totally ATLAS related. May you could also post ATLAS's log or at least the end bit of it where it builds lapack.

It's here.

comment:166 Changed 6 years ago by fbissey

I am not sure what happens at all. I am not convinced that the original lapack archive is getting relinked along with the C interface from ATLAS but that's not easy to establish from the log because of the size. I would need to spend some time looking at it carefully.

comment:167 in reply to: ↑ 144 ; follow-up: Changed 6 years ago by kcrisman

The OSX 10.4 issue is a cvxopt bug. Where is BLAS in the ancient vecLib and why didn't Apple call it libblas? In any case I don't have access to a museum Mac, so somebody else will have to figure that out.

Reporting for duty! Currently building MPIR, with with changes in this ticket (except the doctest/doc patch, which is no biggie).

Would this issue only come up if someone did set SAGE_ATLAS_ARCH=base or at any rate set it? I though that using the system ATLAS was still the default on Mac after this ticket - was that a misunderstanding? I might find out before I leave work today... but if it doesn't break without resetting that variable, I don't think that is as bad, since hopefully no one using this old of a machine is depending on it for fast linear algebra.

comment:168 in reply to: ↑ 167 Changed 6 years ago by fbissey

Replying to kcrisman:

The OSX 10.4 issue is a cvxopt bug. Where is BLAS in the ancient vecLib and why didn't Apple call it libblas? In any case I don't have access to a museum Mac, so somebody else will have to figure that out.

Reporting for duty! Currently building MPIR, with with changes in this ticket (except the doctest/doc patch, which is no biggie).

Would this issue only come up if someone did set SAGE_ATLAS_ARCH=base or at any rate set it? I though that using the system ATLAS was still the default on Mac after this ticket - was that a misunderstanding? I might find out before I leave work today... but if it doesn't break without resetting that variable, I don't think that is as bad, since hopefully no one using this old of a machine is depending on it for fast linear algebra.

That would be a start but most of the spkg using blas have specific rules for OS X and we would need to change them before they start using ATLAS instead of veclib. From the top of my head:

  • iml (actually that would solve some problems)
  • linbox
  • numpy
  • scipy
  • cvxopt
  • R?

I believe sage itself can cope with the change as is but it should be checked.

comment:169 Changed 6 years ago by kcrisman

My point was not that we should switch to ATLAS, but rather that it might be possible to have a different ticket for making ATLAS work optionally on Mac this way, if Sage builds and tests fine with this new ATLAS in the case where Mac does not actually build it. I don't know if that's true, though, since jdemeyer's report could perhaps have been with that env var set.

comment:170 Changed 6 years ago by kcrisman

Well, it turns out that it must be removing the other spkgs that does it.

building 'gsl' extension
creating build/temp.macosx-10.4-ppc-2.7
creating build/temp.macosx-10.4-ppc-2.7/C
gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/student/Desktop/sage-5.3.rc0/local/include -I/Users/student/Desktop/sage-5.3.rc0/local/include/python2.7 -c C/gsl.c -o build/temp.macosx-10.4-ppc-2.7/C/gsl.o
C/gsl.c: In function 'initgsl':
C/gsl.c:198:13: warning: variable 'm' set but not used [-Wunused-but-set-variable]
gcc -bundle -undefined dynamic_lookup -L/Users/student/Desktop/sage-5.3.rc0/local/lib build/temp.macosx-10.4-ppc-2.7/C/gsl.o -L/Users/student/Desktop/sage-5.3.rc0/local/lib -L/Users/student/Desktop/sage-5.3.rc0/local/lib -lm -lgsl -lblas -lgfortran -lm -o build/lib.macosx-10.4-ppc-2.7/cvxopt/gsl.so
/usr/bin/ld: can't locate file for: -lblas
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
Error building/installing cvxopt

real    0m3.866s
user    0m1.281s
sys     0m1.359s
************************************************************************
Error installing package cvxopt-1.1.5
************************************************************************

Now I understand Volker's comment. Maybe we can just have a different configuration when using old Macs, as in François' comment. But I wouldn't know how to do that.

comment:171 Changed 6 years ago by kcrisman

With SAGE_ATLAS_ARCH=base on the same machine, I get

Base configuration on PPC.
Running configure with arch = POWER4, isa extensions (), archdef dir None
Running ../src/configure --prefix=/Users/student/Desktop/sage-5.3.rc0/local --with-netlib-lapack-tarfile=/Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/lapack-3.4.1.tgz --cc="gcc" -Si latune 0 -Fa alg -fPIC -C if "/Users/student/Desktop/sage-5.3.rc0/local/bin/sage_fortran" -C acg "/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc" -b 32 -O 12 -A 2 -V 0
gcc -I/Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/include  -g -w -c /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/src/atlconf_misc.c
gcc -I/Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/include  -g -w -o xconfig /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/src/config.c atlconf_misc.o 
./xconfig -d s /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src/ -d b /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build  -Si lapackref 1 -Si latune 0 -Fa alg -fPIC -C if /Users/student/Desktop/sage-5.3.rc0/local/bin/sage_fortran -C acg /Users/student/Desktop/sage-5.3.rc0/local/bin/gcc -b 32 -O 12 -A 2 -V 0
gcc -I/Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/include  -g -w -o xisgcc /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/src/IsGcc.c atlconf_misc.o 
gcc -I/Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/include  -g -w -c /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/src/probe_comp.c
gcc -I/Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build/../src//CONFIG/include  -g -w -o xprobe_comp probe_comp.o atlconf_misc.o 
rm -f config1.out
make -j1 atlas_run atldir=/Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build exe=xprobe_comp redir=config1.out \
                args="-v 0 -o atlconf.txt -O 12 -A 2 -Si nof77 0 -V 0  -C ic '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa ic '-fPIC' -C sm '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa sm '-fPIC' -C dm '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa dm '-fPIC' -C sk '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa sk '-fPIC' -C dk '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa dk '-fPIC' -C xc '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa xc '-fPIC' -C gc '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa gc '-fPIC' -C if '/Users/student/Desktop/sage-5.3.rc0/local/bin/sage_fortran' -Fa if '-fPIC' -b 32 -d b /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build"
cd /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build ; ./xprobe_comp -v 0 -o atlconf.txt -O 12 -A 2 -Si nof77 0 -V 0  -C ic '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa ic '-fPIC' -C sm '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa sm '-fPIC' -C dm '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa dm '-fPIC' -C sk '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa sk '-fPIC' -C dk '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa dk '-fPIC' -C xc '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa xc '-fPIC' -C gc '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa gc '-fPIC' -C if '/Users/student/Desktop/sage-5.3.rc0/local/bin/sage_fortran' -Fa if '-fPIC' -b 32 -d b /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/ATLAS-build > config1.out
/bin/sh: line 1: ./xctest: Bad CPU type in executable
make[5]: *** [atlas_run] Error 126
make[4]: *** [IRunCComp] Error 2


Unable to find usable compiler for ICC; abortingMake sure compilers are in your path, and specify good compilers to configure
(see INSTALL.txt or 'configure --help' for details)make[3]: *** [atlas_run] Error 1
make[2]: *** [IRun_comp] Error 2
ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 0 -o atlconf.txt -O 12 -A 2 -Si nof77 0 -V 0  -C ic '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa ic '-fPIC' -C sm '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa sm '-fPIC' -C dm '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa dm '-fPIC' -C sk '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa sk '-fPIC' -C dk '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa dk '-fPIC' -C xc '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa xc '-fPIC' -C gc '/Users/student/Desktop/sage-5.3.rc0/local/bin/gcc' -Fa gc '-fPIC' -C if '/Users/student/Desktop/sage-5.3.rc0/local/bin/sage_fortran' -Fa if '-fPIC' -b 32"'

Assembly configured as GAS_PPC (4)

Bad VECFLAG value=0, res='VECFLAG=0
'

Vector ISA Extension configured as   (0,0)

Clock rate configured as 700Mhz

Maximum number of threads configured as  1
Cannot detect CPU throttling.
mkdir src bin tune interfaces
cd src ; mkdir testing auxil blas lapack pthreads threads
cd src/blas ; \
           mkdir f77reference reference gemv ger gemm kbmm \
                 level1 level2 level3 pklevel3
cd src/blas/reference ; mkdir level1 level2 level3
cd src/blas/level2 ; mkdir kernel
cd src/blas/pklevel3 ; mkdir gpmm sprk
cd src/blas/level3 ; mkdir rblas kernel
cd src/pthreads ; mkdir blas misc
cd src/pthreads/blas ; mkdir level1 level2 level3
cd src/threads ; mkdir blas lapack
cd src/threads/blas ; mkdir level3 level2
cd tune ; mkdir blas sysinfo lapack threads
cd tune/blas ; mkdir gemm gemv ger level1 level3
cd interfaces ; mkdir blas lapack
cd interfaces/lapack ; mkdir C F77
cd interfaces/lapack/C ; mkdir src testing
cd interfaces/lapack/F77 ; mkdir src testing
cd interfaces/blas ; mkdir C F77
cd interfaces/blas/C ; mkdir src testing
cd interfaces/blas/F77 ; mkdir src testing
cd interfaces/lapack ; mkdir C2F
cd interfaces/lapack/C2F ; mkdir src
mkdir ARCHS
make -j1 -f Make.top startup
Make.top:1: Make.inc: No such file or directory
Make.top:325: warning: overriding commands for target `/AtlasTest'
Make.top:76: warning: ignoring old commands for target `/AtlasTest'
make[3]: *** No rule to make target `Make.inc'.  Stop.
make[2]: *** [startup] Error 2
mv: rename lib/Makefile to lib/Make.tmp: No such file or directory
../src/configure: line 450: lib/Makefile: No such file or directory
../src/configure: line 451: lib/Makefile: No such file or directory
../src/configure: line 452: lib/Makefile: No such file or directory
../src/configure: line 453: lib/Makefile: No such file or directory
../src/configure: line 509: lib/Makefile: No such file or directory
DONE configure
Finished configuring ATLAS.
Running make -j1
make -j1 -f Make.top build
Make.top:1: Make.inc: No such file or directory
Make.top:325: warning: overriding commands for target `/AtlasTest'
Make.top:76: warning: ignoring old commands for target `/AtlasTest'
make[3]: *** No rule to make target `Make.inc'.  Stop.
make[2]: *** [build] Error 2
------------------------------------------------------------
  File "./spkg-install", line 476, in <module>
    assert_success(rc, bad='Failed to build ATLAS.', good='Finished building ATLAS core.')
  File "./spkg-install", line 76, in assert_success
    traceback.print_stack(file=sys.stdout)
------------------------------------------------------------
Error:  Failed to build ATLAS.

real    1m2.106s
user    0m15.388s
sys     0m25.736s
************************************************************************
Error installing package atlas-3.10.0
************************************************************************

comment:172 Changed 6 years ago by vbraun

Oh I take it your museum piece doesn't have a Power4 CPU. Can you try

SAGE_ATLAS_ARCH=PPCG4 sage -f http://www.stp.dias.ie/~vbraun/Sage/spkg/atlas-3.10.0.spkg

comment:173 Changed 6 years ago by kcrisman

Correct, PowerPC G4, which I think is slightly different. It's currently compiling fine, I'll let you know the results.


In other news, #13408 seems to be a dup of this ticket. I don't know if we support "rhel 5" systems currently, nor whether this particular spkg fixes that person's problem, though.

comment:174 Changed 6 years ago by kcrisman

Finished installing shared ATLAS library.
Copying /Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0/patches/atlas-config to /Users/student/Desktop/sage-5.3.rc0/local/bin

real    1558m23.512s
user    1148m7.019s
sys     243m20.134s
Successfully installed atlas-3.10.0
Deleting temporary build directory
/Users/student/Desktop/sage-5.3.rc0/spkg/build/atlas-3.10.0
Making Python scripts relocatable...
Finished installing atlas-3.10.0.spkg

Good as far as it goes! Is this the record for longest ATLAS build ever?

Typing make after that still leads to the cvxopt can't find file for -lblas error; can someone remind me what the command would be to force rebuilding of dependencies (if that would even make a difference)?

comment:175 Changed 6 years ago by vbraun

So all we have to do is build ATLAS on OSX 10.4, then we don't have to figure out how to drive the ancient accelerate framework. Dima, can you change cvxopt to link against atlas on 10.4?

comment:176 Changed 6 years ago by kcrisman

I see, so that's why the problem is the same. Sounds like either we would do this, or fbissey's idea of a different configuration now.

I've touched cvxopt and am trying to build the rest of Sage now, so don't hold your breath yet that this was a permanent fix (in addition to roughly doubling the build time of Sage, not that this would matter on this platform).

comment:177 Changed 6 years ago by vbraun

I've changed the spkg to build by default on PPC OSX machines (Darwin + uname -p equals powerpc).

comment:178 follow-up: Changed 6 years ago by kcrisman

Like I said, don't count those chickens. I think this is pretty clearly related, given the libatlas reference.

building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/po
byte-compiling package 'graphics'
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/student/Desktop/sage-5.3.rc0/spkg/build/r-2.14.0.p3/src/library/grDevices/libs/grDevices.so':
  dlopen(/Users/student/Desktop/sage-5.3.rc0/spkg/build/r-2.14.0.p3/src/library/grDevices/libs/grDevices.so, 6): Symbol not found: _ATL_DecAtomicCount
  Referenced from: /Users/student/Desktop/sage-5.3.rc0/local/lib/libatlas.2.dylib
  Expected in: dynamic lookup
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
make[6]: *** [../../../library/graphics/R/graphics.rdb] Error 1
make[5]: *** [all] Error 2
make[4]: *** [R] Error 1
make[3]: *** [R] Error 1
make[2]: *** [R] Error 1
Error building R.

real    44m11.283s
user    28m7.249s
sys     6m59.266s
************************************************************************
Error installing package r-2.14.0.p3
************************************************************************

I think that's the last spkg other than rubiks and sagetex, actually, so cvxopt and r might be the only problems with this approach.

comment:179 Changed 6 years ago by kcrisman

Haha, I was wrong. Same error in Scipy:

23, in <module>
    from numpy.linalg import lapack_lite
ImportError: dlopen(/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so, 2): Symbol not found: _ATL_DecAtomicCount
  Referenced from: /Users/student/Desktop/sage-5.3.rc0/local/lib/libatlas.2.dylib
  Expected in: dynamic lookup

Error building scipy.

real    0m3.779s
user    0m0.437s
sys     0m0.840s
************************************************************************
Error installing package scipy-0.9.p1
************************************************************************

comment:180 Changed 6 years ago by kcrisman

And finally:

spkg/pipestatus "./sage --docbuild --no-pdf-links all html  2>&1" "tee -a dochtml.log"
Warning: Could not import sage.calculus.riemann dlopen(/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so, 2): Symbol not found: _ATL_DecAtomicCount
  Referenced from: /Users/student/Desktop/sage-5.3.rc0/local/lib/libatlas.2.dylib
  Expected in: dynamic lookup

Traceback (most recent call last):
  File "/Users/student/Desktop/sage-5.3.rc0/devel/sage/doc/common/builder.py", line 1098, in <module>
    getattr(get_builder(name), type)()
  File "/Users/student/Desktop/sage-5.3.rc0/devel/sage/doc/common/builder.py", line 243, in _wrapper
    getattr(get_builder(document), name)(*args, **kwds)
  File "/Users/student/Desktop/sage-5.3.rc0/devel/sage/doc/common/builder.py", line 363, in _wrapper
    self.write_auto_rest_file(module_name)
  File "/Users/student/Desktop/sage-5.3.rc0/devel/sage/doc/common/builder.py", line 622, in write_auto_rest_file
    title = self.get_module_docstring_title(module_name)
  File "/Users/student/Desktop/sage-5.3.rc0/devel/sage/doc/common/builder.py", line 580, in get_module_docstring_title
    __import__(module_name)
  File "numpy.pxd", line 154, in init sage.calculus.interpolators (sage/calculus/interpolators.c:5716)
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/__init__.py", line 136, in <module>
    import add_newdocs
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 13, in <module>
    from polynomial import *
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 11, in <module>
    import numpy.core.numeric as NX
AttributeError: 'module' object has no attribute 'core'
make: *** [doc-html] Error 1

so it won't even build doc, which is weird, since it did say that Sage started properly.

comment:181 Changed 6 years ago by fbissey

The last two errors are really a misconfiguration/miscompilation of numpy. If you look at /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so with otool -L (I think) you may see something. In fact the deeper problem seem to be that the dynamic lookup doesn't find libatlas.dylib. I am not sure if explicit linking would solve the problem. We should look at the numpy spkg and also atyour numpy log to see how lapack_lite.so was linked.

comment:182 Changed 6 years ago by kcrisman

:~/Desktop/sage-5.3.rc0 student$ otool -L local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so 
local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so:
        /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /Users/student/Desktop/sage-5.3.rc0/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.12)

I've uploaded the log to http://sage.math.washington.edu/home/kcrisman/numpy-1.5.1.p1.log as well. What do you think the R problem is?

comment:183 Changed 6 years ago by fbissey

For R it looks like a similar problem. R uses lapack and compile its own subset if not present. It also looks for ATLAS specific bits. Did you run otool from the sage shell? In this case I don't think it matters but you should look at those library problem from a sage shell to get the right LD_LIBRARY_PATH settings.

comment:184 Changed 6 years ago by kcrisman

$ otool -L local/lib/python2.7/site-pack
ages/numpy/linalg/lapack_lite.so 
local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so:
        /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /Users/student/Desktop/sage-5.3.rc0/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.12)

comment:185 Changed 6 years ago by fbissey

OK that's weird. According to your log of building numpy, lapack_lite.so was compiled against veclib rather than atlas and this is in accord with your otool output. So the problem may steem from a relinking or hiding of the veclib library by atlas. It is probably finding the symbols in the ATLAS install first. The problem in turn seems to be that libatlas.2.dylib is missing a symbol or that it should be provided by an extra library not provided. otool -L -r on libatlas.2.dylib? (I hope the -r does what I except: same thing as -r in ldd in linux), actually on lapack_lite.so while you are at it.

comment:186 Changed 6 years ago by kcrisman

I'm not sure that was what you wanted.

$ otool -L -r local/lib/libatlas.dylib local/lib/libatlas.dylib:
        /Users/student/Desktop/sage-5.3.rc0/local/lib/libatlas.2.dylib (compatibility version 4.0.0, current version 4.0.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /Users/student/Desktop/sage-5.3.rc0/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.12)
External relocation information 0 entries
address  pcrel length extern type    scattered symbolnum/value
Local relocation information 1107 entries
address  pcrel length extern type    scattered symbolnum/value
005a7000 0     2      0      0       0         1
005a7c4c 0     2      0      0       0         1
005a7c48 0     2      0      0       0         1
005a7c44 0     2      0      0       0         1

This continues for a long, long while.

comment:187 Changed 6 years ago by fbissey

It's not. I am not sure there is an otool equivalent for "ldd -r". Another point: from the error you get I am expecting that if you start python from the sage shell and then "import numpy" if will fail with a similar error. Starting python with "-v" may show us what libraries get loaded exactly when you import numpy.

comment:188 Changed 6 years ago by kcrisman

According to the man page for ldd, that option only works on ELF binaries (whatever that means), and this blog post confirms that Mac doesn't use them. This other blog post suggests that dyld might be useful...

Numpy results coming up.

comment:189 Changed 6 years ago by kcrisman

Same symbol not found, all the way at the end. If this is too long let me know and I'll edit (!) this comment.

>>> import numpy
import numpy # directory /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/__init__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/__init__.py
import numpy # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/__init__.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/__config__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/__config__.py
import numpy.__config__ # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/__config__.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/version.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/version.py
import numpy.version # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/version.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/_import_tools.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/_import_tools.py
import numpy._import_tools # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/_import_tools.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/add_newdocs.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/add_newdocs.py
import numpy.add_newdocs # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/add_newdocs.pyc
import numpy.lib # directory /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/__init__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/__init__.py
import numpy.lib # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/__init__.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/info.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/info.py
import numpy.lib.info # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/info.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/type_check.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/type_check.py
import numpy.lib.type_check # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/type_check.pyc
import numpy.core # directory /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/__init__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/__init__.py
import numpy.core # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/__init__.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/info.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/info.py
import numpy.core.info # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/info.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/multiarray.so", 2);
import numpy.core.multiarray # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/multiarray.so
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/umath.so", 2);
import numpy.core.umath # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/umath.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/_internal.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/_internal.py
import numpy.core._internal # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/_internal.pyc
import numpy.compat # directory /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/__init__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/__init__.py
import numpy.compat # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/__init__.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/_inspect.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/_inspect.py
import numpy.compat._inspect # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/_inspect.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/py3k.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/py3k.py
import numpy.compat.py3k # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/compat/py3k.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/numerictypes.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/numerictypes.py
import numpy.core.numerictypes # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/numerictypes.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/_sort.so", 2);
import numpy.core._sort # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/_sort.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/numeric.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/numeric.py
import numpy.core.numeric # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/numeric.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/_dotblas.so", 2);
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/arrayprint.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/arrayprint.py
import numpy.core.arrayprint # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/arrayprint.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/fromnumeric.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/fromnumeric.py
import numpy.core.fromnumeric # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/fromnumeric.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/cPickle.so", 2);
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/cStringIO.so", 2);
import cStringIO # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/cStringIO.so
import cPickle # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/cPickle.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/defchararray.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/defchararray.py
import numpy.core.defchararray # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/defchararray.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/records.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/records.py
import numpy.core.records # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/records.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/memmap.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/memmap.py
import numpy.core.memmap # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/memmap.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/scalarmath.so", 2);
import numpy.core.scalarmath # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/scalarmath.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/function_base.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/function_base.py
import numpy.core.function_base # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/function_base.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/machar.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/machar.py
import numpy.core.machar # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/machar.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/getlimits.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/getlimits.py
import numpy.core.getlimits # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/getlimits.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/shape_base.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/shape_base.py
import numpy.core.shape_base # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/core/shape_base.pyc
import numpy.testing # directory /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/__init__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/__init__.py
import numpy.testing # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/__init__.pyc
import unittest # directory /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/__init__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/__init__.py
import unittest # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/__init__.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/result.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/result.py
import unittest.result # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/result.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/StringIO.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/StringIO.py
import StringIO # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/StringIO.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/util.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/util.py
import unittest.util # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/util.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/collections.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/collections.py
import collections # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/collections.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/_collections.so", 2);
import _collections # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/_collections.so
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/operator.so", 2);
import operator # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/operator.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/keyword.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/keyword.py
import keyword # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/keyword.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/heapq.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/heapq.py
import heapq # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/heapq.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/itertools.so", 2);
import itertools # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/itertools.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/bisect.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/bisect.py
import bisect # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/bisect.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/_bisect.so", 2);
import _bisect # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/_bisect.so
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/_heapq.so", 2);
import _heapq # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/_heapq.so
import thread # builtin
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/functools.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/functools.py
import functools # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/functools.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/_functools.so", 2);
import _functools # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/_functools.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/case.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/case.py
import unittest.case # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/case.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/difflib.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/difflib.py
import difflib # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/difflib.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/pprint.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/pprint.py
import pprint # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/pprint.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/suite.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/suite.py
import unittest.suite # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/suite.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/loader.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/loader.py
import unittest.loader # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/loader.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/fnmatch.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/fnmatch.py
import fnmatch # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/fnmatch.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/main.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/main.py
import unittest.main # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/main.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/runner.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/runner.py
import unittest.runner # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/runner.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/time.so", 2);
import time # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/time.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/signals.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/signals.py
import unittest.signals # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/unittest/signals.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python/weakref.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python/weakref.py
import weakref # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python/weakref.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/decorators.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/decorators.py
import numpy.testing.decorators # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/decorators.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/utils.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/utils.py
import numpy.testing.utils # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/utils.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/nosetester.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/nosetester.py
import numpy.testing.nosetester # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/nosetester.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/numpytest.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/numpytest.py
import numpy.testing.numpytest # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/testing/numpytest.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/ufunclike.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/ufunclike.py
import numpy.lib.ufunclike # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/ufunclike.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/index_tricks.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/index_tricks.py
import numpy.lib.index_tricks # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/index_tricks.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/math.so", 2);
import math # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/lib-dynload/math.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/function_base.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/function_base.py
import numpy.lib.function_base # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/function_base.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/twodim_base.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/twodim_base.py
import numpy.lib.twodim_base # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/twodim_base.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/_compiled_base.so", 2);
import numpy.lib._compiled_base # dynamically loaded from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/_compiled_base.so
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/arraysetops.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/arraysetops.py
import numpy.lib.arraysetops # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/arraysetops.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/utils.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/utils.py
import numpy.lib.utils # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/utils.pyc
import numpy.matrixlib # directory /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/matrixlib
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/matrixlib/__init__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/matrixlib/__init__.py
import numpy.matrixlib # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/matrixlib/__init__.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/matrixlib/defmatrix.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/matrixlib/defmatrix.py
import numpy.matrixlib.defmatrix # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/matrixlib/defmatrix.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/shape_base.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/shape_base.py
import numpy.lib.shape_base # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/shape_base.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/stride_tricks.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/stride_tricks.py
import numpy.lib.stride_tricks # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/stride_tricks.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/scimath.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/scimath.py
import numpy.lib.scimath # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/scimath.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/polynomial.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/polynomial.py
import numpy.lib.polynomial # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/polynomial.pyc
import numpy.linalg # directory /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/__init__.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/__init__.py
import numpy.linalg # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/__init__.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/info.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/info.py
import numpy.linalg.info # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/info.pyc
# /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/linalg.pyc matches /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/linalg.py
import numpy.linalg.linalg # precompiled from /Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/linalg.pyc
dlopen("/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so", 2);
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/__init__.py", line 136, in <module>
    import add_newdocs
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from numpy.lib import add_newdoc
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 13, in <module>
    from polynomial import *
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 17, in <module>
    from numpy.linalg import eigvals, lstsq
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 48, in <module>
    from linalg import *
  File "/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 23, in <module>
    from numpy.linalg import lapack_lite
ImportError: dlopen(/Users/student/Desktop/sage-5.3.rc0/local/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so, 2): Symbol not found: _ATL_DecAtomicCount
  Referenced from: /Users/student/Desktop/sage-5.3.rc0/local/lib/libatlas.2.dylib
  Expected in: dynamic lookup

comment:190 Changed 6 years ago by GeorgSWeber

Hi,

now that I re-read the comments here again, I seem to faintly remember this problem circle from my adventure with lmonade (Gentoo Prefix derivative) on OS X 10.4 last year. See my travel account about this, points "22." and "26." and especially the rant following that in:

https://groups.google.com/d/msg/lmnd-devel/1ZqHx1JBY2Q/syAOZYtZN4IJ

  1. If my memory is correct, the symbol "_ATL_DecAtomicCount" comes from/is resolved in libblas(.dylib), this could be checked independently from the underlying OS. Where is libblas.dylib (libblas.so under Linux) located, is it something like .../lib/blas/reference/?
  1. Karl-Dieter, I try to catch up with what you installed and tried, but till then could you please try

"sage -R"

anyway in the meantime (from the shell prompt) and print the result, probably an error message from the OS X 10.4 less-than-optimal dyld dynamic loader?

  1. If this really is what the problem is about, some symlinks might suffice, but I do not remember exactly how and for which libraries (both R and maxima were affected in a weird way, and Volker's compilerwrapper intervenes in the lmonade setting, too).

Best regards,

Georg

P.S.: Later last year, I ultimately managed somehow to get some 64-bit Sage (lmonade flavour) working on the 32-bit OS X 10.4, so in the course, I definitely had to successfully build and link/reference some new "self-made" 64-bit atlas/blas, since OS X 10.4 only ships with a 32-bit "system copy" of atlas/blas, so this is definitely doable. But even Python itself is not officially supported as 64-bit version on OS X 10.4, so quite some more hackery was needed. (This only might be interesting, if one day the Sage project wants to get rid of the dependency of certain Apple system library headers, which come only with "XCode", or more precisely the "command line tools", on newer OS X versions --- currently these are a prerequisite for building Sage on OS X.)

comment:191 Changed 6 years ago by fbissey

Yeah I remember those bits vaguely now. But lmnd never used libvec unless you hacked something (I have an ebuild to allow that but no-one else has seen it). The location you mention in (1) is specific to gentoo and correspond to netlib blas (otherwise called blas reference) current lmnd uses a different scheme. A lmnd user could pick openblas or gotoblas these days.

The link idea is interesting, having $SAGE_LOCAL/lib/libblas.dylib pointing to libvec could help.

comment:192 Changed 6 years ago by kcrisman

(sage-sh) student@Dasher-03:sage-5.3.rc0$ ./sage -R
/Users/student/Desktop/sage-5.3.rc0/spkg/bin/sage: line 496: /Users/student/Desktop/sage-5.3.rc0/local/bin/R: No such file or directory

But that's expected, since I didn't succeed in building R with this.

comment:193 Changed 6 years ago by GeorgSWeber

With OS X 10.4 on my MacIntel?, I ran with sage-5.3.rc1 into the same problem as earlier reported here (for Sage-5.2 and Sage-5.1, I can confirm the problem exists already for Sage-5.1):

https://groups.google.com/forum/?fromgroups=#!searchin/sage-devel/5.1$205.2/sage-devel/0T4djTzK0BE/4d7dnBJq9YQJ

The fix is trivial (once one knows what the problem is), in module_list.py there is a "-lpari" option missing for the cremona.mat module (for the other cremona.xxx modules, the "-lpari" option is listed with a comment about "Cygiwn might need this" --- obviously the dynamic linker/loader on OS X 10.4 MacIntel? is comparably dumb). Once I sorted out creating a corresponding ticket, uploaded the fix there, and answered to the thread above, I'll continue with the atlas story here.

comment:194 Changed 6 years ago by GeorgSWeber

Hi all, it is really puzzling, why with current Sage-5.3 on OS X 10.4 PPC (yesterday released, it's up on the servers), the cvxopt-1.1.5 spkg finds during its build the blas.dylib --- but with the changes of this ticket here, cvxopt-1.1.5 does not find it anymore (see comments #142 and #170 here).

Some facts:

  • On OS X 10.4 PPC, under the directory "/usr/lib/", there are no "atlas.dylib", "blas.dylib", "cblas.dylib", "lapack.dylib" files or links (on OS X 10.4 Intel, these four entries *do* exist there, as links).
  • On OS X 10.4 (both PPC and Intel), Sage historically does not build atlas nor blas (nor cblas) nor lapack, so there are not corresponding dylibs either under "$SAGE_ROOT/local/lib/".
  • In $SAGE_ROOT/devel/sage-main/module_list.py, there is some magic for the configuration of the "BLAS" and "BLAS2" macros. Given the above fact(s), on OS X 10.4 PPC, I read these as resulting to use "gslblas" (!!) provided by Sage, on OS X 10.4 Intel, I read these as resulting to use the system "cblas" and "atlas".
  • On OS X 10.4 Intel, these "system" atlas, blas, and cblas libraries actually all link to one and the same "blas.dylib" located under /System/Libraries/Frameworks/Accelerate?.framework/version/A/vecLIB.framwork/version/A/ (or some permutation thereof, I can't look up the exact path right now at the moment). These libraries are also located there under OS X 10.4 PPC, but there do not seem to be any links.
  • The old cvxopt-1.1.4(.p1) lists "gslblas" as library to be linked to, but actually, it is unclear at least to me, which kind of "blas" library really got used in the end on OS X 10.4 --- maybe on PPC some different one than on Intel.

Is it possible that currently, the build of cvxopt-1.1.5 on OS X 10.4 PPC succeeds only during a "whole" build of Sagte-5.3, the linker somehow caching the libraries it finds in the course of the build (especially "blas.dylib" somewhen before cvxopt is built) --- and with the changes of this ticket, the build sequence changes somehow so suddenly, "blas.dylib" is not anymore in this cache (or whatever kind of mechansim with the same result)?

comment:195 follow-up: Changed 6 years ago by fbissey

Before this ticket netlib's blas (blas spkg) would be build on OS X if I am not mistaken. So an unoptimized blas would be present to be picked in SAGE_LOCAL/lib. cblas would indeed be provided by gslblas if nothing else.

comment:196 in reply to: ↑ 195 Changed 6 years ago by dimpase

Replying to fbissey:

Before this ticket netlib's blas (blas spkg) would be build on OS X if I am not mistaken. So an unoptimized blas would be present to be picked in SAGE_LOCAL/lib. cblas would indeed be provided by gslblas if nothing else.

hmm, no, I think on OSX there is native blas/lapack (veclib) which was used (and still is used, given the right settings used to build Sage).

comment:197 follow-up: Changed 6 years ago by vbraun

I agree with Francois, we probably never used the ancient accelerate (OSX 10.4) framework correctly. In fact, this ticket makes it pretty clear that we did not.

comment:198 in reply to: ↑ 197 ; follow-up: Changed 6 years ago by dimpase

Replying to vbraun:

I agree with Francois, we probably never used the ancient accelerate (OSX 10.4) framework correctly. In fact, this ticket makes it pretty clear that we did not.

as far as CVXOPT is concerned, it does use MacOSX veclib (there was a OSX 10.7-related ticket which dealt with the fact that veclib changed some undefined behaviour when 10.7 was released, and CVXOPT got hit by this issue).

comment:199 in reply to: ↑ 198 ; follow-ups: Changed 6 years ago by vbraun

Replying to dimpase:

as far as CVXOPT is concerned, it does use MacOSX veclib

Are you sure? I think OSX 10.4 is rather different from modern OSX accelerate. Post the output of otool -L on OSX 10.4 PPC or it didn't happen ;)

comment:200 in reply to: ↑ 199 ; follow-up: Changed 6 years ago by kcrisman

Two hundred comments!

as far as CVXOPT is concerned, it does use MacOSX veclib

Are you sure? I think OSX 10.4 is rather different from modern OSX accelerate. Post the output of otool -L on OSX 10.4 PPC or it didn't happen ;)

Tell me the exact command (otool -L what_file?) and I'll do it as soon as I get to work.

comment:201 in reply to: ↑ 200 Changed 6 years ago by dimpase

Replying to kcrisman:

Two hundred comments!

as far as CVXOPT is concerned, it does use MacOSX veclib

Are you sure? I think OSX 10.4 is rather different from modern OSX accelerate. Post the output of otool -L on OSX 10.4 PPC or it didn't happen ;)

Tell me the exact command (otool -L what_file?) and I'll do it as soon as I get to work.

$ cd $SAGE_LOCAL/lib/python/site-packages/cvxopt
$ otool -L lapack.so

comment:202 follow-ups: Changed 6 years ago by kcrisman

So who was right?

Dasher-03:~/Desktop/sage-4.8/local/lib/python/site-packages/cvxopt student$ otool -L lapack.so 
lapack.so:
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.12)
        /Users/student/Desktop/sage-4.8/local/lib/libgsl.0.dylib (compatibility version 17.0.0, current version 17.0.0)
        /Users/student/Desktop/sage-4.8/local/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

This is with Sage 4.8, the last working binary I have on this box. I foolishly deleted all newer ones in the meantime. Sage 5.3 works on it, of course - in fact, I just used the app bundle yesterday - but it would take some time to start a fresh 5.3 or 5.4.beta0.

comment:203 in reply to: ↑ 202 Changed 6 years ago by dimpase

Replying to kcrisman:

So who was right?

Dasher-03:~/Desktop/sage-4.8/local/lib/python/site-packages/cvxopt student$ otool -L lapack.so 
lapack.so:
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.12)
        /Users/student/Desktop/sage-4.8/local/lib/libgsl.0.dylib (compatibility version 17.0.0, current version 17.0.0)
        /Users/student/Desktop/sage-4.8/local/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

looks like this particular system does not use the veclib framework. Is it Intel, or PPC?

comment:204 Changed 6 years ago by kcrisman

Dasher-03:~/Desktop/sage-4.8/local/lib/python/site-packages/cvxopt student$ uname -a
Darwin Dasher-03.local 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc

At 700 MHz and half a gig of ram, probably one of the lowest-capability machines running Sage today... but it works fine, if slow. But we're just spoiled - I'm sure Gauss or Newton would have been happy to have this :)

comment:205 in reply to: ↑ 202 Changed 6 years ago by GeorgSWeber

Replying to kcrisman:

So who was right?

Dasher-03:~/Desktop/sage-4.8/local/lib/python/site-packages/cvxopt student$ otool -L lapack.so 
lapack.so:
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.12)
        /Users/student/Desktop/sage-4.8/local/lib/libgsl.0.dylib (compatibility version 17.0.0, current version 17.0.0)
        /Users/student/Desktop/sage-4.8/local/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

This is with Sage 4.8, the last working binary I have on this box. I foolishly deleted all newer ones in the meantime. Sage 5.3 works on it, of course - in fact, I just used the app bundle yesterday - but it would take some time to start a fresh 5.3 or 5.4.beta0.

It is not necessary to "start a fresh 5.3 or 5.4.beta0". Instead, one can go to some Sage OS X PPC download page, http://boxen.math.washington.edu/home/sagemath/sage-mirror/osx/powerpc/index.html , download from there e.g. "sage-5.3-OSX-32bit-10.4-PowerMacintosh?-Darwin.dmg", and look inside --- on any OS X system/version. The result is ... surprising, to say the least:

sagebuilder$ otool -L lapack.so
lapack.so:
        /Users/buildbot/build/sage/moufang-1/moufang_binary/build/sage-5.3/local/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /Users/buildbot/build/sage/moufang-1/moufang_binary/build/sage-5.3/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.12)

The two occurences of "libgcc_s.1.dylib" are somewhat fishy, but apparently nothing new, and I'd vote for that topic being a complete different story, and not to be treated here any further. The library "libSystem.B.dylib" is the C runtime on OS X, AFAIK. But then only libfortran.dylib --- and no trace whatsoever of any *las.dylib?!?!? For comparison, on OS X 10.4 Intel, for Sage-5.3.rc1 the analoguous result is:

sagebuilder$ otool -L lapack.so
lapack.so:
        /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib (compatibility version 1.0.0, current version 192.15.0)
        /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 192.15.0)
        /Users/Shared/sage/sage-5.3.rc1/local/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /Users/Shared/sage/sage-5.3.rc1/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.11)

I would conclude that it is problematic, that the OS X 10.4 PPC linker/loader builds at all the current cvxopt-1.1.5 spkg contained in Sage-5.3, producing results with such incomplete dependency information. Looking closely on the command line, it is told to use "-undefined dynamic_lookup" (which seems to save us at runtime later, however only by chance, I guess), so essentially it does what it should --- but then, why does that linker/loader under some very comparable circumstances error out with "/usr/bin/ld: can't locate file for: -lblas"???

Of the different alternatives to come to an end with this ticket here (which is about the new atlas-3.10 spkg), I like the "link idea" (see the comment 191 from Francois), i.e. the atlas spkg, generally on OS X (!), doing no more and no less than creating links in $SAGE_LOCAL/lib/ --- the same as exist in /usr/lib/, at least on OS X 10.4 Intel. More precisely, three links pointing to the "framework" blas library:

libatlas.dylib -> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
libblas.dylib -> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
libcblas.dylib -> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

and one more link for the "framework" lapack library (all link targets being absolute, not relative):

liblapack.dylib -> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

A quick check shows that at least on OS X Intel, the absolute path to these framework libraries is the same for OS X 10.4, 10.5, 10.6, and 10.7 (I can't check for OS X 10.8), and even on OS X 10.7.3, there still is only one version "A", which is the "Current" version of that framework.

This change, for all OS X variants, would be a bit intrusive. But to me, it seems to bring the OS X world a bit closer to the situation on the other OSes. I offer to test a respectively updated atlas spkg on the OS X systems/versions I have access to. (In the "patches" subdir, one also might wish to delete the "edit" duplicates of two files, those with a tilde at the end of their file name.)

Thoughts?

comment:206 Changed 6 years ago by kcrisman

I can't pretend to understand exactly what all the linking is doing here - it seems very much a black box. But those two absolute paths certainly exist on my box, and seem like a good alternative to trying to get ATLAS to build from scratch on OS X for now. I will naturally also volunteer to test on anything I have access to.

comment:207 in reply to: ↑ 199 Changed 6 years ago by dimpase

Replying to vbraun:

Replying to dimpase:

as far as CVXOPT is concerned, it does use MacOSX veclib

Are you sure? I think OSX 10.4 is rather different from modern OSX accelerate. Post the output of otool -L on OSX 10.4 PPC or it didn't happen ;)

On 10.5 PPC it is veclib all right...

$ otool -L lapack.so 
lapack.so:
        /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib (compatibility version 1.0.0, current version 218.0.0)

comment:208 Changed 6 years ago by kcrisman

So you mean that after

if conf['Darwin?'] \
        and not os.environ.has_key('SAGE_ATLAS_ARCH'):
    print 'Skipping build of ATLAS on intel OS X'
    sys.exit(0)


in the spkg-install (well, before the exit) we should add the linking described comment:205? That would seem easy enough, though I don't know what the syntax would be (not just ln, I assume).

Last edited 6 years ago by kcrisman (previous) (diff)

comment:209 Changed 6 years ago by vbraun

  • Description modified (diff)
  • Status changed from needs_work to needs_review

I don't think we should be symlinking system libraries into local/lib if we can avoid it. Really cvxopt is broken, it should be linking against the accelerate blas but doesn't. In particular, we should correctly set BLAS_LIB_DIR in cvxopt on Darwin. The update spkg fixes this. I've also changed the atlas spkg back to not build by default on Darwin. Please test the combination of both spkgs on your OSX machines.

comment:210 Changed 6 years ago by kcrisman

With Sage 5.4.beta1:

applying trac_10508_root_repo.patch
patching file spkg/install
Hunk #2 succeeded at 363 with fuzz 1 (offset 47 lines).
patching file spkg/standard/deps
Hunk #2 succeeded at 60 with fuzz 1 (offset -1 lines).
Hunk #4 FAILED at 525
1 out of 4 hunks FAILED -- saving rejects to file spkg/standard/deps.rej
patch failed, unable to continue (try -v)

This is because of

# Lapack depends on SAGE_ROOT_REPO because it *executes* Fortran code at
# build time.  Therefore, it needs an up-to-date version of sage-env
# which adds $SAGE_LOCAL/lib64 to the LD_LIBRARY_PATH.

which if I recall correctly is from #13395, so this would need to be updated. For now it won't affect me building from source, so I'll just do this by hand, but I don't know the right solution to combining those two things.

comment:211 Changed 6 years ago by kcrisman

  • Reviewers changed from Benjamin Jones to Benjamin Jones, Karl-Dieter Crisman, Dmitrii Pasechnik, Georg Weber, François Bissey, John Palmieri
  • Status changed from needs_review to needs_work

Here's one more issue - I have a feeling this isn't OS X specific ;-)

File "/Users/.../sage-5.4.beta1/devel/sage-main/sage/misc/package.py", line 119:
    sage: install_package()
Expected:
    ['atlas...', 'blas...', ...]
Got:
    ['atlas-3.10.0', 'boehm_gc-7.2.alpha6.p2', 'boost-cropped-1.34.1', 'bzip2-1.0.6', 'cddlib-094f.p11', 'cephes-2.8', 'cliquer-1.2.p11', 
<snip>

This was a change in #11021, apparently introduced in beta0. This was on 10.7; the build will not finish for quite a while on 10.4.

Interestingly, I didn't need to apply the doctest patch, so I guess that is only in certain hardware-specific circumstances.

comment:212 Changed 6 years ago by kcrisman

And just to prove something must have happened, old versus new:

$ otool -L lapack.so 
lapack.so:
	/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Users/.../sage-5.4.beta0/local/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0)
	/Users/.../sage-5.4.beta0/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
$ otool -L lapack.so 
lapack.so:
	/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib (compatibility version 1.0.0, current version 1.0.0)
	/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Users/.../sage-5.4.beta1/local/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0)
	/Users/.../sage-5.4.beta1/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

Changed 6 years ago by vbraun

Updated patch

comment:213 Changed 6 years ago by vbraun

  • Description modified (diff)
  • Status changed from needs_work to needs_review

comment:214 Changed 6 years ago by kcrisman

Edited dumb question. Here is what remains.


Is it ok that there is basically an spkg in an spkg? We just got rid of this in the R/RPy situation, but I assume this is somehow different. Somehow.

Last edited 6 years ago by kcrisman (previous) (diff)

comment:215 Changed 6 years ago by vbraun

The new atlas needs the lapack tarball to build. The only alternative would be to have a separate lapack spkg that saves a tarball of its sources somewhere ;-)

comment:216 follow-ups: Changed 6 years ago by dimpase

it does build OK on MacOSX 10.5 PPC (namely, a G4 processor).

I'll report the result of testlong when it's done.

comment:217 in reply to: ↑ 216 Changed 6 years ago by kcrisman

it does build OK on MacOSX 10.5 PPC (namely, a G4 processor).

Same on my 10.4 PPC G4 machine.

I'll report the result of testlong when it's done.

It's not done, but the failures all seem to be of the following sort - not finding -lblas:

sage -t  -force_lib "devel/sage/sage/misc/preparser.py"     
**********************************************************************
File "/Users/student/Desktop/sage-5.4.beta1/devel/sage/sage/misc/preparser.py", line 1526:
    sage: z=0; sage.misc.preparser.load(t,globals())
Expected:
    Compiling ....pyx...
    hi 0
Got:
    Compiling /Users/student/.sage//temp/Dasher_03.local/6088//tmp_2.pyx...
    Error compiling cython file:
    Error compiling /Users/student/.sage//temp/Dasher_03.local/6088//tmp_2.pyx:
    running build
    running build_ext
    building '_Users_student__sage_temp_Dasher_03_local_6088_tmp_2_pyx_0' extension
    creating build
    creating build/temp.macosx-10.4-ppc-2.7
    gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/student/Desktop/sage-5.4.beta1/local/include/csage/ -I/Users/student/Desktop/sage-5.4.beta1/local/include/ -I/Users/student/Desktop/sage-5.4.beta1/local/include/python2.7/ -I/Users/student/Desktop/sage-5.4.beta1/local/lib/python2.7/site-packages/numpy/core/include -I/Users/student/Desktop/sage-5.4.beta1/devel/sage/sage/ext/ -I/Users/student/Desktop/sage-5.4.beta1/devel/sage/ -I/Users/student/Desktop/sage-5.4.beta1/devel/sage/sage/gsl/ -I/Users/student/.sage//temp/Dasher_03.local/6088 -I/Users/student/Desktop/sage-5.4.beta1/local/include/python2.7 -c _Users_student__sage_temp_Dasher_03_local_6088_tmp_2_pyx_0.c -o build/temp.macosx-10.4-ppc-2.7/_Users_student__sage_temp_Dasher_03_local_6088_tmp_2_pyx_0.o -w -O2
    creating build/lib.macosx-10.4-ppc-2.7
    gcc -bundle -undefined dynamic_lookup -L/Users/student/Desktop/sage-5.4.beta1/local/lib build/temp.macosx-10.4-ppc-2.7/_Users_student__sage_temp_Dasher_03_local_6088_tmp_2_pyx_0.o -L/Users/student/Desktop/sage-5.4.beta1/local//lib/ -lmpfr -lgmp -lgmpxx -lstdc++ -lpari -lm -ljc -lgsl -lgslcblas -lblas -lntl -lcsage -o build/lib.macosx-10.4-ppc-2.7/_Users_student__sage_temp_Dasher_03_local_6088_tmp_2_pyx_0.so -L/Users/student/Desktop/sage-5.4.beta1/local//lib
    <BLANKLINE>
    /usr/bin/ld: can't locate file for: -lblas
    collect2: ld returned 1 exit status
    error: command 'gcc' failed with exit status 1
    <BLANKLINE>

comment:218 Changed 6 years ago by vbraun

Can you try to make a symlink

 cd $SAGE_LOCAL/lib
 ln -s /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib .

and run the doctests again?

comment:219 Changed 6 years ago by kcrisman

I'm pretty sure all the non-timeouts are related to this.

        sage -t  -force_lib "devel/sage/sage/misc/cachefunc.pyx"
        sage -t  -force_lib "devel/sage/sage/misc/cython.py"
        sage -t  -force_lib "devel/sage/sage/misc/lazy_attribute.py"
        sage -t  -force_lib "devel/sage/sage/misc/package.py"
        sage -t  -force_lib "devel/sage/sage/misc/preparser.py"
        sage -t  -force_lib "devel/sage/sage/misc/sagedoc.py"
        sage -t  -force_lib "devel/sage/sage/misc/sageinspect.py"
        sage -t  -force_lib "devel/sage/sage/misc/superseded.py"
        sage -t  -force_lib "devel/sage/sage/parallel/decorate.py"
        sage -t  -force_lib "devel/sage/sage/plot/contour_plot.py" # Time out
        sage -t  -force_lib "devel/sage/sage/plot/graphics.py" # Time out
        sage -t  -force_lib "devel/sage/sage/plot/plot.py" # Time out
        sage -t  -force_lib "devel/sage/sage/rings/number_field/number_field_element.pyx" # Time out
        sage -t  -force_lib "devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py" # Time out
        sage -t  -force_lib "devel/sage/sage/schemes/elliptic_curves/heegner.py" # Time out
        sage -t  -force_lib "devel/sage/sage/structure/element.pyx"
        sage -t  -force_lib "devel/sage/sage/structure/misc.pyx"

I'll try the symlink now.

comment:220 Changed 6 years ago by kcrisman

This seems to work fine. I think that if just putting this link in the top for only PPC machines (or even only 10.4 PPC machines if Dima's tests turn out fine) would be fine. Or even some of the other links e.g. to lapack, if appropriate.

I also feel your frustration with not having an easy machine to test with. I would really like to make this one available, but the way I understand it that's not an option - at least, I tried the ssh method above and it didn't seem to work properly.

comment:221 Changed 6 years ago by vbraun

I've updated the spkg to symlink the veclib blas and lapack to $SAGE_LOCAL/lib/ on OSX PPC. This should finally work now. Please test and review!

Karl-Dieter, you went beyond your duty to debug this. But every platform dies eventually, you just have to notice the signs. E.g. when it starts getting more difficult than finding a SPARC box ;)

comment:222 Changed 6 years ago by kcrisman

Haha! Anyway, I'll still try it out.

By the way, I presume the cvxopt changes might not be necessary (at least not the Accelerate-related one) now, but that it also wouldn't hurt to keep them in for all Macs?

comment:223 Changed 6 years ago by GeorgSWeber

I ran also into the problem of comment 211, but I see that one is already cared for.

The latest "pyx_preparse()" problem might not be entirely due to what is done about "BLAS configuration/setup", and how it is done in .../sage/misc/cython.py (see especially lines 64-67 in conjunction with lines 78-79 and line 265 in that file), but certainly creates pretty exactly the kind of problem observed in comment 216, and healed by the symlink in comment 218. (It's quite a miracle to me, how that could have ever worked before under OS X 10.4 PPC --- which I know it did!)

Which leaves us with either adjusting every occurence of BLAS configuration/setup (sage/module_list.py lines 22-44, sage/misc/cython.py lines as above, cvxopt and possibly yet another spkg or two, ...) for the "OS X 10.4 PPC case" (we already *do* search for "/usr/lib/libclas.{so, dylib}" in those places, and use that one if one can be found there, just extend the search to "/System/Library/Frameworks/Accelerate?.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib" in case the former search failed), or else try the symlink approach. Or some "hybrid" approach, symlinking only on OS X 10.4 PPC.

@Volker:

In comment 209 you wrote:

I don't think we should be symlinking system libraries into local/lib if we can avoid it.

So if you think that creating symlinks to "outside-of-sage" libraries in $SAGE_ROOT/local/lib/ (and possibly to header files like "cblas.h" and "clapack.h" in $SAGE_ROOT/local/include/, too) should be avoided, could you please give some insights about the reasoning behind?

P.S.:

I can't find the following note about trying to actually *build and use* ATLAS on OS X in the comments so far, so here it is: If we want to be able to do so one day, at least the numpy build system needs to be patched (somewhere in src/numpy/distutils/system_info.py, classes "lapack_opt_info" and "blas_opt_info"), since there the usage of the Accelerate framework on OS X is hardcoded --- which seems to be problematic, if other parts of Sage do not use the same underlying LAPACK and BLAS libraries. Essentially, one should be able to "just" re-use patches from the respective Gentoo ebuilds, it has the air of a "reine Fleissarbeit" (dict.leo.org: "a diligent but routine piece of work"). Of course, any OS X 10.4 PPC specific bits and pieces would then have to "behave well", too ... (the "symlinking approach" would probably make that part rather straightforward).

P.P.S.:

Now that quite a few people are involved, wouldn't it make sense to try to clean up that current BLAS configuration/setup code parts a bit? At least between module_list.py, cython.py and the cvxopt spkg install, more or less the same functionality is tripled. Possibly by moving all this to setting (or taking over from the parent environment) "SAGE_BLAS_LIB", "SAGE_CBLAS_LIB", "SAGE_ATLAS_LIB" or the like environment variables, ensuring these are sanely set at both the start of a Sage build (prereq spkg?!), as well as in the Sage environment at runtime (sage-shell?!), and then in "module_list.py", "misc/cython.py", cvxopt spkg install, ... simply referring to/using/relying on these env vars ... just letting the thoughts flow, sorry :-)

P.P.P.S.:

Unfortunately, it took me so long to write this, that it this message already mostly outdated (by comments 221, 222).

comment:224 Changed 6 years ago by vbraun

While ugly, its not really a problem if some parts of the Sage install link to alternative blas implementations. Though for now I think we'll just do the symlink workaround for OSX PPC.

I'm totally against new environment variables. The proper solution IMHO is a blas-config script that can spit out the required options. For example, blas-config --cflags --f77blas would give you the f77 compiler flags. Then we can step by step replace all hardcoded blas guesses by blas-config calls. But this is stuff for a future ticket ;-)

comment:225 follow-up: Changed 6 years ago by kcrisman

I'm getting a really weird build error I didn't get before on 5.4.beta1 with this stuff in it. This is on OS X 10.7.

Traceback (most recent call last):
  File "setup.py", line 199, in <module>
    check_for_dependencies()
  File "/Users/.../sage-5.4.beta1-atlas/spkg/build/ipython-0.10.2.$
    check_for_pexpect()
  File "/Users/.../sage-5.4.beta1-atlas/spkg/build/ipython-0.10.2.$
    print_status("pexpect", pexpect.__version__)
AttributeError: 'module' object has no attribute '__version__'
Error building IPython.

real    0m0.298s
user    0m0.194s
sys     0m0.056s
************************************************************************
Error installing package ipython-0.10.2.p1
************************************************************************

Granted, I was using six threads, but it is repeatable. I'm going to try this again, and I really can't understand it. I haven't seen anyone give this kind of report. I also get

****************************************************
nothing changed
pulling from /Users/.../sage-5.4.beta1-atlas/spkg/build/extcode-5.4.beta1
searching for changes
abort: repository is unrelated
abort: merging with a working directory ancestor has no effect
nothing changed
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
./spkg-install: line 33: /Users/.../sage-5.4.beta1-atlas/data/extcode/.hg/hgrc: No such file or directory

real	0m0.464s
user	0m0.344s
sys	0m0.108s
************************************************************************
Error installing package extcode-5.4.beta1
************************************************************************

I don't see how this could be related, but wanted to report it.

comment:226 in reply to: ↑ 216 Changed 6 years ago by dimpase

Replying to dimpase:

it does build OK on MacOSX 10.5 PPC (namely, a G4 processor).

I'll report the result of testlong when it's done.

all tests pass, no problem, without any workarounds needed for 10.4. Thus 10.5 behaves quite well.

comment:227 in reply to: ↑ 225 ; follow-up: Changed 6 years ago by kcrisman

I don't see how this could be related, but wanted to report it.

It must have been some kind of weird race condition - I did another build from scratch on 5.4.beta1 on 10.7 with these changes and only had the expected misc/package.py error taken care of by the attached patch. Sorry for the noise, and I'm certainly not going to try to track down the race condition.

Anyway, things are looking good!

comment:228 in reply to: ↑ 227 ; follow-up: Changed 6 years ago by vbraun

Replying to kcrisman:

Anyway, things are looking good!

You are supposed to set the ticket to positive review in that case.

comment:229 in reply to: ↑ 228 ; follow-up: Changed 6 years ago by kcrisman

Anyway, things are looking good!

You are supposed to set the ticket to positive review in that case.

Am I now? There are tons of things on this ticket I know absolutely nothing about. Was this the last outstanding issue, according to the other reviewers? Will this last change cause trouble on computers other than the ones I tested it on? (I'm taking it from Georg's word that that is indeed the relevant path for those libraries on all Macs, possibly not including Mountain Lion.)

comment:230 in reply to: ↑ 229 ; follow-up: Changed 6 years ago by vbraun

Replying to kcrisman:

Will this last change cause trouble on computers other than the ones I tested it on?

Well we either wait until this ticket is obsoleted by the next ATLAS version, test it manually on each computer on skynet, or we let the buildbot do it.

comment:231 in reply to: ↑ 230 Changed 6 years ago by kcrisman

Will this last change cause trouble on computers other than the ones I tested it on?

Well we either wait until this ticket is obsoleted by the next ATLAS version, test it manually on each computer on skynet, or we let the buildbot do it.

Fair enough. I was mainly worried about Dima's computer, actually. So you're saying the rest of the ticket has already been positively reviewed? For instance, in comment:162, John says "On mark (Solaris), I see a problem building scipy." and I don't see anything resolving that (in fact, he edits it to indicate ATLAS is the problem). I am comfortable with positive review from my p.o.v., but I won't incur the wrath of Solaris fans by overriding that.

comment:232 Changed 6 years ago by vbraun

Sparc solaris isn't first-tier platform so we can always clean that up later. There is already way too much on this ticket to even pick out the comments that relate to SPARC only. And dima just reported that it worked fine for him.

comment:233 Changed 6 years ago by kcrisman

  • Status changed from needs_review to positive_review

Be it on your head, then! Jeroen, send all buildbot log failures to Volker directly ;)

Also, Dima reported it worked fine before the change to linking the system library directly in, though presumably if my computers on either end worked, his should.

comment:234 Changed 6 years ago by kcrisman

  • Status changed from positive_review to needs_work

Hah! I should have known... The symlink by hand worked, but

Skipping build of ATLAS on intel OS X
Traceback (most recent call last):
  File "./spkg-install", line 106, in <module>
    ln(os.path.join(veclib_dir, lib), 
NameError: name 'ln' is not defined

real    0m1.290s
user    0m0.334s
sys     0m0.501s
************************************************************************
Error installing package atlas-3.10.0
************************************************************************

That's probably because this is #!/usr/bin/env python. I think what we need is Python's os.symlink. I can't explain why this doesn't raise a problem on 10.7, but apparently on 10.4 it does.

comment:235 Changed 6 years ago by kcrisman

I've uploaded a package at http://sage.math.washington.edu/home/kcrisman/atlas-3.10.0.spkg for Volker to look at. Hopefully this will solve this last minor problem. Then he can either put this change in his or link to this one if he feels it's now positive review.

It didn't cause trouble on my other machine because it is Intel, which doesn't use this branch of the code! But it would have broken Dima's 10.5 PPC machine.

Last edited 6 years ago by kcrisman (previous) (diff)

comment:236 follow-up: Changed 6 years ago by vbraun

I thought you had tried the spkg on your machine ;-)

I fixed the ln (which is actually a python function that I forgot to import). The replaced spkg should work now. And the ln is only used on OSX PPC, which is also why I can't test it myself.

Last edited 6 years ago by vbraun (previous) (diff)

comment:237 in reply to: ↑ 236 ; follow-up: Changed 6 years ago by kcrisman

  • Status changed from needs_work to needs_review

I thought you had tried the spkg on your machine ;-)

Nope, just the solution, which I thought you'd properly written ;-)

I fixed the ln (which is actually a python function that I forgot to import). The replaced spkg should work now. And the ln is only used on OSX PPC, which is also why I can't test it myself.

Ok. I might be able to try this with my home box in a bit, otherwise it'll have to wait for the last test. But that ln looks like a good one too.

comment:238 Changed 6 years ago by jdemeyer

  • Description modified (diff)

Is the ATLAS spkg mentioned in the description still the correct link?

comment:239 Changed 6 years ago by vbraun

Jeroen: Yes, that is the correct link.

comment:240 in reply to: ↑ 237 Changed 6 years ago by kcrisman

  • Status changed from needs_review to positive_review

I fixed the ln (which is actually a python function that I forgot to import). The replaced spkg should work now. And the ln is only used on OSX PPC, which is also why I can't test it myself.

Ok. I might be able to try this with my home box in a bit, otherwise it'll have to wait for the last test. But that ln looks like a good one too.

It built fine.

comment:241 Changed 6 years ago by jdemeyer

  • Dependencies changed from #13160 to #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415
  • Description modified (diff)

comment:242 Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work

There is still a problem because the new atlas package runs automake and autoconf, probably some timestamps are messed up:

make[3]: Entering directory `/release/merger/sage-5.4.beta2/spkg/build/atlas-3.10.0/ATLAS-lib'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /release/merger/sage-5.4.beta2/spkg/build/atlas-3.10.0/ATLAS-lib/missing --run aclocal-1.1
1 -I m4
/release/merger/sage-5.4.beta2/spkg/build/atlas-3.10.0/ATLAS-lib/missing: line 52: aclocal-1.11: command not found
WARNING: `aclocal-1.11' is missing on your system.  You should only need it if
         you modified `acinclude.m4' or `configure.ac'.  You might want
         to install the `Automake' and `Perl' packages.  Grab them from
         any GNU archive site.
 cd . && /bin/bash /release/merger/sage-5.4.beta2/spkg/build/atlas-3.10.0/ATLAS-lib/missing --run automake-1.11 --gnu
/release/merger/sage-5.4.beta2/spkg/build/atlas-3.10.0/ATLAS-lib/missing: line 52: automake-1.11: command not found
WARNING: `automake-1.11' is missing on your system.  You should only need it if
         you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
         You might want to install the `Automake' and `Perl' packages.
         Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /release/merger/sage-5.4.beta2/spkg/build/atlas-3.10.0/ATLAS-lib/missing --run autoconf
WARNING: `autoconf' is missing on your system.  You should only need it if
         you modified `configure.ac'.  You might want to install the
         `Autoconf' and `GNU m4' packages.  Grab them from any GNU
         archive site.
/bin/bash ./config.status --recheck

comment:243 Changed 6 years ago by jdemeyer

It looks like somebody copied the atlas tree on 11 July without -p option, therefore destroying all timestamps.

comment:244 Changed 6 years ago by jdemeyer

Fixing this, hang on...

comment:245 Changed 6 years ago by jdemeyer

  • Description modified (diff)
  • Status changed from needs_work to needs_review

comment:246 Changed 6 years ago by jdemeyer

Changes w.r.t. to Volker's spkg: atlas-3.10.0.p0.diff

comment:247 Changed 6 years ago by vbraun

  • Status changed from needs_review to positive_review

Looks good to me!

comment:248 Changed 6 years ago by jdemeyer

This failed to build on arando (Ubuntu 12.04 i686) with a very obscure error message:

BEGIN BASIC KERNEL TESTS:
make[6]: *** [res/dMVNK.sum] Error 255
make[6]: Leaving directory `/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/tune/blas/gemv'
make[5]: *** [/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/tune/blas/gemv/res/dMVNK.sum] Error 2
make[5]: Target `INSTALL_LOG/dMVNK.sum' not remade because of errors.
make[5]: Leaving directory `/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin'
ERROR 915 DURING MVNTUNE!!.  CHECK INSTALL_LOG/dMVNTUNE.LOG FOR DETAILS.

full log: http://build.sagemath.org/sage/builders/NTU%20arando%20%28Ubuntu%2012.04%20i686%29/builds/68/steps/shell_5/logs/atlas

Now rebuilding...

comment:249 Changed 6 years ago by jdemeyer

Same error on hawk (OpenSolaris 06.2009-32):

BEGIN BASIC KERNEL TESTS:
make[6]: *** [res/dMVNK.sum] Error 255
make[6]: Leaving directory `/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/tune/blas/gemv'
make[5]: *** [/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/tune/blas/gemv/res/dMVNK.sum] Error 2
make[5]: Target `INSTALL_LOG/dMVNK.sum' not remade because of errors.
make[5]: Leaving directory `/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin'
ERROR 915 DURING MVNTUNE!!.  CHECK INSTALL_LOG/dMVNTUNE.LOG FOR DETAILS.

comment:250 Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work

The arando failure is reproducible, I found this in the logs:

OUTPUT OF system():
make[7]: Entering directory `/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/tune/blas/gemv'
cd /var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin ; make xextract
make[8]: Entering directory `/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin'
/usr/bin/gcc -DL2SIZE=4194304 -I/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/include -I/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//include -I/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_x86SSE3 -DATL_CPUMHZ=3301 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632 -m32 -DATL_FULL_LAPACK -DATL_NCPU=4 -O -fomit-frame-pointer -fPIC -m32 -o xextract /var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//bin/extract.c
/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//bin/extract.c: In function ‘Extract’:
/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//bin/extract.c:3196:4: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘struct EXTENV *’ [-Wformat]
/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//bin/extract.c:3252:4: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘struct EXTENV *’ [-Wformat]
/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//bin/extract.c: In function ‘LnIsExtCmnd’:
/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//bin/extract.c:3566:16: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
make[8]: Leaving directory `/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin'
mkdir EXTDIR
/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin/xextract -b /var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//tune/blas/gemv/atlas-l2g.base -langC \
                           order=clmajor rout=mvn_C nu=1 type=DREAL \
                           -def MU 8  -o EXTDIR/dmvn_C.c
make[7]: *** [dmvnext_C] Aborted (core dumped)
make[7]: Leaving directory `/var/lib/buildbot/build/sage/arando-1/arando_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/tune/blas/gemv'

The hawk failure is reproducible, I found this in the logs:

OUTPUT OF system():
make[7]: Entering directory `/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/tune/blas/gemv'
cd /export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin ; make xextract
make[8]: Entering directory `/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin'
/usr/local/bin/gcc -DL2SIZE=4194304 -I/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/include -I/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//include -I/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_SunOS -DATL_ARCH_Corei1 -DATL_CPUMHZ=3325 -DSUN_HR -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632 -m32 -DATL_FULL_LAPACK -DATL_NCPU=8 -O -fomit-frame-pointer -fPIC -m32 -o xextract /export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//bin/extract.c
make[8]: Leaving directory `/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin'
mkdir EXTDIR
/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/bin/xextract -b /export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/../src//tune/blas/gemv/atlas-l2g.base -langC \
                           order=clmajor rout=mvn_C nu=8 type=DREAL \
                           -def MU 2  -o EXTDIR/dmvn_C.c
make[7]: *** [dmvnext_C] Segmentation Fault (core dumped)
make[7]: Leaving directory `/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.4.beta2/spkg/build/atlas-3.10.0.p0/ATLAS-build/tune/blas/gemv'

Conjecture: this happens on all Intel i386 32-bit systems.

Last edited 6 years ago by jdemeyer (previous) (diff)

comment:251 Changed 6 years ago by jdemeyer

  • Description modified (diff)

comment:252 follow-up: Changed 6 years ago by jdemeyer

The error on arando and hawk is with the xextract.c program, which is over 3000 lines of string-handling code in C. There seems to be some heap corruption, so I'm pretty sure it's a genuine bug in ATLAS.

comment:253 follow-up: Changed 6 years ago by vbraun

I agree, seems to be triggered by the very long path names in the buildbot. I'll try to narrow it down.

comment:254 in reply to: ↑ 253 Changed 6 years ago by jdemeyer

Replying to vbraun:

I agree, seems to be triggered by the very long path names in the buildbot. I'll try to narrow it down.

Not sure, I tried to increase all fixed-sized buffers in xextract.c and that didn't solve the problem.

comment:255 in reply to: ↑ 252 ; follow-up: Changed 6 years ago by dimpase

Replying to jdemeyer:

The error on arando and hawk is with the xextract.c program, which is over 3000 lines of string-handling code in C. There seems to be some heap corruption, so I'm pretty sure it's a genuine bug in ATLAS.

I'd look for an error caused by the fact that arando has a 64-bit capable CPU, but runs a 32-bit kernel.

If it's about the path lengths then it should be possible to do a standalone install of Sage on arando in /tmp, say, and see whether the new Atlas works.

comment:256 in reply to: ↑ 255 ; follow-up: Changed 6 years ago by jdemeyer

Replying to dimpase:

I'd look for an error caused by the fact that arando has a 64-bit capable CPU, but runs a 32-bit kernel.

I haven't been able to reproduce this on sage.math in 32-bit mode.

If it's about the path lengths then it should be possible to do a standalone install of Sage on arando in /tmp, say, and see whether the new Atlas works.

I doubt that filenames have anything to do with it.

comment:257 in reply to: ↑ 256 Changed 6 years ago by dimpase

Replying to jdemeyer:

Replying to dimpase:

I'd look for an error caused by the fact that arando has a 64-bit capable CPU, but runs a 32-bit kernel.

I haven't been able to reproduce this on sage.math in 32-bit mode.

well, it's a different, older, CPU, isn't it?

comment:258 Changed 6 years ago by vbraun

Well file names get definitely truncated to 128 characters in extract.c. Here is a stack backtrace on eno/skynet:

(gdb) bt
#0  0xf7ffd430 in __kernel_vsyscall ()
#1  0x4212798f in raise () from /lib/libc.so.6
#2  0x421292d5 in abort () from /lib/libc.so.6
#3  0x4216802a in __libc_message () from /lib/libc.so.6
#4  0x4216ef12 in malloc_printerr () from /lib/libc.so.6
#5  0x42170068 in _int_free () from /lib/libc.so.6
#6  0x4214c006 in _IO_vfscanf_internal () from /lib/libc.so.6
#7  0x4215c592 in __isoc99_vsscanf () from /lib/libc.so.6
#8  0x4215c4df in __isoc99_sscanf () from /lib/libc.so.6
#9  0x080490db in Wstr2int (str=0xffffb290 "1 -1 + ", iptr=0xffffb0d8)
    at /home/vbraun/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/ATLAS/build/..//bin/extract.c:473
#10 0x0804daf0 in icalc (EE=0xffffbb0c, line=0xffffb290 "1 -1 + ")
    at /home/vbraun/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/ATLAS/build/..//bin/extract.c:2052
#11 0x08053195 in LnIsExtCmnd (EE=0xffffbb0c, line=0xffffbb54 "NUm1")
    at /home/vbraun/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/ATLAS/build/..//bin/extract.c:3514
#12 0x080541a8 in HandleLine (EE=0xffffbb0c, line=0xffffbb54 "NUm1")
    at /home/vbraun/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/ATLAS/build/..//bin/extract.c:3797
#13 0x08052435 in Extract (OldEnv=0x0, wp=0x8058008)
    at /home/vbraun/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/ATLAS/build/..//bin/extract.c:3205
#14 0x080543fb in main (nargs=13, args=0xffffcc44)
    at /home/vbraun/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/ATLAS/build/..//bin/extract.c:3840
(gdb) frame 10
#10 0x0804daf0 in icalc (EE=0xffffbb0c, line=0xffffb290 "1 -1 + ")
    at /home/vbraun/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/ATLAS/build/..//bin/extract.c:2052
2052          i = Wstr2int(line, &istack[k]);
(gdb) print EE->FpIn.Fnam
$19 = "/home/vbraun/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/0123456789/01234"

comment:259 Changed 6 years ago by vbraun

  • Description modified (diff)

comment:260 Changed 6 years ago by jdemeyer

When I was debugging, I made further changes to the buffer sizes in that file, so it could be that I accidentally introduced a different segfault. Anyway, testing your patch now...

comment:261 Changed 6 years ago by jdemeyer

  • Status changed from needs_work to positive_review

comment:262 Changed 6 years ago by jdemeyer

  • Description modified (diff)

comment:263 Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work

Building ATLAS on iras hangs at some point. After

/home/jdemeyer/iras/sage-5.4.beta1/local/bin/gcc -o ATL_dtrsv.o -c -DL2SIZE=4194304 -I/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/include -I/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/../src//include -I/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/../src//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_IA64Itan2 -DATL_CPUMHZ=1594 -DATL_USE64BITS -DATL_MAXNREG=128 -DATL_IntelIccBugs -DATL_FULL_LAPACK -DATL_NCPU=4 -O -fomit-frame-pointer -fPIC -DDREAL /home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/../src//src/blas/level2//ATL_trsv.c
/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/../src//src/blas/level2//ATL_trsv.c: In function 'ATL_trsvUN_k':
/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/../src//src/blas/level2//ATL_trsv.c:105:6: warning: assignment discards 'const' qualifier from pointer target type [enabled by default]
ar r /home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/lib/libatlas.a ATL_L2AIsOverlapped.o ATL_dgbmv.o ATL_dgpmv.o ATL_dgpr.o ATL_dsbmv.o ATL_dspmv.o ATL_dspr.o ATL_dspr2.o ATL_dsymv.o ATL_dsyr.o ATL_dsyr2.o ATL_dtbmv.o ATL_dtbsv.o ATL_dtpmv.o ATL_dtpsv.o ATL_dtrmv.o ATL_dtrsv.o
echo /home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/lib/libatlas.a
/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/lib/libatlas.a
touch dblas2.grd
make[4]: Leaving directory `/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/src/blas/level2'
make[3]: Leaving directory `/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/tune/blas/ger'
make[2]: Leaving directory `/home/jdemeyer/iras/sage-5.4.beta1/spkg/build/atlas-3.10.0.p1/ATLAS-build/bin'

the build simply gets stuck, with nothing happening anymore.

comment:264 Changed 6 years ago by jhpalmieri

Are you sure it got stuck? When I built on iras (admittedly with an earlier version of the spkg), it would stop for hours at a time, but eventually continue. It ended up taking about 37 hours to complete.

comment:265 follow-up: Changed 6 years ago by vbraun

I think the occasional nap times are when ATLAS is trying to find the compiler etc by walking various directory trees. Except that skynet has such a slow NFS that this literally takes hours. Of course you can always attach strace to the process to see what it is really doing.

comment:267 in reply to: ↑ 265 Changed 6 years ago by jdemeyer

Replying to vbraun:

I think the occasional nap times are when ATLAS is trying to find the compiler etc by walking various directory trees.

If this is true, it should be fixed. That isn't a proper way to find a compiler.

comment:268 Changed 6 years ago by jdemeyer

Can we force ATLAS to use the value of the $CC environment variable for the C compiler and skip the crazy find stuff?

comment:269 Changed 6 years ago by jdemeyer

  • Milestone changed from sage-5.4 to sage-5.5

comment:270 Changed 6 years ago by vbraun

I'm passing the fqn of the compiler, this should make ATLAS not use find. Though it might do something similar for another binary. The only way to tell is to attach strace when it appears stuck. I've started a compilation on iras...

comment:271 Changed 6 years ago by vbraun

I've built ATLAS on iras and it completed successfully. Just took two days or so. At times it gets quiet for a few hours while computing some timings but it did not get stuck.

comment:272 Changed 6 years ago by vbraun

  • Status changed from needs_work to positive_review

Switching this back to positive review since build does not get stuck in fact.

comment:273 Changed 6 years ago by jdemeyer

  • Authors changed from Volker Braun to Volker Braun, Jeroen Demeyer

comment:274 Changed 6 years ago by jdemeyer

Concerning iras: it does indeed build properly. I actually wrote a small script to take snapshots of the ATLAS log file and noticed that the build seemingly gets stuck for almost 19 hours!

I still agree with the positive_review, even though this is a substantial regression in ATLAS build time.

comment:275 Changed 6 years ago by vbraun

Of course you can always set SAGE_ATLAS_ARCH=fast if you are in a hurry, then it won't attempt to go through the tuning process. On the other hand there isn't anything else for the buildbot to do on iras so do we care?

comment:276 Changed 6 years ago by jdemeyer

  • Status changed from positive_review to needs_work

I'm seeing Segmentation Faults with the ATLAS built on iras (ia64):

$ ./sage -t -verbose devel/sage/sage/matrix/matrix_double_dense.pyx
[...]
Trying:
    R = random_matrix(CDF, Integer(200))###line 3810:_sage_    >>> R = random_matrix(CDF, 200)
Expecting nothing
ok
Trying:
    H = R.conjugate_transpose()*R###line 3811:_sage_    >>> H = R.conjugate_transpose()*R
Expecting nothing
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libcsage.so(print_backtrace-0x909d460)[0x2000000000a09400]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libcsage.so(sigdie-0x909d3c0)[0x2000000000a094b0]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libcsage.so(sage_signal_handler-0x107d800)[0x2000000000a08b90]
[0xa0000000000107e0]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_zupNBmm0_1_0_b0-0x5e39d80)[0x2000000003c6cb10]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_zpNBmm_b0+0x22020c0)[0x2000000003c93a60]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_zMBJBmm-0x5fd54d0)[0x2000000003ad13d0]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_zmmJIK2-0x5ef2ac0)[0x2000000003bb3df0]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_zmmJIK+0x2122b50)[0x2000000003bb49f0]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_ztgemmNN-0x5e79660)[0x2000000003c2d260]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_ztsvgemmNN+0x21971b0)[0x2000000003c29350]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_DoWorkMM-0x727360)[0x20000000035bccb0]
/home/buildbot/build/sage/iras-1/iras_full/build/sage-5.5.beta0/local/lib/libatlas.so.2(ATL_dyntlaunch+0x1eb7310)[0x2000000003948e60]
/lib/libpthread.so.0[0x20000000004395d0]
/lib/libc.so.6.1(__clone2-0x93b9dc0)[0x20000000006ecb10]

comment:278 Changed 6 years ago by tmonteil

You might be interested in ticket #13706

Changed 6 years ago by Snark

Log of compilation of atlas-3.10.0.p1 with SAGE_ATLAS_ARCH=ARMv7 on a native box

Changed 6 years ago by Snark

Log of compilation of atlas-3.10.0.p1 with SAGE_ATLAS_ARCH=ARMv7 in a qemu vm

comment:279 Changed 6 years ago by Snark

As seen in the two attached log files, I didn't manage to get that spkg to compile for ARMv7. No 'fast' or 'base' for these processors... so it doesn't work on arm!

comment:280 Changed 6 years ago by vbraun

The qemu failure is because of hard/soft abi mix (/usr/bin/ld: error: xctest uses VFP register arguments, /tmp/ccZXPvWa.o does not). It seems that something wrong with gcc/gfortran here.

On the native box, did you try SAGE_ATLAS_ARCH=ARMv7,NEON? Assuming that it has NEON support? It seems that the configuration dies because it doesn't deal with the case of no ISA extension.

Changed 6 years ago by Snark

Log of compilation of atlas-3.10.0.p1 with SAGE_ATLAS_ARCH=ARMv7,NEON on a real box

comment:281 Changed 6 years ago by Snark

It still doesn't work. I'll now try native compilation without any SAGE_ATLAS_* to see what happens.

comment:282 Changed 6 years ago by Snark

That falls back on 'fast', which doesn't make sence for this processor!?

I'll see if it's an upstream bug...

comment:283 follow-up: Changed 6 years ago by vbraun

The "base" and "fast" targets are my invention. Of course they are only implemented when I know a working configuration ;-)

At least the SAGE_ATLAS_ARCH=ARMv7,NEON version seems to get a little bit further. But it fails to detect the clock rate and then dies: "Clock rate configured as 0Mhz"

comment:284 Changed 6 years ago by Snark

In any case, that package breaks the arm port...

comment:285 follow-up: Changed 6 years ago by Snark

There's a question to ask there: has atlas that good performances to compensate for its shortcomings?

comment:286 in reply to: ↑ 285 Changed 6 years ago by dimpase

Replying to Snark:

There's a question to ask there: has atlas that good performances to compensate for its shortcomings?

Atlas is the only BLAS implementation around that does tuning on the fly, AFAIK. Why is this needed for the vast majority of users, it's unclear. And Atlas is mostly a 1-man project.

I'd say that ideally Sage should accept any (sufficiently compatible) BLAS/LAPACK implementation.

comment:287 Changed 6 years ago by jhpalmieri

Would it make sense to special case ia64 machines like iras, and just build the old ATLAS (and then would we also need lapack and blas)? It would increase the size of the spkg considerably to include the old and new versions, but disk space is cheap. If the new version is much better on most platforms, it might be worth it.

comment:288 Changed 6 years ago by vbraun

Using the reference BLAS, say, will be an order of magnitude slower. Its not an option if you want to rival the big M's. Maple for Unix uses (or at least used) ATLAS.

Intel MKL or Goto/Openblas are faster on the latest Intel chips. ATLAS is the only high-performance library that works at least somewhat across a larger range of processors.

I agree that Sage should be able to work with more than one BLAS/LAPACK. I'm looking into this now and will post to sage-devel with a concrete proposal.

comment:289 Changed 6 years ago by fbissey

It is doable in that we do it in sage on gentoo. Iml needs patching too work with anything else than atlas (configuration not functionality) . Linbox numpy scipy need careful handling sage itself needs patching in setup.py as well. I know you are looking at lmnd Volker I guess that will give you an idea of what we do. Of course the pkgconfig and alternatives thing could be way simplified in vanilla sage.

comment:290 Changed 6 years ago by Snark

I have tried the upstream atlas sources, failed, and opened a bug report there -- the developer already answered.

Where there's life, there's hope :-)

comment:291 Changed 6 years ago by vbraun

Any followup discussion that is not specific to the ATLAS-3.10 spkg should go here: https://groups.google.com/d/topic/sage-devel/FmQqale37X4/discussion

comment:292 Changed 6 years ago by jpflori

Just a few random remarks:

  • there is an updated cvxopt spkg at #13799 (it has been merged, so we need rebasing here), it seems to me it at least addresses the same kind of underlinking issue after the too aggressive fixes of #13160, but on Cygwin rather than OS X (I've not read all the comments in detail so excuse me if this is wrong),
  • I don't think building ATLAS really needs to be disabled on Cygwin, I could at least build the static libraries for ATLAS 3.8.4 (although the shared make target would fail), not sure about ATLAS 3.10, it failed during tuning on my computer, but that's because of memory leaks unrelated to ATLAS, using SAGE_ATLAS_ARCH I should be able to get through this, at least get static libs, and see what's up with the shared ones. My feeling is that his should be postponed in a later ticket (unless this one never gets merged).
  • If the only blocker is some obscure bug on ia64, why not merge it anyway and mention somewhere visible that we are aware of the failure? Or disable building ATLAS on ia64? Wouldn't it be better than using an unsupported version of ATLAS?

comment:293 follow-up: Changed 6 years ago by novoselt

For the record: I failed to build Sage-5.6.rc0 in a virtual machine on Xeon X5650 due to ATLAS - neither default behaviour nor using SAGE_ATLAS_ARCH worked. The new package worked fine with default settings.

comment:294 in reply to: ↑ 293 Changed 6 years ago by ppurka

Replying to novoselt:

For the record: I failed to build Sage-5.6.rc0 in a virtual machine on Xeon X5650 due to ATLAS - neither default behaviour nor using SAGE_ATLAS_ARCH worked. The new package worked fine with default settings.

What is blocking this ticket anyway? Is it only the ia64 problem? I think it a bad idea that all current/common archs are blocked because of a failure in some arch that not many people are using. I have been patching and installing these patches on my machine for 3 months now because the older atlas refuses to build successfully.

comment:295 follow-up: Changed 6 years ago by jpflori

Let's jsut request a system-wide atlas on ia64. We do that on Mac OS X that a bunch of people actually use, they perfectly live with this, and it does not prevent us from updating Sage.

comment:296 in reply to: ↑ 295 ; follow-up: Changed 6 years ago by fbissey

Replying to jpflori:

Let's jsut request a system-wide atlas on ia64. We do that on Mac OS X that a bunch of people actually use, they perfectly live with this, and it does not prevent us from updating Sage.

Most spkg using blas/lapack have a special section to deal with OS X. This spkg would mean we can actually switch to ATLAS on OS X and most of the spkg in question will have to be touched. So in fact we don't ask for anything to be set on OS X, it finds the vectorize framework all by itself.

comment:297 in reply to: ↑ 296 Changed 6 years ago by jpflori

Replying to fbissey:

Replying to jpflori:

Let's jsut request a system-wide atlas on ia64. We do that on Mac OS X that a bunch of people actually use, they perfectly live with this, and it does not prevent us from updating Sage.

Most spkg using blas/lapack have a special section to deal with OS X. This spkg would mean we can actually switch to ATLAS on OS X and most of the spkg in question will have to be touched. So in fact we don't ask for anything to be set on OS X, it finds the vectorize framework all by itself.

I don't really get your answer.

To make my point more clear, can't we ask the user to install "something" that would replace what the atlas spkg provides on ia64, just as on Cygwin if you prefer, rather than on OS X where it is more tricky.

comment:298 Changed 6 years ago by fbissey

Ah, I see. You want to add specific logic for ia64 in this spkg. Why not? I think you should just go ahead and add it (baring that, at least tell us how you want it implemented).

comment:299 Changed 6 years ago by jpflori

Updated ATLAS and LAPACK at http://boxen.math.washington.edu/home/jpflori/atlas-3.10.1.p0.spkg and a properly rebased cvxopt at http://boxen.math.washington.edu/home/jpflori/cvxopt-1.1.5.p1.spkg

Maybe the following change helps on ia64:

   * Fixed premature KillAllMMNodes in emit_mm.c

Some random strings look like the bug report at http://sourceforge.net/p/math-atlas/support-requests/863/ :)

Could someone test it on the previously failing (and working) archs?

At least it builds on a Corei7 with SAGE_ATLAS_aRCH=Corei2,AVX,SSE3,SSE2,SSE1 Ill try a proper Sage build later.

I should also have access to some armv7l and ia64 on GCC Compile Farm and will try to build 5.7 + patches here there.

Changed 6 years ago by jpflori

Rebased spkg diff, for review only.

comment:300 Changed 6 years ago by jpflori

(Ive not implemented a workaround requesting a system wide cblas for ia64 yet as wed better confirm the problem is still present first)

comment:301 Changed 6 years ago by jhpalmieri

On Solaris (skynet machine mark), I see the same problem as reported in 162. On ia64 (skynet machine iras), things don't look good: the ATLAS spkg has been building for at least 4 hours, and is currently stalled -- no changes to the install log in about 3 1/2 hours. This is what happened before, when it took 37 hours to build the spkg. I'll check back in a day or two to see if it's finished, but I think the upgrade from 3.10.0 to 3.10.1 didn't fix the problem.

comment:302 Changed 6 years ago by vbraun

The problem is that some ATLAS kernel crashes no ia64, not the long build time.

comment:303 Changed 6 years ago by jpflori

On gcc60, the Sage 5.7 + #10508 build I launched this morning is now stuck in ATLAS since about a couple of hours at:

make[6]: Entering directory `/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/tune/sysinfo'
/usr/bin/gcc -c -DL2SIZE=4194304 -I/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/include -I/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//include -I/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_IA64Itan2 -DATL_CPUMHZ=1300 -DATL_USE64BITS -DATL_MAXNREG=128 -DATL_IntelIccBugs -DATL_FULL_LAPACK -DATL_NCPU=2 -fomit-frame-pointer -O2 -fno-tree-loop-optimize -fPIC /home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//tune/sysinfo/emit_lamch.c
/usr/bin/gcc -DL2SIZE=4194304 -I/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/include -I/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//include -I/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_IA64Itan2 -DATL_CPUMHZ=1300 -DATL_USE64BITS -DATL_MAXNREG=128 -DATL_IntelIccBugs -DATL_FULL_LAPACK -DATL_NCPU=2 -fomit-frame-pointer -O2 -fno-tree-loop-optimize -fPIC -o xemit_lamch emit_lamch.o -lpthread -lm
/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/bin/ATLrun.sh /home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/tune/sysinfo xemit_lamch /home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/include
make[6]: Leaving directory `/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/tune/sysinfo'
make[5]: Leaving directory `/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/bin'

I'll report when it hopefully finishes.

comment:304 Changed 6 years ago by jpflori

There are some *.tar.bz2 files in the patch directory, are they used anywhere? I can't spot anything in our scripts.

comment:305 Changed 6 years ago by jpflori

Im aware of what's said in the ticket description, but could you precise why we do not use upstream build system to generate the shared libraries, but rather repack the static ones? After looking at http://math-atlas.sourceforge.net/atlas_install/node22.html which is not that crystal clear and at the Makefile used upstream it seems that more or less one big (sequential or parallel/ including fortran or not) library is built, and not 3 or 4 separate ones. Is that correct?

comment:306 follow-ups: Changed 6 years ago by jpflori

About the Itanium build, after a previous modification at 12:45, the log was modified again at 16:50 :)

comment:307 in reply to: ↑ 306 Changed 6 years ago by leif

Replying to jpflori:

About the Itanium build, after a previous modification at 12:45, the log was modified again at 16:50 :)

Keep us informed... #sagemath on irc.freenode.net

Or does ATLAS have a feature to tweet its build progress? (I guess many Sage users would like that.)

comment:308 follow-up: Changed 6 years ago by vbraun

Upstream has just completely changed the shared library names, so we would have to change all spkgs to hardcode different libatlas names. Instead I'd rather change Sage to use a pkgconfig-style script to get the blas/lapack libraries.

comment:309 in reply to: ↑ 308 Changed 6 years ago by jpflori

Replying to vbraun:

Upstream has just completely changed the shared library names, so we would have to change all spkgs to hardcode different libatlas names.

Could you please state from what to what as I couldn't determine that easily by just looking around on my computer? And I can't use my computer to build different ATLAS version just for fun, so if its in the corner of you head, that would be greatly appreciated.

Instead I'd rather change Sage to use a pkgconfig-style script to get the blas/lapack libraries.

If that could also let other BLAS/LAPACK implementations be plugged into Sage, that would be really great. I remember some discussion on sage-devel recently, but the proposed solution looked quite more complicated, don't remmeber why.

comment:310 follow-ups: Changed 6 years ago by vbraun

Its not just a name change for libraries, its also a change of which symbols are where. So basically you'll have to trial-build your way through all spkgs to see what you need to link in. Let me know when you are finished ;-)

The tar.bz files are architectural defaults, they are used by the atlas build system if you copy then into the right place.

comment:311 in reply to: ↑ 310 Changed 6 years ago by jpflori

Replying to vbraun:

The tar.bz files are architectural defaults, they are used by the atlas build system if you copy then into the right place.

I got their potential use, but are they actually used by the spkg scripts? That's what I did not get. I could not find any doc either about them.

comment:312 Changed 6 years ago by jpflori

Except for

# add extra architectural defaults
# currently none
# cp('patches/ARCH.tgz', 'src/CONFIG/ARCHS')

comment:313 in reply to: ↑ 310 Changed 6 years ago by jpflori

Replying to vbraun:

Its not just a name change for libraries, its also a change of which symbols are where. So basically you'll have to trial-build your way through all spkgs to see what you need to link in. Let me know when you are finished ;-)

Ok, I took the time to actually rebuild ATLAS 3.10.1 and do as advertised at: http://math-atlas.sourceforge.net/atlas_install/node22.html and there is indeed just one serial/parallel shared library built now called libatlas.so/libtatlas.so which contains all of libcblas.a libf77blas.a libatlas.a liblapack.a (or pt version of them). Its also possible to rule out the fortran symbols.

I don't know what ATLAS 3.8.4 offered if it did offer anything for shared libraries.

Anyway, Im happy with your autotools script which basically do the same thing as upstream but in separate libraries.

comment:314 in reply to: ↑ 306 ; follow-up: Changed 6 years ago by jpflori

Replying to jpflori:

About the Itanium build, after a previous modification at 12:45, the log was modified again at 16:50 :)

Next sign of activity around 00:32, then somehow regularly until 2:19, and nothing since. I hope it won't take more than 48 hours...

comment:315 in reply to: ↑ 314 ; follow-up: Changed 6 years ago by jpflori

Replying to jpflori:

Replying to jpflori:

About the Itanium build, after a previous modification at 12:45, the log was modified again at 16:50 :)

Next sign of activity around 00:32, then somehow regularly until 2:19, and nothing since. I hope it won't take more than 48 hours...

Some activity (I really mean writing into the log) between 14:14 and 14:20, not finished yet.

comment:316 Changed 6 years ago by jhpalmieri

The build on iras finished after 36 hours, apparently successfully. We'll see how doctests go.

comment:317 follow-up: Changed 6 years ago by jhpalmieri

On iras, I get several doctest failures:

The following tests failed:

        sage -t  --long -force_lib devel/sage/sage/calculus/interpolators.pyx # Killed/crashed
        sage -t  --long -force_lib devel/sage/sage/calculus/riemann.pyx # Killed/crashed
        sage -t  --long -force_lib devel/sage/sage/matrix/matrix_double_dense.pyx # Killed/crashed

In the log file, it just says "The doctested process was killed by signal 11" for each one.

comment:318 follow-up: Changed 6 years ago by jhpalmieri

On iras, I rebuilt all of the packages that come after ATLAS with SAGE_CHECK=yes. I got one failure, iml:

mkdir .libs
gcc -I/../src -I/home/palmieri/iras/sage-5.8.beta1-10508/local/include -I. -g -O2 -o .lib\
s/test-smallentry test_smallentry-test-smallentry.o  ../src/.libs/libiml.so -L/home/palmi\
eri/iras/sage-5.8.beta1-10508/local/lib -lm /home/palmieri/iras/sage-5.8.beta1-10508/loca\
l/lib/libgmp.so -Wl,--rpath -Wl,/home/palmieri/iras/sage-5.8.beta1-10508/local/lib
../src/.libs/libiml.so: undefined reference to `cblas_dswap'
../src/.libs/libiml.so: undefined reference to `cblas_dgemv'
../src/.libs/libiml.so: undefined reference to `cblas_dgemm'
../src/.libs/libiml.so: undefined reference to `cblas_dger'
../src/.libs/libiml.so: undefined reference to `cblas_dcopy'
collect2: ld returned 1 exit status
make[5]: *** [test-smallentry] Error 1
make[5]: Leaving directory `/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/iml-1.0.1\
.p14/src/tests'
make[4]: *** [check-am] Error 2
make[4]: Leaving directory `/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/iml-1.0.1\
.p14/src/tests'
make[3]: *** [check-recursive] Error 1
make[3]: Leaving directory `/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/iml-1.0.1\
.p14/src'
Error testing IML

(gsl also failed, but it failed with the old ATLAS package, too.)

comment:319 follow-up: Changed 6 years ago by jpflori

Unrelated, but Sage's build later failed building PARI:

gcc  -c -I. -I../src/headers -fPIC -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer  -g   -o krasner.o ../src/modules/krasner.c
../src/modules/krasner.c: In function 'GetRamifiedPol':
../src/modules/krasner.c:878: error: unrecognizable insn:
(insn 3685 2258 3694 56 (parallel [
            (set (reg:DI 134 f6)
                (asm_operands:DI ("xma.hu %0 = %2, %3, f0
        ;;
        xma.l %1 = %2, %3, f0") ("=&f") 0 [
                        (reg:DI 135 f7)
                        (reg/v:DI 130 f2 [orig:495 pmodg ] [495])
                    ]   
                     [
                        (asm_input:DI ("f") 0)
                        (asm_input:DI ("f") 0)
                    ] 3266574))
            (set (reg:DI 135 f7)
                (asm_operands:DI ("xma.hu %0 = %2, %3, f0
        ;;
        xma.l %1 = %2, %3, f0") ("=f") 1 [
                        (reg:DI 135 f7)
                        (reg/v:DI 130 f2 [orig:495 pmodg ] [495])
                    ]   
                     [
                        (asm_input:DI ("f") 0)
                        (asm_input:DI ("f") 0)
                    ] 3266574))
        ]) -1 (nil))
../src/modules/krasner.c:878: internal compiler error: in internal_dfa_insn_code, at config/ia64/itanium2.md:1676

I'll give gcc-4.7.2.p0 a shot.

comment:320 in reply to: ↑ 315 Changed 6 years ago by jpflori

Replying to jpflori:

Replying to jpflori:

Replying to jpflori:

About the Itanium build, after a previous modification at 12:45, the log was modified again at 16:50 :)

Next sign of activity around 00:32, then somehow regularly until 2:19, and nothing since. I hope it won't take more than 48 hours...

Some activity (I really mean writing into the log) between 14:14 and 14:20, not finished yet.

Oh and ATLAS finished at 2:02. So that must be about 38/40 hours.

comment:321 in reply to: ↑ 319 Changed 6 years ago by jpflori

Replying to jpflori:

Unrelated, but Sage's build later failed building PARI:

gcc  -c -I. -I../src/headers -fPIC -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer  -g   -o krasner.o ../src/modules/krasner.c
../src/modules/krasner.c: In function 'GetRamifiedPol':
../src/modules/krasner.c:878: error: unrecognizable insn:
(insn 3685 2258 3694 56 (parallel [
            (set (reg:DI 134 f6)
                (asm_operands:DI ("xma.hu %0 = %2, %3, f0
        ;;
        xma.l %1 = %2, %3, f0") ("=&f") 0 [
                        (reg:DI 135 f7)
                        (reg/v:DI 130 f2 [orig:495 pmodg ] [495])
                    ]   
                     [
                        (asm_input:DI ("f") 0)
                        (asm_input:DI ("f") 0)
                    ] 3266574))
            (set (reg:DI 135 f7)
                (asm_operands:DI ("xma.hu %0 = %2, %3, f0
        ;;
        xma.l %1 = %2, %3, f0") ("=f") 1 [
                        (reg:DI 135 f7)
                        (reg/v:DI 130 f2 [orig:495 pmodg ] [495])
                    ]   
                     [
                        (asm_input:DI ("f") 0)
                        (asm_input:DI ("f") 0)
                    ] 3266574))
        ]) -1 (nil))
../src/modules/krasner.c:878: internal compiler error: in internal_dfa_insn_code, at config/ia64/itanium2.md:1676

I'll give gcc-4.7.2.p0 a shot.

For the record, this is #9897, closed as duplicate from #10572.

comment:322 follow-up: Changed 6 years ago by jpflori

And then failed building Linbox

make[7]: Entering directory `/home/jpflori/sage-5.7/spkg/build/linbox-1.3.2.p0/src/linbox/algorithms'
/bin/bash ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../..   -DDISABLE_COMMENTATOR -O2    -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR  -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include  -I/home/jpflori/sage-5.7/local/include  -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include  -g -fPIC -c -o diophantine-solver.lo diophantine-solver.C
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -DDISABLE_COMMENTATOR -O2 -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -g -fPIC -c diophantine-solver.C  -fPIC -DPIC -o .libs/diophantine-solver.o
In file included from ../../linbox/blackbox/compose.h:34,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:25:
../../linbox/matrix/blas-matrix.h:238: error: 'template<class _Field> template<class T> LinBox::BlasMatrix::BlasMatrix(const _Field&, const int64_t&, const T&)' cannot be overloaded
../../linbox/matrix/blas-matrix.h:220: error: with 'template<class _Field> template<class T> LinBox::BlasMatrix::BlasMatrix(const _Field&, const long int&, const T&)'
In file included from ../../linbox/matrix/blas-matrix.h:1196,
                 from ../../linbox/blackbox/compose.h:34,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:25:
../../linbox/matrix/blas-matrix.inl:259: error: redefinition of 'LinBox::BlasMatrix<_Field>::BlasMatrix(const _Field&, const long int&, const T&)'
../../linbox/matrix/blas-matrix.inl:245: error: 'LinBox::BlasMatrix<_Field>::BlasMatrix(const _Field&, const int64_t&, const T&)' previously declared here
make[7]: *** [diophantine-solver.lo] Error 1

comment:323 Changed 6 years ago by ppurka

Overall, sounds like a disaster on ia64. :-/

comment:324 Changed 6 years ago by jpflori

Please note the PARI/GP problem is completely unrelated, and the Linbox surely is. I just posted them here in order not to "lose" them.

comment:325 in reply to: ↑ 322 ; follow-up: Changed 6 years ago by jpflori

Replying to jpflori:

And then failed building Linbox

make[7]: Entering directory `/home/jpflori/sage-5.7/spkg/build/linbox-1.3.2.p0/src/linbox/algorithms'
/bin/bash ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../..   -DDISABLE_COMMENTATOR -O2    -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR  -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include  -I/home/jpflori/sage-5.7/local/include  -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include  -g -fPIC -c -o diophantine-solver.lo diophantine-solver.C
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -DDISABLE_COMMENTATOR -O2 -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -g -fPIC -c diophantine-solver.C  -fPIC -DPIC -o .libs/diophantine-solver.o
In file included from ../../linbox/blackbox/compose.h:34,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:25:
../../linbox/matrix/blas-matrix.h:238: error: 'template<class _Field> template<class T> LinBox::BlasMatrix::BlasMatrix(const _Field&, const int64_t&, const T&)' cannot be overloaded
../../linbox/matrix/blas-matrix.h:220: error: with 'template<class _Field> template<class T> LinBox::BlasMatrix::BlasMatrix(const _Field&, const long int&, const T&)'
In file included from ../../linbox/matrix/blas-matrix.h:1196,
                 from ../../linbox/blackbox/compose.h:34,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:25:
../../linbox/matrix/blas-matrix.inl:259: error: redefinition of 'LinBox::BlasMatrix<_Field>::BlasMatrix(const _Field&, const long int&, const T&)'
../../linbox/matrix/blas-matrix.inl:245: error: 'LinBox::BlasMatrix<_Field>::BlasMatrix(const _Field&, const int64_t&, const T&)' previously declared here
make[7]: *** [diophantine-solver.lo] Error 1

This one looks related to https://groups.google.com/d/topic/linbox-devel/ogc_XyBEJNg/discussion I'll try tweaking stuff.

comment:326 in reply to: ↑ 325 ; follow-up: Changed 6 years ago by jpflori

Replying to jpflori:

Replying to jpflori:

And then failed building Linbox

make[7]: Entering directory `/home/jpflori/sage-5.7/spkg/build/linbox-1.3.2.p0/src/linbox/algorithms'
/bin/bash ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../..   -DDISABLE_COMMENTATOR -O2    -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR  -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include  -I/home/jpflori/sage-5.7/local/include  -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include  -g -fPIC -c -o diophantine-solver.lo diophantine-solver.C
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -DDISABLE_COMMENTATOR -O2 -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -g -fPIC -c diophantine-solver.C  -fPIC -DPIC -o .libs/diophantine-solver.o
In file included from ../../linbox/blackbox/compose.h:34,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:25:
../../linbox/matrix/blas-matrix.h:238: error: 'template<class _Field> template<class T> LinBox::BlasMatrix::BlasMatrix(const _Field&, const int64_t&, const T&)' cannot be overloaded
../../linbox/matrix/blas-matrix.h:220: error: with 'template<class _Field> template<class T> LinBox::BlasMatrix::BlasMatrix(const _Field&, const long int&, const T&)'
In file included from ../../linbox/matrix/blas-matrix.h:1196,
                 from ../../linbox/blackbox/compose.h:34,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:25:
../../linbox/matrix/blas-matrix.inl:259: error: redefinition of 'LinBox::BlasMatrix<_Field>::BlasMatrix(const _Field&, const long int&, const T&)'
../../linbox/matrix/blas-matrix.inl:245: error: 'LinBox::BlasMatrix<_Field>::BlasMatrix(const _Field&, const int64_t&, const T&)' previously declared here
make[7]: *** [diophantine-solver.lo] Error 1

This one looks related to https://groups.google.com/d/topic/linbox-devel/ogc_XyBEJNg/discussion I'll try tweaking stuff.

Got it, the fix used defines something if using GCC 4.4.5 on non x86_64 because its needed on 32 bits. Unfortunately this breaks ia64 (maybe other 64 bits systems? anybody wants to try out GCC 4.4.5 on sparc64 or ppc64 :)), so the problem it the filtering on "non x86_64", rather than "32 bits".

comment:327 in reply to: ↑ 326 Changed 6 years ago by jpflori

Replying to jpflori:

Replying to jpflori:

Replying to jpflori:

And then failed building Linbox

make[7]: Entering directory `/home/jpflori/sage-5.7/spkg/build/linbox-1.3.2.p0/src/linbox/algorithms'
/bin/bash ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../..   -DDISABLE_COMMENTATOR -O2    -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR  -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include  -I/home/jpflori/sage-5.7/local/include  -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include  -g -fPIC -c -o diophantine-solver.lo diophantine-solver.C
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -DDISABLE_COMMENTATOR -O2 -g -DNDEBUG -U_LB_DEBUG -DDISABLE_COMMENTATOR -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -I/home/jpflori/sage-5.7/local/include -g -fPIC -c diophantine-solver.C  -fPIC -DPIC -o .libs/diophantine-solver.o
In file included from ../../linbox/blackbox/compose.h:34,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:25:
../../linbox/matrix/blas-matrix.h:238: error: 'template<class _Field> template<class T> LinBox::BlasMatrix::BlasMatrix(const _Field&, const int64_t&, const T&)' cannot be overloaded
../../linbox/matrix/blas-matrix.h:220: error: with 'template<class _Field> template<class T> LinBox::BlasMatrix::BlasMatrix(const _Field&, const long int&, const T&)'
In file included from ../../linbox/matrix/blas-matrix.h:1196,
                 from ../../linbox/blackbox/compose.h:34,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:25:
../../linbox/matrix/blas-matrix.inl:259: error: redefinition of 'LinBox::BlasMatrix<_Field>::BlasMatrix(const _Field&, const long int&, const T&)'
../../linbox/matrix/blas-matrix.inl:245: error: 'LinBox::BlasMatrix<_Field>::BlasMatrix(const _Field&, const int64_t&, const T&)' previously declared here
make[7]: *** [diophantine-solver.lo] Error 1

This one looks related to https://groups.google.com/d/topic/linbox-devel/ogc_XyBEJNg/discussion I'll try tweaking stuff.

Got it, the fix used defines something if using GCC 4.4.5 on non x86_64 because its needed on 32 bits. Unfortunately this breaks ia64 (maybe other 64 bits systems? anybody wants to try out GCC 4.4.5 on sparc64 or ppc64 :)), so the problem it the filtering on "non x86_64", rather than "32 bits".

Reported upstream: https://groups.google.com/d/topic/linbox-devel/NuD24slLFyY/discussion

comment:328 follow-up: Changed 6 years ago by jpflori

I cannot use the fast target on ia64 because the python module "platform" seems broken:

>>> platform.uname()
('Linux', 'tic', '2.6.32-5-mckinley', '#1 SMP Sun May 6 08:36:37 UTC 2012', 'ia64', '')

so that

>>> platform.processor()
''

Indeed

% uname -a
Linux tic 2.6.32-5-mckinley #1 SMP Sun May 6 08:36:37 UTC 2012 ia64 GNU/Linux

and

% uname -p
unknown
Last edited 6 years ago by jpflori (previous) (diff)

comment:329 in reply to: ↑ 328 ; follow-up: Changed 6 years ago by leif

Replying to jpflori:

Indeed

% uname -a
Linux tic 2.6.32-5-mckinley #1 SMP Sun May 6 08:36:37 UTC 2012 ia64 GNU/Linux

and

% uname -p
unknown

And uname -m ?

comment:330 in reply to: ↑ 329 Changed 6 years ago by jpflori

Replying to leif:

Replying to jpflori:

Indeed

% uname -a
Linux tic 2.6.32-5-mckinley #1 SMP Sun May 6 08:36:37 UTC 2012 ia64 GNU/Linux

And uname -m ?

That's where the ia64 comes from. Both "uname -p" and "uname -i" spit "unknown".

comment:331 follow-up: Changed 6 years ago by jpflori

FYI, I tried building ATLAS on another similar ia64 (gcc66) with SAGE_ATLAS_ARCH=IA64Itan2 and it still took ages:

real    2778m46.611s
user    2184m3.292s
sys     13m49.536s
Successfully installed atlas-3.10.1.p0

and its quite similar to what happened without SAGE_ATLAS_ARCH set (and fast does not work, but I assume it would be the same as IA64Itan2):

real    2269m37.705s
user    2230m5.724s
sys     14m31.728s

Maybe that's because the other core is busy? (can't do nothing about that...)

Both logs are at

comment:332 Changed 6 years ago by jpflori

Result of make testlong on gcc60 at http://boxen.math.washington.edu/home/jpflori/testlong-gcc63-ia64-debian.log

Most failures from gap seem to be of type

gap(22997): unaligned access to 0x60000fffffffa46f, ip=0x40000000001a7ba0

The one from gfan with assertions failures surely due to similar reasons. It reminds me of #13151.

Some other failures involve permutation and symmetric stuff.

In particular I got no segfault in sage/matrix/matrix_double_dense.pyx.

comment:333 in reply to: ↑ 331 Changed 6 years ago by jpflori

Replying to jpflori:

FYI, I tried building ATLAS on another similar ia64 (gcc66) with SAGE_ATLAS_ARCH=IA64Itan2 and it still took ages:

real    2778m46.611s
user    2184m3.292s
sys     13m49.536s
Successfully installed atlas-3.10.1.p0

and its quite similar to what happened without SAGE_ATLAS_ARCH set (and fast does not work, but I assume it would be the same as IA64Itan2):

real    2269m37.705s
user    2230m5.724s
sys     14m31.728s

Maybe that's because the other core is busy? (can't do nothing about that...)

Both logs are at

After copying the tar.bz2 archdefs files in the patches directory into the src/CONFIG/ARCHS I indeed get a much faster (something between 40 minutes and 1 hour) build, so I guess you put them there in that intention and we should trigger the copy in spkg-install.

I'll put an updated spkg with that and a fix for detection of ia64 online soon.

comment:334 Changed 6 years ago by jpflori

It seems the spkg also takes a quite huge amount of time to build on sparc64 in 32 bits mode. The log is at http://boxen.math.washington.edu/home/jpflori/atlas-3.10.1.p0-gcc63-sparc64-32.log

comment:335 in reply to: ↑ 318 Changed 6 years ago by jpflori

Replying to jhpalmieri:

On iras, I rebuilt all of the packages that come after ATLAS with SAGE_CHECK=yes. I got one failure, iml:

mkdir .libs
gcc -I/../src -I/home/palmieri/iras/sage-5.8.beta1-10508/local/include -I. -g -O2 -o .lib\
s/test-smallentry test_smallentry-test-smallentry.o  ../src/.libs/libiml.so -L/home/palmi\
eri/iras/sage-5.8.beta1-10508/local/lib -lm /home/palmieri/iras/sage-5.8.beta1-10508/loca\
l/lib/libgmp.so -Wl,--rpath -Wl,/home/palmieri/iras/sage-5.8.beta1-10508/local/lib
../src/.libs/libiml.so: undefined reference to `cblas_dswap'
../src/.libs/libiml.so: undefined reference to `cblas_dgemv'
../src/.libs/libiml.so: undefined reference to `cblas_dgemm'
../src/.libs/libiml.so: undefined reference to `cblas_dger'
../src/.libs/libiml.so: undefined reference to `cblas_dcopy'
collect2: ld returned 1 exit status
make[5]: *** [test-smallentry] Error 1
make[5]: Leaving directory `/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/iml-1.0.1\
.p14/src/tests'
make[4]: *** [check-am] Error 2
make[4]: Leaving directory `/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/iml-1.0.1\
.p14/src/tests'
make[3]: *** [check-recursive] Error 1
make[3]: Leaving directory `/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/iml-1.0.1\
.p14/src'
Error testing IML

(gsl also failed, but it failed with the old ATLAS package, too.)

Did it segfault as before during "make ptest"? I guess it was one of the main reason to withhold this package, so it would be great to know. At least on the setup I used, there was no problem.

comment:336 in reply to: ↑ 317 Changed 6 years ago by jpflori

Replying to jhpalmieri:

On iras, I get several doctest failures:

The following tests failed:

        sage -t  --long -force_lib devel/sage/sage/calculus/interpolators.pyx # Killed/crashed
        sage -t  --long -force_lib devel/sage/sage/calculus/riemann.pyx # Killed/crashed
        sage -t  --long -force_lib devel/sage/sage/matrix/matrix_double_dense.pyx # Killed/crashed

In the log file, it just says "The doctested process was killed by signal 11" for each one.

Oh yeah, it did... Not sure what to do then.

comment:337 in reply to: ↑ 178 ; follow-up: Changed 6 years ago by jpflori

Replying to kcrisman:

Like I said, don't count those chickens. I think this is pretty clearly related, given the libatlas reference.

building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/po
byte-compiling package 'graphics'
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/student/Desktop/sage-5.3.rc0/spkg/build/r-2.14.0.p3/src/library/grDevices/libs/grDevices.so':
  dlopen(/Users/student/Desktop/sage-5.3.rc0/spkg/build/r-2.14.0.p3/src/library/grDevices/libs/grDevices.so, 6): Symbol not found: _ATL_DecAtomicCount
  Referenced from: /Users/student/Desktop/sage-5.3.rc0/local/lib/libatlas.2.dylib
  Expected in: dynamic lookup
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
make[6]: *** [../../../library/graphics/R/graphics.rdb] Error 1
make[5]: *** [all] Error 2
make[4]: *** [R] Error 1
make[3]: *** [R] Error 1
make[2]: *** [R] Error 1
Error building R.

real    44m11.283s
user    28m7.249s
sys     6m59.266s
************************************************************************
Error installing package r-2.14.0.p3
************************************************************************

I think that's the last spkg other than rubiks and sagetex, actually, so cvxopt and r might be the only problems with this approach.

I get similar problems on sparc hardware. There must be something wrong in the build system because some asm routines are not available for sparc and it does not fallback to generic routines but rather leaves undefined symbol for DecAtomicCount? (and two other related functions).

By the way these functions seem thread related but passing again -t 0 to configure as used to be the case in our previous spkg does not solve the problem, the thread part still gets built, even if it may be not used.

comment:338 in reply to: ↑ 337 ; follow-ups: Changed 6 years ago by jpflori

Replying to jpflori:

Replying to kcrisman:

Like I said, don't count those chickens. I think this is pretty clearly related, given the libatlas reference.

building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/po
byte-compiling package 'graphics'
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/student/Desktop/sage-5.3.rc0/spkg/build/r-2.14.0.p3/src/library/grDevices/libs/grDevices.so':
  dlopen(/Users/student/Desktop/sage-5.3.rc0/spkg/build/r-2.14.0.p3/src/library/grDevices/libs/grDevices.so, 6): Symbol not found: _ATL_DecAtomicCount
  Referenced from: /Users/student/Desktop/sage-5.3.rc0/local/lib/libatlas.2.dylib
  Expected in: dynamic lookup
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
make[6]: *** [../../../library/graphics/R/graphics.rdb] Error 1
make[5]: *** [all] Error 2
make[4]: *** [R] Error 1
make[3]: *** [R] Error 1
make[2]: *** [R] Error 1
Error building R.

real    44m11.283s
user    28m7.249s
sys     6m59.266s
************************************************************************
Error installing package r-2.14.0.p3
************************************************************************

I think that's the last spkg other than rubiks and sagetex, actually, so cvxopt and r might be the only problems with this approach.

I get similar problems on sparc hardware. There must be something wrong in the build system because some asm routines are not available for sparc and it does not fallback to generic routines but rather leaves undefined symbol for DecAtomicCount? (and two other related functions).

By the way these functions seem thread related but passing again -t 0 to configure as used to be the case in our previous spkg does not solve the problem, the thread part still gets built, even if it may be not used.

From what I've seen on a Debian ppc64, by default the correct mut implementation of DecAtomicCount? and the two other functions get picked up (note there is a ppc assembly implem but its commented as unstable and an #error statement is put in the assembly file).

But if I put back the "-t 0" param when configuring ATLAS, then these three functions do not get defined, which would be ok if other thread related functions which point to these functions were not defined... So if I explicitely disable thread, ATLAS still builds some (but not all!) of the thread related functions and if I tried to dlopen the library the runtime linker fails with undefined symbols as reported by Karl Dieter.

Nonetheless I don't think that the problem I just stated is what Karl Dieter encountered as he used the default configuration and so should get the fallback implementaiton of DecAtomicCount? and related. I also encountered such a behavior on sparc where there is no assembly routines and somehow the fallback implementation is not picked as well.

Karl Dieter, could you post your ATLAS build log somewhere please?

comment:339 in reply to: ↑ 338 ; follow-up: Changed 6 years ago by leif

Replying to jpflori:

Replying to jpflori:

Replying to kcrisman:

Like I said, don't count those chickens. I think this is pretty clearly related, given the libatlas reference.

building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/po
byte-compiling package 'graphics'
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/student/Desktop/sage-5.3.rc0/spkg/build/r-2.14.0.p3/src/library/grDevices/libs/grDevices.so':
  dlopen(/Users/student/Desktop/sage-5.3.rc0/spkg/build/r-2.14.0.p3/src/library/grDevices/libs/grDevices.so, 6): Symbol not found: _ATL_DecAtomicCount
  Referenced from: /Users/student/Desktop/sage-5.3.rc0/local/lib/libatlas.2.dylib
  Expected in: dynamic lookup
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
make[6]: *** [../../../library/graphics/R/graphics.rdb] Error 1
make[5]: *** [all] Error 2
make[4]: *** [R] Error 1
make[3]: *** [R] Error 1
make[2]: *** [R] Error 1
Error building R.

real    44m11.283s
user    28m7.249s
sys     6m59.266s
************************************************************************
Error installing package r-2.14.0.p3
************************************************************************

I think that's the last spkg other than rubiks and sagetex, actually, so cvxopt and r might be the only problems with this approach.

I get similar problems on sparc hardware. There must be something wrong in the build system because some asm routines are not available for sparc and it does not fallback to generic routines but rather leaves undefined symbol for DecAtomicCount? (and two other related functions).

By the way these functions seem thread related but passing again -t 0 to configure as used to be the case in our previous spkg does not solve the problem, the thread part still gets built, even if it may be not used.

From what I've seen on a Debian ppc64, by default the correct mut implementation of DecAtomicCount? and the two other functions get picked up (note there is a ppc assembly implem but its commented as unstable and an #error statement is put in the assembly file).

But if I put back the "-t 0" param when configuring ATLAS, then these three functions do not get defined, which would be ok if other thread related functions which point to these functions were not defined... So if I explicitely disable thread, ATLAS still builds some (but not all!) of the thread related functions and if I tried to dlopen the library the runtime linker fails with undefined symbols as reported by Karl Dieter.

Well, this might be due to how Sage builds shared libraries from ATLAS' static ones, as statically linking by default does some kind of dead code elimination ("removing" unused modules and hence potentially dead references).


Nonetheless I don't think that the problem I just stated is what Karl Dieter encountered as he used the default configuration and so should get the fallback implementaiton of DecAtomicCount? and related. I also encountered such a behavior on sparc where there is no assembly routines and somehow the fallback implementation is not picked as well.

comment:340 in reply to: ↑ 339 ; follow-up: Changed 6 years ago by jpflori

Replying to leif:

Well, this might be due to how Sage builds shared libraries from ATLAS' static ones, as statically linking by default does some kind of dead code elimination ("removing" unused modules and hence potentially dead references).

Same problem (at least there is an undefined ATL_DecAtomicCount and defined ATL_GetAtomicCount in the generated libsatlas.so) with the shared libs generated using ATLAS build system rather than Volker's autotools based one.

I'm giving it a shot on Linux just to see what happens if I try to disable threads there as well.

comment:341 Changed 6 years ago by jpflori

I have the same undefined symbols in the Linux shared libs if I build ATLAS with "-t 0" but R does not seem to care.

comment:342 Changed 6 years ago by jpflori

In fact the Debian ppc64 install does not care either.

comment:343 in reply to: ↑ 340 ; follow-up: Changed 6 years ago by leif

Replying to jpflori:

Replying to leif:

Well, this might be due to how Sage builds shared libraries from ATLAS' static ones, as statically linking by default does some kind of dead code elimination ("removing" unused modules and hence potentially dead references).

Same problem (at least there is an undefined ATL_DecAtomicCount and defined ATL_GetAtomicCount in the generated libsatlas.so) with the shared libs generated using ATLAS build system rather than Volker's autotools based one.

And there are no additional NEEDED tags either (?) I guess...

comment:344 in reply to: ↑ 343 ; follow-up: Changed 6 years ago by jpflori

Replying to leif:

Replying to jpflori:

Replying to leif:

Well, this might be due to how Sage builds shared libraries from ATLAS' static ones, as statically linking by default does some kind of dead code elimination ("removing" unused modules and hence potentially dead references).

Same problem (at least there is an undefined ATL_DecAtomicCount and defined ATL_GetAtomicCount in the generated libsatlas.so) with the shared libs generated using ATLAS build system rather than Volker's autotools based one.

And there are no additional NEEDED tags either (?) I guess...

Hum, you got me. What's that and how to check it?

From what I just reported it seems the undefined symbols are no problem with a non threaded build (also I guess it would be cleaner not to include all these defined thread related functions).

The problem might arise when one actually try to build a threaded lib but ATLAS fails to pick assembly or fallback code for ATL_DecAtomicCount. I'm currently trying to build R (it never went that far, don't remember why) on a sparc system which failed to build a real threaded lib just like Karl Dieter ppc system. It's quite slow but I should be able to report today.

comment:345 in reply to: ↑ 344 ; follow-up: Changed 6 years ago by leif

Replying to jpflori:

Replying to leif:

Replying to jpflori:

Replying to leif:

Well, this might be due to how Sage builds shared libraries from ATLAS' static ones, as statically linking by default does some kind of dead code elimination ("removing" unused modules and hence potentially dead references).

Same problem (at least there is an undefined ATL_DecAtomicCount and defined ATL_GetAtomicCount in the generated libsatlas.so) with the shared libs generated using ATLAS build system rather than Volker's autotools based one.

And there are no additional NEEDED tags either (?) I guess...

Hum, you got me. What's that and how to check it?

On ELF systems, e.g. with readelf -d foo.so [ | grep -w NEEDED ]. :-)

These are the entries where shared libraries needed by the program / the shared library itself are recorded.


(also I guess it would be cleaner not to include all these defined thread related functions).

Presumably... ;-)


The problem might arise when one actually try to build a threaded lib but ATLAS fails to pick assembly or fallback code for ATL_DecAtomicCount.

If it fails in that case (too), that's an ATLAS bug I'd say. (Unless it would use some to-be-linked-in external functions instead, but the ATL_ prefix indicates it doesn't [try to].)


I'm currently trying to build R (it never went that far, don't remember why) on a sparc system which failed to build a real threaded lib just like Karl Dieter ppc system.

R is often built quite "late", not just because of its dependencies, but perhaps also due to our deps, i.e., the order [otherwise independent] packages are listed there (I thinkTM).

comment:346 Changed 6 years ago by jpflori

Last info of the day, on the Debian sparc system where ATLAS failed to build a threaded lib, R did not complain either, so this may be PPC/OS X specific.

comment:347 in reply to: ↑ 345 Changed 6 years ago by jdemeyer

Replying to leif:

R is often built quite "late"

On a fast multi-core system, R will usually be the last package to finish building. But that's more because R depends on ATLAS (so it has to be built "late") and it's built mainly single-threaded.

comment:348 in reply to: ↑ 338 ; follow-up: Changed 6 years ago by kcrisman

Karl Dieter, could you post your ATLAS build log somewhere please?

Well, I can look tomorrow, but I strongly doubt that I kept that. The machine doesn't have tons of disk space, so I only keep one or two old builds around on it for testing. In any case, at least at one point the spkg for this ticket had resolved the issue, or so it seems after reading through the (very lengthy) notes...

I might try starting a build with gcc 4.7 and this ticket, though, sometime later tonight.

comment:349 in reply to: ↑ 348 ; follow-up: Changed 6 years ago by jpflori

Replying to kcrisman:

Karl Dieter, could you post your ATLAS build log somewhere please?

Well, I can look tomorrow, but I strongly doubt that I kept that. The machine doesn't have tons of disk space, so I only keep one or two old builds around on it for testing. In any case, at least at one point the spkg for this ticket had resolved the issue, or so it seems after reading through the (very lengthy) notes...

I might try starting a build with gcc 4.7 and this ticket, though, sometime later tonight.

Ok, so I'll assume the ATLAS spkg is ok for the R one now. Nonetheless I'll report the problem of threads related stuff upstream.

comment:350 Changed 6 years ago by jpflori

FYI, it builded ok on the Solaris 10 I have access to, including the use of the fallback mutex implementation for the DecAtomic? function etal.

comment:351 in reply to: ↑ 349 ; follow-up: Changed 6 years ago by kcrisman

I might try starting a build with gcc 4.7 and this ticket, though, sometime later tonight.

Somehow I forgot to do this, though I definitely built Sage. I'll try this later today for sure.

Ok, so I'll assume the ATLAS spkg is ok for the R one now.

I think you should assume so.

comment:352 in reply to: ↑ 351 Changed 6 years ago by kcrisman

I might try starting a build with gcc 4.7 and this ticket, though, sometime later tonight.

Somehow I forgot to do this, though I definitely built Sage. I'll try this later today for sure.

Sorry, I got confused and thought you were talking about Cygwin. I will be able to check on this build in about four hours, when I am physically present at that machine.

comment:353 Changed 6 years ago by kcrisman

Aargh, it failed early on, while building the gcc-4.7 spkg. So I'll have to put gcc-4.6.3.spkg back in, and restart the build from there. Sorry, now I won't know until Monday - but like I said, I don't anticipate any problems, given prior experience.

comment:354 Changed 6 years ago by jpflori

I've just updated the spkg at http://boxen.math.washington.edu/home/jpflori/atlas-3.10.1.p0.spkg with:

  • copy the archdefs so they are used,
  • better detection of ia64,
  • check return code of patch command.

I've put another devel spkg at http://boxen.math.washington.edu/home/jpflori/atlas-3.11.8.p0.spkg where I only updated the src folder and removed the long_filename patch which is now upstream.

comment:355 in reply to: ↑ 162 Changed 6 years ago by jpflori

Replying to jhpalmieri:

Builds on cicero and flavius. On mark (Solaris), I see a problem building scipy. Could this be related? Log here.

Edit: more info, from the numpy log:

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not found in /home/palmieri/mark/sage-5.3.beta1-ATLAS/local/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
/home/palmieri/mark/sage-5.3.beta1-ATLAS/spkg/build/numpy-1.5.1.p1/src/numpy/distutils/system_info.py:1010: UserWarning:
*********************************************************************
    Lapack library (from ATLAS) is probably incomplete:
      size of /home/palmieri/mark/sage-5.3.beta1-ATLAS/local/lib/liblapack.so is 360k (expected >4000k)

    Follow the instructions in the KNOWN PROBLEMS section of the file
    numpy/INSTALL.txt.
*********************************************************************

If you have an account on skynet, feel free to look around /home/palmieri/mark/sage-5.3.beta1-ATLAS/.

Same problem on my Solaris, scipy fails and in numpy log:

/infres/post/flori/sage-5.7-infres2/spkg/build/numpy-1.5.1.p1/src/numpy/distutil
s/system_info.py:1010: UserWarning: 
*********************************************************************
    Lapack library (from ATLAS) is probably incomplete:
      size of /infres/post/flori/sage-5.7-infres2/local/lib/liblapack.so is 333k
 (expected >4000k)

    Follow the instructions in the KNOWN PROBLEMS section of the file
    numpy/INSTALL.txt.
*********************************************************************

comment:356 Changed 6 years ago by jpflori

On the debian sparc where the ATL_DecAtomic etal symbols are missing, scipy also fails because of these symbols:

ImportError: /infres/post/flori/sage-5.7-lame5/local/lib/libatlas.so.2: undefined symbol: ATL_DecAtomicCount

comment:357 follow-up: Changed 6 years ago by jpflori

It seems to me the current spkg does not install static libraries.

And I have an undefined ATL_sammm symbol in libatlas.so which makes the check for "-lcblas -latals" fail on Linux. Checking for LAPACK fails for the same reason. In fact it only succeeds on my system potentially because there is a system wide libblas...

comment:358 in reply to: ↑ 357 Changed 6 years ago by jpflori

Replying to jpflori:

It seems to me the current spkg does not install static libraries.

And I have an undefined ATL_sammm symbol in libatlas.so which makes the check for "-lcblas -latals" fail on Linux. Checking for LAPACK fails for the same reason. In fact it only succeeds on my system potentially because there is a system wide libblas...

This reports on Linux are with ATLAS 3.11.8, checking now with 3.10.1

comment:359 follow-up: Changed 6 years ago by jhpalmieri

I just noticed on iras (ia64), near the beginning of the build, I get lots of error messages

/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S: Assembler messages:
/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S:32: Error: Unknown opcode `subl $8,%esp'
/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S:33: Error: bad expression
/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S:33: Error: Illegal operand separator `e'
/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S:34: Error: bad expression
...

These are present when building the old spkg (3.8.4.p1) as well as the just posted 3.10.1.p0. Are they important?

comment:360 Changed 6 years ago by vbraun

The spkg intentionally does not install static libraries because static libraries suck.

Errors during compilation are normal, its just trying out different asm routines to see which ones work.

comment:361 Changed 6 years ago by jhpalmieri

With the latest 3.10.1.p0 spkg on iras, the build completed in 45 minutes! Far better than the 36 hours the last time. We'll see how it handles tests...

comment:362 Changed 6 years ago by kcrisman

On Cygwin with this ticket, apparently Scipy doesn't know where to find lapack any more.

$ ./sage -i scipy
Found package scipy in spkg/standard/scipy-0.11.0.p1.spkg
scipy-0.11.0.p1
====================================================
Extracting package /home/sagetest/sage-5.9.beta0/spkg/standard/scipy-0.11.0.p1.spkg
-rw-r--r-- 1 Administrator None 5480829 Jan 29 19:13 /home/sagetest/sage-5.9.beta0/spkg/standard/scipy-0.11.0.p1.spkg
Finished extraction
****************************************************
Host system:
CYGWIN_NT-6.1-WOW64 CETGORD-J5FGIPM 1.7.17(0.262/5/3) 2012-10-19 14:39 i686 Cygwin
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-pc-cygwin/4.5.3/lto-wrapper.exe
Target: i686-pc-cygwin
Configured with: /gnu/gcc/releases/respins/4.5.3-3/gcc4-4.5.3-3/src/gcc-4.5.3/configure --srcdir=/gnu/gcc/releases/respins/4.5.3-3/gcc4-4.5.3-3/src/gcc-4.5.3 --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --datarootdir=/usr/share --docdir=/usr/share/doc/gcc4 -C --datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v --with-gmp=/usr --with-mpfr=/usr --enable-bootstrap --enable-version-specific-runtime-libs --libexecdir=/usr/lib --enable-static --enable-shared --enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld --with-gnu-as --with-dwarf2 --disable-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,lto,objc,obj-c++ --enable-graphite --enable-lto --enable-java-awt=gtk --disable-symvers --enable-libjava --program-suffix=-4 --enable-libgomp --enable-libssp --enable-libada --enable-threads=posix --with-arch=i686 --with-tune=generic --enable-libgcj-sublibs CC=gcc-4 CXX=g++-4 CC_FOR_TARGET=gcc-4 CXX_FOR_TARGET=g++-4 GNATMAKE_FOR_TARGET=gnatmake GNATBIND_FOR_TARGET=gnatbind --with-ecj-jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.5.3 (GCC)
****************************************************
Note: CFLAGS, CXXFLAGS and SHAREDFLAGS are taken from distutils,
      so their current settings are ignored.
patching file scipy/weave/catalog.py
Running from scipy source directory.
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /home/sagetest/sage-5.9.beta0/local/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /home/sagetest/sage-5.9.beta0/local
  libraries ptf77blas,ptcblas,atlas not found in /home/sagetest/sage-5.9.beta0/local/include
  libraries ptf77blas,ptcblas,atlas not found in /home/sagetest/sage-5.9.beta0/local/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in /home/sagetest/sage-5.9.beta0/local
  libraries f77blas,cblas,atlas not found in /home/sagetest/sage-5.9.beta0/local/include
  libraries f77blas,cblas,atlas not found in /home/sagetest/sage-5.9.beta0/local/lib
  NOT AVAILABLE

<snip a lot of similar stuff>

  File "/home/sagetest/sage-5.9.beta0/local/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 461, in get_info
    raise self.notfounderror(self.notfounderror.__doc__)
numpy.distutils.system_info.LapackNotFoundError:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
Error building scipy.

real    0m0.827s
user    0m0.264s
sys     0m0.542s
************************************************************************
Error installing package scipy-0.11.0.p1
************************************************************************

Indeed, local/lib has liblapack.a and libblas.a when I don't use this ticket, but not with this ticket (though both have libblas.dll.a).

And I guess this is unsurprising, because we don't really do anything on Cygwin!

Copying /usr/lib/libblas.dll.a to /home/sagetest/sage-5.9.beta0/local/lib

is the extent of the log for atlas in both cases, whereas before lapack was definitely built (lots of sage_fortran etc. in the log) and of course now it's MIA by design.

So... do we have to now build atlas on Cygwin? I can do

cp /usr/lib/liblapack.a /home/sagetest/sage-5.9.beta0/local/lib

for now, hopefully that will work...

This ticket still has

# On Cygwin we simply require that the system-wide lapack is installed.
# This includes BLAS and is enough to build the rest of Sage.
if conf['CYGWIN?']:
    lib = '/usr/lib/libblas.dll.a'
    if not os.path.exists(lib):
        print '*'*75
        print 'On Cygwin you must install the standard LAPACK Cygwin package'
        print 'via the Cygwin setup.exe program in the "Math" category.'
        print '*'*75 
        sys.exit(1)
    cp(lib, os.path.join(conf['SAGE_LOCAL'], 'lib'))
    sys.exit(0)

but I think that now we'll have to add to it to copy liblapack.a (or build lapack, of course).

So I think that probably some update to this needs to be included. Maybe this would still be enough?

Last edited 6 years ago by kcrisman (previous) (diff)

comment:363 Changed 6 years ago by jpflori

Indeed, now ATLAS builds LAPACK itself, so if you don't build ATLAS, you don't build LAPACK either (in addition to the lapack spkg, the cblas ref implem one was also removed).

comment:364 follow-up: Changed 6 years ago by kcrisman

Right, but in the past we still needed the lapack stuff from Cygwin.

Also, cvxopt now fails.

building 'glpk' extension
gcc -I/usr/include/ncurses -fno-strict-aliasing -std=gnu99 -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/home/sagetest/sage-5.9.beta0/local/include -I/home/sagetest/sage-5.9.beta0/$
gcc -shared -Wl,--enable-auto-image-base -L/home/sagetest/sage-5.9.beta0/local/lib build/temp.cygwin-1.7.17-i686-2.7/C/glpk.o -L/home/sagetest/sage-5.9.beta0/local/lib -L/home/sagetest/sage-5.9.b$
/home/sagetest/sage-5.9.beta0/local/lib/libglpk.a(glpapi07.o): In function `set_d_eps':
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:111: undefined reference to `__imp____gmpq_init'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:112: undefined reference to `__imp____gmpq_set_d'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:114: undefined reference to `__imp____gmpq_div'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:115: undefined reference to `__imp____gmpq_set_si'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:117: undefined reference to `__imp____gmpq_add'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:119: undefined reference to `__imp____gmpq_mul'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:122: undefined reference to `__imp____gmpq_clear'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:125: undefined reference to `__imp____gmpq_get_d'

Looks like a missing include of MPIR, maybe?

comment:365 in reply to: ↑ 364 ; follow-up: Changed 6 years ago by jpflori

Replying to kcrisman:

Right, but in the past we still needed the lapack stuff from Cygwin.

Yup to get the BLAS thing. But although it also provided the LAPACK part we built it anyway.

Also, cvxopt now fails.

building 'glpk' extension
gcc -I/usr/include/ncurses -fno-strict-aliasing -std=gnu99 -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/home/sagetest/sage-5.9.beta0/local/include -I/home/sagetest/sage-5.9.beta0/$
gcc -shared -Wl,--enable-auto-image-base -L/home/sagetest/sage-5.9.beta0/local/lib build/temp.cygwin-1.7.17-i686-2.7/C/glpk.o -L/home/sagetest/sage-5.9.beta0/local/lib -L/home/sagetest/sage-5.9.b$
/home/sagetest/sage-5.9.beta0/local/lib/libglpk.a(glpapi07.o): In function `set_d_eps':
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:111: undefined reference to `__imp____gmpq_init'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:112: undefined reference to `__imp____gmpq_set_d'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:114: undefined reference to `__imp____gmpq_div'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:115: undefined reference to `__imp____gmpq_set_si'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:117: undefined reference to `__imp____gmpq_add'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:119: undefined reference to `__imp____gmpq_mul'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:122: undefined reference to `__imp____gmpq_clear'
/home/sagetest/sage-5.9.beta0/spkg/build/glpk-4.44.p0/src/src/glpapi07.c:125: undefined reference to `__imp____gmpq_get_d'

Looks like a missing include of MPIR, maybe?

Did you use the p1 spkg I posted and linked toward the end of the comments?

comment:366 Changed 6 years ago by jhpalmieri

On iras, the most recent 3.10.1.p0 spkg fails its self-tests:

RHS=76, nrm=291.507111
RHS=77, nrm=337.993896
RHS=78, nrm=335.039612
RHS=79, nrm=477.389954
RHS=80, nrm=334.815796
make[6]: *** [csanity_test] Error 1
make[6]: *** Waiting for unfinished jobs....
Last edited 6 years ago by jhpalmieri (previous) (diff)

comment:367 in reply to: ↑ 359 Changed 6 years ago by jdemeyer

Replying to jhpalmieri:

I just noticed on iras (ia64), near the beginning of the build, I get lots of error messages

/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S: Assembler messages:
/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S:32: Error: Unknown opcode `subl $8,%esp'
/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S:33: Error: bad expression
/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S:33: Error: Illegal operand separator `e'
/home/palmieri/iras/sage-5.8.beta1-10508/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//CONFIG/src/backend/cpuid.S:34: Error: bad expression
...

These are present when building the old spkg (3.8.4.p1) as well as the just posted 3.10.1.p0. Are they important?

Not really. ATLAS does some kind of "brute force" CPU detection where it tries to compile with various options for various kinds of CPUs until one succeeds.

comment:368 in reply to: ↑ 365 ; follow-up: Changed 6 years ago by kcrisman

  • Description modified (diff)

Right, but in the past we still needed the lapack stuff from Cygwin.

Yup to get the BLAS thing. But although it also provided the LAPACK part we built it anyway.

Well, anyway that needs to be fixed so that Cygwin knows where to find what.

Looks like a missing include of MPIR, maybe?

Did you use the p1 spkg I posted and linked toward the end of the comments?

No, it was in comment:299 - that's scores of comments ago. If that is really what is needed, then you should update the ticket description (which I have now done).

Does that mean I shouldn't have used Volker's spkg for atlas either? Does yours behave properly w.r.t. Cygwin?

comment:369 in reply to: ↑ 368 Changed 6 years ago by kcrisman

Looks like a missing include of MPIR, maybe?

Did you use the p1 spkg I posted and linked toward the end of the comments?

No, it was in comment:299 - that's scores of comments ago. If that is really what is needed, then you should update the ticket description (which I have now done).

Anyway, that works.

Does that mean I shouldn't have used Volker's spkg for atlas either? Does yours behave properly w.r.t. Cygwin?

It doesn't, at least not automatically - it just copies libblas.dll.a but not liblapack.a, and then exits.

And for Scipy's spkg-install, that's a problem when it's not in $SAGE_LOCAL:

if [ "$UNAME" = "Darwin" ]; then
    unset ATLAS
    unset BLAS
    unset LAPACK
    export LDFLAGS="-bundle -undefined dynamic_lookup $LDFLAGS"
else
    export ATLAS="$SAGE_LOCAL"  
    export BLAS="$SAGE_LOCAL"
    export LAPACK="$SAGE_LOCAL"
    export LDFLAGS="-shared $LDFLAGS"
fi

I think it doesn't really make sense to change Scipy's spkg. I think it does make sense to copy liblapack in the same way and some messages about exactly what lapack stuff to install on Cygwin here, and then someone can use SAGE_ATLAS_INSTALL=??? to try out atlas building on Cygwin. Since there is a lot of other stuff going on here, I'm not going to attempt to confuse the issue by uploading my own spkg now, but JP knows what's needed and can surelyTM take care of it :-)

comment:370 Changed 6 years ago by jpflori

My 3.10.1.p0 spkg is the most up to date. You can also give the 3.11.8.p0 spkg a shot but it should not work because of the ATL_samm issue. As this is not really working yet, I was too lazy to update the ticket descritpion.

And I did not take care of Cygwin yet; just for info the needed packge are lapack (or liblapack0) and liblapack-devel.

I first tried a little bit of ia64 and then Debian/Solaris? sparc and things are quite horrible already. There is this boring fallback threads code which is not correctly picked when configured to use threads and no assembly is available, and unfortunately the build system seems a little broken and the same broken pieces get picked up when configured not to use threads as well. In fact I think getting it to properly install on Cygwin will be easier.

And finally there is the case of your PPC OS X 14 which seems to have similar problems as what I got on ia64/sparc.

comment:371 follow-ups: Changed 6 years ago by kcrisman

  • Description modified (diff)
  • Milestone changed from sage-5.8 to sage-5.9

Yours still has Volker's fix

if conf['Darwin?'] and not os.environ.has_key('SAGE_ATLAS_ARCH'):
    print 'Skipping build of ATLAS on intel OS X'
    if conf['PPC?']:   # OSX 10.4 PPC linker needs help to find the accelerate blas
        veclib_dir = '/System/Library/Frameworks/Accelerate.framework/' + \
            'Versions/A/Frameworks/vecLib.framework/Versions/A'
        for lib in [ 'libBLAS.dylib', 'libLAPACK.dylib']:
            ln(os.path.join(veclib_dir, lib), 
               os.path.join(conf['SAGE_LOCAL'], 'lib', lib))
    sys.exit(0)

so this should be okay. And ia64 works fine now for installing (according to jhpalmieri - what about tests, I assume not done yet on iras?).


What are the work issues for this ticket? It's hard to tell from all the comments - maybe they should be put in "work issues" :-)

comment:372 in reply to: ↑ 371 Changed 6 years ago by jhpalmieri

Replying to kcrisman:

And ia64 works fine now for installing (according to jhpalmieri - what about tests, I assume not done yet on iras?).

See my comment above: self tests fail for the new spkg. When I build Sage without SAGE_CHECK=yes, all tests pass (make ptestlong).

Last edited 6 years ago by jhpalmieri (previous) (diff)

comment:373 in reply to: ↑ 162 Changed 6 years ago by jpflori

Replying to jhpalmieri:

Builds on cicero and flavius. On mark (Solaris), I see a problem building scipy. Could this be related? Log here.

Edit: more info, from the numpy log:

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not found in /home/palmieri/mark/sage-5.3.beta1-ATLAS/local/lib
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
/home/palmieri/mark/sage-5.3.beta1-ATLAS/spkg/build/numpy-1.5.1.p1/src/numpy/distutils/system_info.py:1010: UserWarning:
*********************************************************************
    Lapack library (from ATLAS) is probably incomplete:
      size of /home/palmieri/mark/sage-5.3.beta1-ATLAS/local/lib/liblapack.so is 360k (expected >4000k)

    Follow the instructions in the KNOWN PROBLEMS section of the file
    numpy/INSTALL.txt.
*********************************************************************

If you have an account on skynet, feel free to look around /home/palmieri/mark/sage-5.3.beta1-ATLAS/.

I had the same problem on my Solaris, it just seems that Solaris test does not like the -e flag:

if [ -e /infres/post/flori/sage-5.7-infres2/spkg/build/atlas-3.10.1.p0/ATLAS-bui
ld/src/lapack/reference/liblapack.a ]; then \
           ln -s /infres/post/flori/sage-5.7-infres2/spkg/build/atlas-3.10.1.p0/
ATLAS-build/src/lapack/reference/liblapack.a /infres/post/flori/sage-5.7-infres2
/spkg/build/atlas-3.10.1.p0/ATLAS-build/src/lapack/reference/lapack_UST232.a ; \
        fi
/bin/sh: test: argument expected

comment:374 Changed 6 years ago by jpflori

And this is somehow in http://math-atlas.sourceforge.net/errata.html .

So we should:

  • sed -e for -f on Solaris.

So I think we have more or less two problems left for ATLAS 3.10.1:

  • investigate problems with threads related functions:
    • fallback code not used when assembly is not available on some systems (i.e. my Debian sparc, but not the Solaris sparc...), a first try seems that going to the build dir and retrying to build the thread related functions solves the problem as suggested here: http://sourceforge.net/p/math-atlas/bugs/170/#6a80
    • threads functions are still included even though "-t 0" is passed, so the above problem cannot be fixed by disabling threads, it seems this is known upstream and is problematic because we use shared libraries, static should be ok, see http://sourceforge.net/p/math-atlas/support-requests/855/
  • segfaults on ia64, that will be a lot of fun :)

And later:

  • fix Cygwin stuff
  • solve ATL_samm for ATLAS 3.11.8

comment:375 Changed 6 years ago by jpflori

For Cygwin: libtool (which already rants on linux for this) will refuse to build .la libs from .o objects directly. Unfortunately, I don't think there is a magical option to make it more sensible and just try (and succeed).

comment:376 follow-up: Changed 6 years ago by jpflori

For Cygwin, using a combinaison of gcc and gfortran rather than libtool with tag=xxx to produce the shaed libs seems to be fine. Numpy and Scipy compiled seemingly ok.

comment:377 in reply to: ↑ 376 Changed 6 years ago by kcrisman

For Cygwin, using a combinaison of gcc and gfortran rather than libtool with tag=xxx to produce the shaed libs seems to be fine. Numpy and Scipy compiled seemingly ok.

Give me the explicit instructions (including what to set SAGE_ATLAS_ARCH to) and I will try this at some point over the weekend. I assume I'd have to muck about in the spkg-install but hopefully that won't be too annoying to do.

comment:378 follow-up: Changed 6 years ago by jpflori

I set

SAGE_ATLAS_ARCH=Corei2,AVX,SSE3,SSE2,SSE1

which was sensible for my harware, nothing different from Linux. Anything not empty will trigger the build, so just choose what fits your hardware; I guess "base" and "fast" should do if you have no idea.

And then I issued make (MAKE="make -j4").

It failed in the end because of libttool

blabla libtool cannot link non-libtool object blabla on this host blabla

So in a Sage shell just cd to the ($SAGE_ROOT/spkg/build/atlas-3.10.1.p0/)ATLAS-lib dir, open Makefile.am and just do what is done for the different lib*.la target but more or less replace @LIBTOOL@ by gcc (or gfortran if there is as well --tag=F77) for the compilation line (and don't forget lib deps -l...). For instance to build a minimally fancy libatlas.dll:

mkdir libatlas-objs
cd libatlas-objs
ar x ../libatlas.a
cd ..
gcc -shared -o libatlas.dll libatlas-objs/*.o
cp libatlas.dll $SAGE_LOCAL/lib/

and for a fortran one for instance

mkdir liblapack-objs
cd liblapack-objs
ar x ../liblapack.a
cd ..
gfortran -shared -o liblapack.dll liblapack-objs/*.o -latlas -lcblas -lf77blas -lm
cp liblapack.dll $SAGE_LOCAL/lib

We could add fancy versioning and creating an import lib and so on, but let's try that first.

comment:379 in reply to: ↑ 371 ; follow-up: Changed 6 years ago by kcrisman

Yours still has Volker's fix so this should be okay.

And it is; OS X 10.4 PPC is doing just fine, passing various combinat tests as we speak, certainly no build problems (with Sage's gcc 4.6, not 4.7).

I'll try the Cygwin thing later this week, did not get a chance yet.

comment:380 in reply to: ↑ 379 ; follow-up: Changed 6 years ago by jpflori

Replying to kcrisman:

Yours still has Volker's fix so this should be okay.

And it is; OS X 10.4 PPC is doing just fine, passing various combinat tests as we speak, certainly no build problems (with Sage's gcc 4.6, not 4.7).

Did it actually build ATLAS or did it use the framework thing Apple provides? I thought that was the solution actually used. If that's the case (look at the log), could you also try actually buliding ATLAS, by setting SAGE_ATLAS_ARCH to something non empty I guess,

I'll try the Cygwin thing later this week, did not get a chance yet.

comment:381 in reply to: ↑ 380 Changed 6 years ago by kcrisman

And it is; OS X 10.4 PPC is doing just fine, passing various combinat tests as we speak, certainly no build problems (with Sage's gcc 4.6, not 4.7).

Did it actually build ATLAS or did it use the framework thing Apple provides? I thought that was the solution actually used.

Of course, and I pointed out that code. We've always done this.

If that's the case (look at the log), could you also try actually buliding ATLAS, by setting SAGE_ATLAS_ARCH to something non empty I guess,

I guess I could try this... seems overkill.

comment:382 follow-up: Changed 6 years ago by kcrisman

Cygwin update, completely different problem from JP, though also Win 7. SAGE_ATLAS_ARCH=base, three threads (though I don't think this was using them?)

make[6]: Entering directory `/cygdrive/c/cygwin/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/tune/blas/gemv'
/usr/bin/gcc -c -DL2SIZE=4194304 -I/cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/include -I/cygdrive/c/cygwin//home/sagetese-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//include -I/cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//de/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_WinNT -DATL_ARCH_x86x87 -DATL_CPUMHZ=2893 -DGCCWIN -DUseClock -DATL_3DNow -DATL_GAS_x8632 -m32 -DATL_FUPACK -DATL_NCPU=4 -O -fomit-frame-pointer -fPIC -m32  -mstackrealign -o mvtksearch.o /cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAld/../src//tune/blas/gemv/mvtksearch.c
/cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//tune/blas/gemv/mvtksearch.c:1:0: warning: -fPIC ignored for target (ade is position independent)
/usr/bin/gcc -DL2SIZE=4194304 -I/cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/include -I/cygdrive/c/cygwin//home/sagetest/s.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//include -I/cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//inccontrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_WinNT -DATL_ARCH_x86x87 -DATL_CPUMHZ=2893 -DGCCWIN -DUseClock -DATL_3DNow -DATL_GAS_x8632 -m32 -DATL_FULL_K -DATL_NCPU=4 -O -fomit-frame-pointer -fPIC -m32  -mstackrealign -o xmvtksearch mvtksearch.o
./xmvtksearch -p d
assertion "kpB" failed: file "/cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/../src//tune/blas/gemv/mvtksearch.c", line 1239ction: TuneBestPF
Makefile:514: recipe for target `res/dMVTK.sum' failed
make[6]: *** [res/dMVTK.sum] Aborted (core dumped)
make[6]: Leaving directory `/cygdrive/c/cygwin/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/tune/blas/gemv'
Makefile:321: recipe for target `/cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/tune/blas/gemv/res/dMVTK.sum' failed
make[5]: *** [/cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/tune/blas/gemv/res/dMVTK.sum] Error 2
make[5]: Leaving directory `/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/bin'
ERROR 949 DURING MVTTUNE!!.  CHECK INSTALL_LOG/dMVTTUNE.LOG FOR DETAILS.
make[5]: Entering directory `/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/bin'
cd /cygdrive/c/cygwin//home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build ; make -j1 error_report
make[6]: Entering directory `/cygdrive/c/cygwin/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build'
make -j1 -f Make.top error_report
make[7]: Entering directory `/cygdrive/c/cygwin/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build'
uname -a 2>&1 >> bin/INSTALL_LOG/ERROR.LOG
/usr/bin/gcc -v 2>&1  >> bin/INSTALL_LOG/ERROR.LOG
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-pc-cygwin/4.5.3/lto-wrapper.exe
Target: i686-pc-cygwin
Configured with: /gnu/gcc/releases/respins/4.5.3-3/gcc4-4.5.3-3/src/gcc-4.5.3/configure --srcdir=/gnu/gcc/releases/respins/4.5.3-3/gcc4-4.5.3-3/src/gcc-4.5.3 --prefir --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --libexecdir=/usr/lib --datadir=/usr/share --localstatedir=/var --sysconfdir=/etc --datarootdir=/usr/sharecdir=/usr/share/doc/gcc4 -C --datadir=/usr/share --infodir=/usr/share/info --mandir=/usr/share/man -v --with-gmp=/usr --with-mpfr=/usr --enable-bootstrap --enable-ve-specific-runtime-libs --libexecdir=/usr/lib --enable-static --enable-shared --enable-shared-libgcc --disable-__cxa_atexit --with-gnu-ld --with-gnu-as --with-dwarf2 able-sjlj-exceptions --enable-languages=ada,c,c++,fortran,java,lto,objc,obj-c++ --enable-graphite --enable-lto --enable-java-awt=gtk --disable-symvers --enable-libjaprogram-suffix=-4 --enable-libgomp --enable-libssp --enable-libada --enable-threads=posix --with-arch=i686 --with-tune=generic --enable-libgcj-sublibs CC=gcc-4 CXX=gCC_FOR_TARGET=gcc-4 CXX_FOR_TARGET=g++-4 GNATMAKE_FOR_TARGET=gnatmake GNATBIND_FOR_TARGET=gnatbind --with-ecj-jar=/usr/share/java/ecj.jar
Thread model: posix
gcc version 4.5.3 (GCC)
/usr/bin/gcc -V 2>&1  >> bin/INSTALL_LOG/ERROR.LOG
gcc: '-V' option must have argument
Make.top:4: recipe for target `error_report' failed
make[7]: [error_report] Error 1 (ignored)
/usr/bin/gcc --version 2>&1  >> bin/INSTALL_LOG/ERROR.LOG
tar cf error_x86x87323DNow.tar Make.inc bin/INSTALL_LOG/*
bzip2 error_x86x87323DNow.tar
make[7]: Leaving directory `/cygdrive/c/cygwin/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build'
make[6]: Leaving directory `/cygdrive/c/cygwin/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build'
make[5]: Leaving directory `/home/sagetest/sage-5.9.beta0/spkg/build/atlas-3.10.1.p0/ATLAS-build/bin'
Error report error_<ARCH>.tgz has been created in your top-level ATLAS
directory.  Be sure to include this file in any help request.
cat: ../../CONFIG/error.txt: No such file or directory
cat: ../../CONFIG/error.txt: No such file or directory

Then there was some other stuff that presumably shouldn't have kept going but did, but soon after that it realized it didn't have some of the stuff and failed. I'd upload the complete log but didn't install scp before and now cygwin.com is not responding.

Last edited 6 years ago by kcrisman (previous) (diff)

comment:383 follow-up: Changed 6 years ago by kcrisman

On OS X 10.4 PPC with SAGE_ATLAS_ARCH=base:

Finished installing shared ATLAS library.
Copying /Users/student/Desktop/sage-5.9.beta0/spkg/build/atlas-3.10.0.p1/patche$

real    1563m59.216s
user    1156m43.959s
sys     249m26.773s
Successfully installed atlas-3.10.0.p1
Deleting temporary build directory
/Users/student/Desktop/sage-5.9.beta0/spkg/build/atlas-3.10.0.p1
Finished installing atlas-3.10.0.p1.spkg

Everything seems to be going fine thus far after that. But please don't default to Macs using this spkg nontrivially!

comment:384 Changed 6 years ago by kcrisman

I hate to point it out, but a slight rebase may end up being necessary for #14344 if it is merged soon. It's pretty trivial and fixes a potentially failing doctest, so I presume it will go in soon.

Changed 6 years ago by kini

apply to $SAGE_ROOT/devel/sage

comment:385 Changed 6 years ago by kini

  • Dependencies changed from #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415 to #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415, #14344
  • Description modified (diff)

Rebased.

comment:386 in reply to: ↑ 383 ; follow-up: Changed 6 years ago by jpflori

Replying to kcrisman:

On OS X 10.4 PPC with SAGE_ATLAS_ARCH=base:

Finished installing shared ATLAS library.
Copying /Users/student/Desktop/sage-5.9.beta0/spkg/build/atlas-3.10.0.p1/patche$

real    1563m59.216s
user    1156m43.959s
sys     249m26.773s
Successfully installed atlas-3.10.0.p1
Deleting temporary build directory
/Users/student/Desktop/sage-5.9.beta0/spkg/build/atlas-3.10.0.p1
Finished installing atlas-3.10.0.p1.spkg

Everything seems to be going fine thus far after that. But please don't default to Macs using this spkg nontrivially!

Could you try running "nm libatlas.dylib|grep "DecAtomic?"" on the produced shared libraries (assuming its called libatlas.dylib on OS X)?

I'll also try to build ATLAS on a more recent OS X running on Intel next week to see what happens.

comment:387 in reply to: ↑ 386 Changed 6 years ago by kcrisman

Could you try running "nm libatlas.dylib|grep "DecAtomic?"" on the produced shared libraries (assuming its called libatlas.dylib on OS X)?

I don't have to; R (and a fortiori rpy2) failed for this reason.

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/student/Desktop/sage-5.9.beta0/spkg/build/r-2.15.2.p1/src/library/grDevices/libs/grDevices.so':
  dlopen(/Users/student/Desktop/sage-5.9.beta0/spkg/build/r-2.15.2.p1/src/library/grDevices/libs/grDevices.so, 6): Symbol not found: _ATL_DecAtomicCount
  Referenced from: /Users/student/Desktop/sage-5.9.beta0/local/lib/libatlas.2.dylib
  Expected in: dynamic lookup
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
make[7]: *** [../../../library/graphics/R/graphics.rdb] Error 1
make[6]: *** [all] Error 2
make[5]: *** [R] Error 1
make[4]: *** [R] Error 1
make[3]: *** [R] Error 1
Error building R.

Matplotlib also didn't build because it couldn't find numpy, which doesn't make any sense since numpy built fine, but anyway... Then scipy failed because of this same symbol missing.

Last edited 6 years ago by kcrisman (previous) (diff)

comment:388 follow-up: Changed 6 years ago by jpflori

Could somehow make the build log of ATLAS available and link it on the ATLAS support ticket I created at https://sourceforge.net/p/math-atlas/support-requests/895/

Your problem is the same I have on sparc: the lack of assembly implem should lead to the pick up of the C implem but it does not...

comment:389 in reply to: ↑ 388 Changed 6 years ago by kcrisman

Could somehow make the build log of ATLAS available and link it on the ATLAS support ticket I created at https://sourceforge.net/p/math-atlas/support-requests/895/

Done. I should note that this shouldn't hold up this ticket.

comment:390 Changed 6 years ago by jpflori

Indeed, and nor should the similar problem on debian/sparc (I did not have problems on solaris/sparc).

So I guess the only real problems left are:

  • to include the [test -f] / [test -e] fix for Solaris (I have done it at some point but don't think I've packaged it yet, I don't really remember, but quite sure I did not uploaded it anywhere).
  • investigate the segfaults on iras (cannot do anything about that, no access to skynet and the ia64 computers I have access to are not problematic).

comment:391 in reply to: ↑ 382 Changed 6 years ago by kcrisman

Then there was some other stuff that presumably shouldn't have kept going but did, but soon after that it realized it didn't have some of the stuff and failed. I'd upload the complete log but didn't install scp before and now cygwin.com is not responding.

See here for the log. Not that I think it will be enlightening per se.

comment:392 in reply to: ↑ 378 ; follow-up: Changed 6 years ago by kcrisman

It failed in the end because of libttool

blabla libtool cannot link non-libtool object blabla on this host blabla

Yup, now I got that far - apparently whatever happened before was a blip.

So in a Sage shell just cd to the ($SAGE_ROOT/spkg/build/atlas-3.10.1.p0/)ATLAS-lib dir, open Makefile.am and just do what is done for the different lib*.la target but more or less replace @LIBTOOL@ by gcc (or gfortran if there is as well --tag=F77) for the compilation line (and don't forget lib deps -l...).

Eventually I was able to figure this out. The additional step (since I didn't have automake) was to change Makefile.in and then rerun configure with the same options as before. Oh, and apparently tabs are very necessary in make-speak, unlike Sage, and instead of $VAR you need $(VAR). Aargh.

Anyway, let's cross our fingers that this works - I'd call that enough for a positive review of whenever you put something up about it on another ticket. Yikes, you are going to turn me into someone who knows about build systems yet - that is a scary prospect.

comment:393 in reply to: ↑ 392 ; follow-up: Changed 6 years ago by kcrisman

Replying to kcrisman:

It failed in the end because of libttool

blabla libtool cannot link non-libtool object blabla on this host blabla

So in a Sage shell just cd to the ($SAGE_ROOT/spkg/build/atlas-3.10.1.p0/)ATLAS-lib dir, open Makefile.am and just do what is done for the different lib*.la target but more or less replace @LIBTOOL@ by gcc (or gfortran if there is as well --tag=F77) for the compilation line (and don't forget lib deps -l...).

Eventually I was able to figure this out. The additional step (since I didn't have automake) was to change Makefile.in and then rerun configure with the same options as before. Oh, and apparently tabs are very necessary in make-speak, unlike Sage, and instead of $VAR you need $(VAR). Aargh.

Okay, this worked. Scipy, Numpy, and R all built fine and sage -ipython importing scipy worked too. Matplotlib failed for rebasing again - this seems to be a theme - but otherwise we're okay on Cygwin with building this in that case, so hopefully we now have good information for a future ticket o make it "really" work on Cygwin. Though I still think that the default there should be to require lapack and use the fix I outlined above.

comment:394 in reply to: ↑ 393 ; follow-up: Changed 6 years ago by jpflori

Replying to kcrisman:

Eventually I was able to figure this out. The additional step (since I didn't have automake) was to change Makefile.in and then rerun configure with the same options as before. Oh, and apparently tabs are very necessary in make-speak, unlike Sage, and instead of $VAR you need $(VAR). Aargh.

Okay, this worked. Scipy, Numpy, and R all built fine and sage -ipython importing scipy worked too. Matplotlib failed for rebasing again - this seems to be a theme - but otherwise we're okay on Cygwin with building this in that case, so hopefully we now have good information for a future ticket o make it "really" work on Cygwin. Though I still think that the default there should be to require lapack and use the fix I outlined above.

If you produced a patch for the autotools build system Volker crafted, it would be very welcome, otherwise, I'll take care of it. In fact, i don't think libtool should be used, but whatever.

And yes, i think we should still default to prereqing ATLAS on Cygwin, I just forgot to add this point to the one to be dealt with before hoping for a needs_review state.

comment:395 in reply to: ↑ 394 Changed 6 years ago by kcrisman

If you produced a patch for the autotools build system Volker crafted, it would be very welcome, otherwise, I'll take care of it. In fact, i don't think libtool should be used, but whatever.

I just meant that we put a check in spkg-install for Cygwin and then copy the appropriate libraries to $SAGE_LOCAL/lib/. See comment:362. I don't have time to do that right now, though.

And yes, i think we should still default to prereqing ATLAS on Cygwin, I just forgot to add this point to the one to be dealt with before hoping for a needs_review state.

Well, Cygwin isn't supported yet, so I don't think it needs to be here for things to be positive review.

comment:396 follow-up: Changed 6 years ago by jpflori

  • Description modified (diff)

I've updated:

to include:

  • the Solaris fix,
  • copy correct libs on Cygwin,
  • hopefully better messages about setting SAGE_ATLAS_ARCH for Cygwin and Darwin.

About Cywgin libs, I don't copy the static LAPACK archive but rather the import library "/usr/lib/liblapack.dll.a" (just as we did fo the BLAS one "/usr/lib/libblas.dll.a"). This should work ok and let link to the shared LAPACK library which in my opinion (and Volker's apparently) is better. Note I've not actually tested this.

I did not:

  • test on problematic ia64 systems, the ones I have access to (gcc60 and gcc66) seem fine, waiting for report of people having access to skynet, that may be considered a blocker although ia64 is not that common anymore and not all ia64 systems seem affected...
  • craft or include a fixed shared library build system for Cygwin yet, but that should be postponed for a later ticket,
  • fix the problems with fallback code/thread related functions which prevent building on exotic systems such as linux/sparc or (old?) darwin/ppc, but we don't support them anyway.

Note that every problem we encountered here has been reported upstream.

comment:397 in reply to: ↑ 396 ; follow-up: Changed 6 years ago by jhpalmieri

Replying to jpflori:

  • test on problematic ia64 systems, the ones I have access to (gcc60 and gcc66) seem fine, waiting for report of people having access to skynet, that may be considered a blocker although ia64 is not that common anymore and not all ia64 systems seem affected...

As I said earlier, it builds on iras now, although it fails its self-tests. However, Sage's tests pass. On the systems you have access to, installing with SAGE_CHECK=yes or with sage -i -c atlas... succeeds?

comment:398 in reply to: ↑ 397 ; follow-up: Changed 6 years ago by jpflori

Replying to jhpalmieri:

Replying to jpflori:

  • test on problematic ia64 systems, the ones I have access to (gcc60 and gcc66) seem fine, waiting for report of people having access to skynet, that may be considered a blocker although ia64 is not that common anymore and not all ia64 systems seem affected...

As I said earlier, it builds on iras now, although it fails its self-tests. However, Sage's tests pass.

Oh, I overlooked the end of your comment and did not get the "make ptestlong" part.

On the systems you have access to, installing with SAGE_CHECK=yes or with sage -i -c atlas... succeeds?

I did not, but will do try it tonight. Now I got all the info you provided, I must say I fear it will not, but should it block this ticket? (Ok its bad, but...) Did the previous ATLAS 3.8.x pass its testsuite?

comment:399 in reply to: ↑ 398 Changed 6 years ago by jhpalmieri

Replying to jpflori:

Did the previous ATLAS 3.8.x pass its testsuite?

I just tried, and it passed.

comment:400 Changed 6 years ago by jpflori

Self tests indeed fails on gcc60 and gcc66 ith something like

/home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/bin/ATLrun.sh /home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/bin xcslvtst -n 167 -r 83 -O 2 c r \
                  >> /home/jpflori/sage-5.7/spkg/build/atlas-3.10.1.p0/ATLAS-build/bin/sanity.out
RHS=1, nrm=474.804962
RHS=2, nrm=428.154633
RHS=3, nrm=349.179718
RHS=4, nrm=336.438446
RHS=5, nrm=199.859177
RHS=6, nrm=219.271439
RHS=7, nrm=235.146393
RHS=8, nrm=559.355835
RHS=9, nrm=280.106232
RHS=10, nrm=527.885193
RHS=11, nrm=492.888306
RHS=12, nrm=305.108643
RHS=13, nrm=275.606659
RHS=14, nrm=129.143158
RHS=15, nrm=343.576660
...

comment:401 Changed 6 years ago by jpflori

I'm trying to build the spkg again on Solaris and I cannot get it to work with the Sun ld, getting "option -dn and -P are incompatible". No troubles (to build at least) with the GNU ld.

Did the spkg work on mark with the Sun ld? Or was it with the GNU ld?

I've tried different versions of PATH, LD and LD_ALTEXEC but could not through the configure step with Sun ld... Any idea of what could be wrong?

comment:402 Changed 6 years ago by jpflori

Maybe the GCC Sage buit is ill configured. It spits

$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/infres/post/flori/sage-5.7-infres2/local/libexec/gcc/sparc-sun-solaris2.10/4.6.3/lto-wrapper
Target: sparc-sun-solaris2.10
Configured with: ../src/configure --prefix=/infres/post/flori/sage-5.7-infres2/local --with-local-prefix=/infres/post/flori/sage-5.7-infres2/local --with-gmp=/infres/post/flori/sage-5.7-infres2/local --with-mpfr=/infres/post/flori/sage-5.7-infres2/local --with-mpc=/infres/post/flori/sage-5.7-infres2/local --with-system-zlib --disable-multilib --with-as=/usr/ccs/bin/as --with-ld=/usr/ccs/bin/ld
Thread model: posix
gcc version 4.6.3 (GCC)

It seems GCC tries to run

/infres/post/flori/sage-5.7-infres2/local/libexec/gcc/sparc-sun-solaris2.10/4.6.3/collect2  -rpath-link /usr/lib -Qy -o xconfig /infres/post/flori/sage-5.7-infres2/local/lib/gcc/sparc-sun-solaris2.10/4.6.3/crt1.o /infres/post/flori/sage-5.7-infres2/local/lib/gcc/sparc-sun-solaris2.10/4.6.3/crti.o /usr/ccs/lib/values-Xa.o /infres/post/flori/sage-5.7-infres2/local/lib/gcc/sparc-sun-solaris2.10/4.6.3/crtbegin.o -L/infres/post/flori/sage-5.7-infres2/local/lib -L/infres/post/flori/sage-5.7-infres2/local/lib/gcc/sparc-sun-solaris2.10/4.6.3 -L/usr/ccs/lib -L/infres/post/flori/sage-5.7-infres2/local/lib/gcc/sparc-sun-solaris2.10/4.6.3/../../.. config.o atlconf_misc.o -lgcc -lgcc_eh -lc -lgcc -lgcc_eh -lc /infres/post/flori/sage-5.7-infres2/local/lib/gcc/sparc-sun-solaris2.10/4.6.3/crtend.o /infres/post/flori/sage-5.7-infres2/local/lib/gcc/sparc-sun-solaris2.10/4.6.3/crtn.o

but whatever "collect2" is does not like "rpath-link"

comment:403 Changed 6 years ago by jpflori

About my GCC rant, it seems it was indeed built using a mixture of Sun/GNU tools and was kind of broken, it is now rebuilt and looks sane.

I've also reuploaded the atlas-3.10.1.p0.spkg with a minor change in spkg-install about the Cygwin packages to install (I replaced liblapack by lapack).

comment:404 follow-up: Changed 6 years ago by jpflori

  • Authors changed from Volker Braun, Jeroen Demeyer to Volker Braun, Jeroen Demeyer, Jean-Pierre Flori
  • Keywords spkg added
  • Work issues set to ia64 testsuite

And I guess we're left with one problem:

Could we put this as positive review anyway? At least Sage passes all its own testsuite. And I'm sure some other spkgs do not pass their testsuites on some platform, even not so unusual ones.

comment:405 in reply to: ↑ 404 Changed 6 years ago by jhpalmieri

Replying to jpflori:

And I guess we're left with one problem:

Could we put this as positive review anyway? At least Sage passes all its own testsuite. And I'm sure some other spkgs do not pass their testsuites on some platform, even not so unusual ones.

I would tentatively agree with this, especially since ia64 might be a bit of a fringe platform for Sage support.

comment:406 Changed 6 years ago by jpflori

  • Description modified (diff)
  • Status changed from needs_work to needs_review
  • Summary changed from Update ATLAS to stable version 3.10 to Update ATLAS to stable version 3.10.1

Upstream should look at our ia64 provided they get access to such hardware.

So I'm putting this as needs_review as:

  • the ia64 ATLAS testsuite failure does not affect Sage tests currently,
  • nobody actually uses ia64,
  • the bug should be fixed upstream quickly and we'll integrate the corresponding fix in an upgrade/patch.

comment:407 Changed 6 years ago by jpflori

On Solaris I had trouble building FFLAS-FFLAPACK because cblas needs to be built with -latlas (ok, expected) and -lrt (realtime library, providing sched_yield).

Once again not sure why the linker is so picky at link time. I had a similar issue with polybori testing for -lpng12, but that was with a seemingly ill biult GCC with GNU as and ld, and now my GCC looks saner and uses Sun ld and as.

comment:408 follow-up: Changed 6 years ago by jpflori

And FFLAS-FFLAPACK tries to detect LAPACK with the same linker flags, but needs -llapack to find it...

comment:409 in reply to: ↑ 408 Changed 6 years ago by jpflori

Replying to jpflori:

And FFLAS-FFLAPACK tries to detect LAPACK with the same linker flags, but needs -llapack to find it...

This is not Solaris specific, I've opened #14390.

comment:410 Changed 6 years ago by jpflori

I've opened #14410 for the ATLAS on Cygwin stuff.

comment:411 Changed 6 years ago by jdemeyer

OK, I plan to test this on the buildbot over the next few days.

comment:412 Changed 6 years ago by jdemeyer

  • Description modified (diff)

comment:413 Changed 6 years ago by jdemeyer

  • Description modified (diff)
  • Work issues ia64 testsuite deleted

comment:414 follow-up: Changed 6 years ago by jdemeyer

  • Description modified (diff)

spkg has uncommitted changes, fixed now.

comment:415 follow-up: Changed 6 years ago by jdemeyer

Also fixed

rc = os.system(command)
status = (rc >> 8) & 0xff    # see http://docs.python.org/library/os.html#os.wait

to

import subprocess
return subprocess.call(command, shell=True)
Version 1, edited 6 years ago by jdemeyer (previous) (next) (diff)

comment:416 in reply to: ↑ 414 ; follow-up: Changed 6 years ago by jpflori

Replying to jdemeyer:

spkg has uncommitted changes, fixed now.

Was it only the fact that solris.patch was uncommited? That seems to be the last version I crafted. Sorry about that. I've done several version of the spkg and fears something got messed up now...

comment:417 in reply to: ↑ 415 ; follow-up: Changed 6 years ago by jpflori

Replying to jdemeyer:

Also fixed

rc = os.system(command)
status = (rc >> 8) & 0x7f    # see http://docs.python.org/library/os.html#os.wait

to

import subprocess
return subprocess.call(command, shell=True)

That's on Volker's side, cannot really comment (without thinking first).

comment:418 in reply to: ↑ 416 Changed 6 years ago by jdemeyer

Replying to jpflori:

Was it only the fact that solaris.patch was uncommited?

Yes, I also renamed that patch to shell.patch since it's not really about Solaris but about non-portable shell tests.

comment:419 in reply to: ↑ 417 Changed 6 years ago by jdemeyer

There are at least two bugs in the command

status = (rc >> 8) & 0x7f    # see http://docs.python.org/library/os.html#os.wait

The first is that 0x7f should obviously be 0xff (we need the high byte and bytes are still 8 bits). The second is that the low byte is completely ignored: if the process got killed by a signal, we want to know that too.

I think subprocess.call() is a good solution since Python recommends it anyway over os.system() and there is no need to fiddle with the return code (signals are returned as negative return codes).

Changed 6 years ago by jdemeyer

comment:420 Changed 6 years ago by jdemeyer

  • Description modified (diff)

Rebased SAGE_ROOT patch.

comment:421 Changed 6 years ago by jdemeyer

I added all auto-generated files in patches/ATLAS-lib to .hgignore, removed empty files likes NEWS, added the foreign option to AM_INIT_AUTOMAKE and removed the redundant and deprecated AM_PROG_LIBTOOL macro. I reran autotools and rewrote the Mercurial history.

Last edited 6 years ago by jdemeyer (previous) (diff)

comment:422 Changed 6 years ago by jdemeyer

Also removed all trailing whitespace in SPKG.txt.

Changed 6 years ago by jdemeyer

comment:423 Changed 6 years ago by jdemeyer

  • Description modified (diff)

comment:424 Changed 6 years ago by jpflori

For info, I had a look and agree with Jeroen's modifications. I'm testing it right now.

comment:425 Changed 6 years ago by jpflori

Running hg status gives me

? patches/ARCHS/IA64Itan264.tar.bz2
? patches/ARCHS/x86SSE264SSE2.tar.bz2
? patches/ATLAS-lib/Makefile.am
? patches/ATLAS-lib/README
? patches/Makefile.patch
? patches/atlas-config
? patches/long_filenames.patch
? patches/shell.patch

comment:426 Changed 6 years ago by jdemeyer

jpflori: I indeed messed up, should be fixed now.

comment:427 follow-up: Changed 6 years ago by jpflori

FYI, I tried this on FreeBSD 9.0 x86 and it succeeds but leaves undefined ATL_*Atomic symbols inside as on Debian sparc or OS X 10.4 ppc which makes loading numpy fail. The previosu ATLAS 3.8.4 spkg is broken in a similar way, but the undefined symbols there are more worrying, its some cblas_* thing...

On a FreeBSD 8.3 amd64, the build fails quite early when a "cd" command fails. It might be a "make" issue.

comment:428 in reply to: ↑ 427 Changed 6 years ago by jpflori

Replying to jpflori:

On a FreeBSD 8.3 amd64, the build fails quite early when a "cd" command fails. It might be a "make" issue.

Indeed for some reason the GNU make was not first in my PATH anymore...

comment:429 Changed 6 years ago by jdemeyer

  • Milestone changed from sage-5.9 to sage-5.10

comment:430 Changed 6 years ago by jdemeyer

Why the change from

    cmd += ' -C if sage_fortran' 

to

    cmd += ' -C if "' + which('sage_fortran') + '"' 

Doesn't ATLAS use $PATH to execute stuff?

comment:431 Changed 6 years ago by jdemeyer

Besides, we should move away from the deprecated sage_fortran and use $FC instead.

comment:432 follow-up: Changed 6 years ago by vbraun

You should always specify full path names for stuff that you hand the atlas configuration script. Atlas does not use $PATH but will use find to locate files otherwise.

comment:433 in reply to: ↑ 432 ; follow-up: Changed 6 years ago by jdemeyer

Replying to vbraun:

Atlas does not use $PATH but will use find to locate files otherwise.

find? As in: search all files on the system? Seriously?

comment:434 Changed 6 years ago by jdemeyer

In any case, the which() function should support commands with options, like gcc -m64.

comment:435 in reply to: ↑ 433 Changed 6 years ago by jpflori

Replying to jdemeyer:

Replying to vbraun:

Atlas does not use $PATH but will use find to locate files otherwise.

find? As in: search all files on the system? Seriously?

I fear so, e.g. see https://sourceforge.net/p/math-atlas/bugs/206/.

comment:436 Changed 6 years ago by jpflori

  • Status changed from needs_review to needs_work
  • Work issues set to which compilers fc sage_fortran

Changed 6 years ago by jpflori

Use FC instead of sage_fortran and preserve compiler options.

comment:437 Changed 6 years ago by jpflori

  • Description modified (diff)
  • Status changed from needs_work to needs_review
  • Work issues which compilers fc sage_fortran deleted

I've taken Jeroen's comments into account. It's commited on top of the latest spkg he provided as a separate commit. See compilers.patch. The spkg is at:

comment:438 Changed 6 years ago by jdemeyer

Buildbot machine lena (Fedora 16 x86_64):

Finished configuring shared ATLAS library.
Running make -j1
make[3]: Entering directory `/home/buildbot/build/sage/lena-1/lena_full/build/sage-5.10.beta1/spkg/build/atlas-3.10.1.p0/ATLAS-lib'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
rm -r -f libatlas-obj
mkdir libatlas-obj
cd libatlas-obj && ar x ../libatlas.a
/bin/sh ./libtool --tag=CC --mode=link gcc -shared \
    -o libatlas.la libatlas-obj/*.o \
    -lpthread -lm \
    -rpath /home/buildbot/build/sage/lena-1/lena_full/build/sage-5.10.beta1/local/lib -version-info 3:0:1

*** Warning: Linking the shared library libatlas.la against the non-libtool
*** objects  libatlas-obj/ATL_DecAtomicCount_amd64.o libatlas-obj/ATL_DecAtomicCount_mut.o libatlas-obj/ATL_DecGlobalAtomicCount.o libatlas-obj/ATL_FreeAtomicCount_arch.o libatlas-obj/ATL_FreeAtomicCount_mut.o libatlas-obj/ATL_FreeGlobalAtomicCount.o libatlas-obj/ATL_GetAtomicCount.o libatlas-obj/ATL_GetGlobalAtomicCount.o libatlas-obj/ATL_L2AIsOverlapped.o libatlas-obj/ATL_ResetAtomicCount_amd64.o libatlas-obj/ATL_ResetAtomicCount_mut.o libatlas-obj/ATL_ResetGlobalAtomicCount.o libatlas-obj/ATL_SetAtomicCount_arch.o libatlas-obj/ATL_SetAtomicCount_mut.o libatlas-obj/ATL_SetGlobalAtomicCount.o libatlas-obj/ATL_Xtgemm.o libatlas-obj/ATL_Xtsyr2k.o libatlas-obj/ATL_Xtsyrk.o libatlas-obj/ATL_buildinfo.o libatlas-obj/ATL_cAgemmCC.o libatlas-obj/ATL_cAgemmCN.o libatlas-obj/ATL_cAgemmCT.o libatlas-obj/ATL_cAgemmNC.o libatlas-obj/ATL_cAgemmNN.o libatlas-obj/ATL_cAgemmNT.o libatlas-obj/ATL_cAgemmTC.o libatlas-obj/ATL_cAgemmTN.o libatlas-obj/ATL_cAgemmTT.o libatlas-obj/ATL_cCNBmm_b0.o 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libatlas-obj/ATL_zupKBmm2_2_1_b1.o libatlas-obj/ATL_zupKBmm2_2_1_bX.o libatlas-obj/ATL_zupKBmm30_2_1_b0.o libatlas-obj/ATL_zupKBmm30_2_1_b1.o libatlas-obj/ATL_zupKBmm30_2_1_bX.o libatlas-obj/ATL_zupKBmm31_1_1_b0.o libatlas-obj/ATL_zupKBmm31_1_1_b1.o libatlas-obj/ATL_zupKBmm31_1_1_bX.o libatlas-obj/ATL_zupKBmm32_2_1_b0.o libatlas-obj/ATL_zupKBmm32_2_1_b1.o libatlas-obj/ATL_zupKBmm32_2_1_bX.o libatlas-obj/ATL_zupKBmm33_1_1_b0.o libatlas-obj/ATL_zupKBmm33_1_1_b1.o libatlas-obj/ATL_zupKBmm33_1_1_bX.o libatlas-obj/ATL_zupKBmm34_2_1_b0.o libatlas-obj/ATL_zupKBmm34_2_1_b1.o libatlas-obj/ATL_zupKBmm34_2_1_bX.o libatlas-obj/ATL_zupKBmm35_1_1_b0.o libatlas-obj/ATL_zupKBmm35_1_1_b1.o libatlas-obj/ATL_zupKBmm35_1_1_bX.o libatlas-obj/ATL_zupKBmm36_2_1_b0.o libatlas-obj/ATL_zupKBmm36_2_1_b1.o libatlas-obj/ATL_zupKBmm36_2_1_bX.o libatlas-obj/ATL_zupKBmm37_1_1_b0.o libatlas-obj/ATL_zupKBmm37_1_1_b1.o libatlas-obj/ATL_zupKBmm37_1_1_bX.o libatlas-obj/ATL_zupKBmm38_2_1_b0.o libatlas-obj/ATL_zupKBmm38_2_1_b1.o libatlas-obj/ATL_zupKBmm38_2_1_bX.o libatlas-obj/ATL_zupKBmm39_1_1_b0.o libatlas-obj/ATL_zupKBmm39_1_1_b1.o libatlas-obj/ATL_zupKBmm39_1_1_bX.o libatlas-obj/ATL_zupKBmm3_1_1_b0.o libatlas-obj/ATL_zupKBmm3_1_1_b1.o libatlas-obj/ATL_zupKBmm3_1_1_bX.o libatlas-obj/ATL_zupKBmm4_2_1_b0.o libatlas-obj/ATL_zupKBmm4_2_1_b1.o libatlas-obj/ATL_zupKBmm4_2_1_bX.o libatlas-obj/ATL_zupKBmm5_1_1_b0.o libatlas-obj/ATL_zupKBmm5_1_1_b1.o libatlas-obj/ATL_zupKBmm5_1_1_bX.o libatlas-obj/ATL_zupKBmm6_2_1_b0.o libatlas-obj/ATL_zupKBmm6_2_1_b1.o libatlas-obj/ATL_zupKBmm6_2_1_bX.o libatlas-obj/ATL_zupKBmm7_1_1_b0.o libatlas-obj/ATL_zupKBmm7_1_1_b1.o libatlas-obj/ATL_zupKBmm7_1_1_bX.o libatlas-obj/ATL_zupKBmm8_2_1_b0.o libatlas-obj/ATL_zupKBmm8_2_1_b1.o libatlas-obj/ATL_zupKBmm8_2_1_bX.o libatlas-obj/ATL_zupKBmm9_1_1_b0.o libatlas-obj/ATL_zupKBmm9_1_1_b1.o libatlas-obj/ATL_zupKBmm9_1_1_bX.o libatlas-obj/ATL_zupKBmm_b0.o libatlas-obj/ATL_zupKBmm_b1.o libatlas-obj/ATL_zupKBmm_bX.o libatlas-obj/ATL_zupMBmm0_2_0_b0.o libatlas-obj/ATL_zupMBmm0_2_0_b1.o libatlas-obj/ATL_zupMBmm0_2_0_bX.o libatlas-obj/ATL_zupMBmm0_4_0_b0.o libatlas-obj/ATL_zupMBmm0_4_0_b1.o libatlas-obj/ATL_zupMBmm0_4_0_bX.o libatlas-obj/ATL_zupMBmm0_6_0_b0.o libatlas-obj/ATL_zupMBmm0_6_0_b1.o libatlas-obj/ATL_zupMBmm0_6_0_bX.o libatlas-obj/ATL_zupMBmm_b0.o libatlas-obj/ATL_zupMBmm_b1.o libatlas-obj/ATL_zupMBmm_bX.o libatlas-obj/ATL_zupNBmm0_1_0_b0.o libatlas-obj/ATL_zupNBmm0_1_0_b1.o libatlas-obj/ATL_zupNBmm0_1_0_bX.o libatlas-obj/ATL_zupNBmm0_2_0_b0.o libatlas-obj/ATL_zupNBmm0_2_0_b1.o libatlas-obj/ATL_zupNBmm0_2_0_bX.o libatlas-obj/ATL_zupNBmm_b0.o libatlas-obj/ATL_zupNBmm_b1.o libatlas-obj/ATL_zupNBmm_bX.o is not portable!
libtool: link: gcc -shared  -fPIC -DPIC   libatlas-obj/ATL_DecAtomicCount_amd64.o libatlas-obj/ATL_DecAtomicCount_mut.o libatlas-obj/ATL_DecGlobalAtomicCount.o libatlas-obj/ATL_FreeAtomicCount_arch.o libatlas-obj/ATL_FreeAtomicCount_mut.o libatlas-obj/ATL_FreeGlobalAtomicCount.o libatlas-obj/ATL_GetAtomicCount.o libatlas-obj/ATL_GetGlobalAtomicCount.o libatlas-obj/ATL_L2AIsOverlapped.o libatlas-obj/ATL_ResetAtomicCount_amd64.o libatlas-obj/ATL_ResetAtomicCount_mut.o libatlas-obj/ATL_ResetGlobalAtomicCount.o libatlas-obj/ATL_SetAtomicCount_arch.o libatlas-obj/ATL_SetAtomicCount_mut.o libatlas-obj/ATL_SetGlobalAtomicCount.o libatlas-obj/ATL_Xtgemm.o libatlas-obj/ATL_Xtsyr2k.o libatlas-obj/ATL_Xtsyrk.o libatlas-obj/ATL_buildinfo.o libatlas-obj/ATL_cAgemmCC.o libatlas-obj/ATL_cAgemmCN.o libatlas-obj/ATL_cAgemmCT.o libatlas-obj/ATL_cAgemmNC.o libatlas-obj/ATL_cAgemmNN.o libatlas-obj/ATL_cAgemmNT.o libatlas-obj/ATL_cAgemmTC.o libatlas-obj/ATL_cAgemmTN.o libatlas-obj/ATL_cAgemmTT.o libatlas-obj/ATL_cCNBmm_b0.o libatlas-obj/ATL_cCNBmm_b1.o libatlas-obj/ATL_cCNBmm_bX.o libatlas-obj/ATL_cCtrsmKL.o libatlas-obj/ATL_cCtrsmKR.o libatlas-obj/ATL_cGetNB.o libatlas-obj/ATL_cGetNCNB.o libatlas-obj/ATL_cIBJBmm.o libatlas-obj/ATL_cIBNBmm.o libatlas-obj/ATL_cMBJBmm.o libatlas-obj/ATL_cNBmm_b0.o libatlas-obj/ATL_cNBmm_b1.o libatlas-obj/ATL_cNBmm_bX.o libatlas-obj/ATL_cNCCUmmNN.o libatlas-obj/ATL_cNCCUmmNN_K.o libatlas-obj/ATL_cNCCUmmNT.o libatlas-obj/ATL_cNCCUmmNT_K.o libatlas-obj/ATL_cNCCUmmTN.o libatlas-obj/ATL_cNCCUmmTN_K.o libatlas-obj/ATL_cNCCUmmTT.o libatlas-obj/ATL_cNCCUmmTT_K.o libatlas-obj/ATL_cNCmmIJK.o libatlas-obj/ATL_cNCmmIJK_c.o libatlas-obj/ATL_cNCmmJIK.o libatlas-obj/ATL_cNCmmJIK_c.o libatlas-obj/ATL_cNCmmNN_a1_b0.o libatlas-obj/ATL_cNCmmNN_a1_b1.o libatlas-obj/ATL_cNCmmNN_a1_bX.o libatlas-obj/ATL_cNCmmNN_aX_b0.o libatlas-obj/ATL_cNCmmNN_aX_b1.o libatlas-obj/ATL_cNCmmNN_aX_bX.o libatlas-obj/ATL_cNCmmNT_a1_b0.o libatlas-obj/ATL_cNCmmNT_a1_b1.o libatlas-obj/ATL_cNCmmNT_a1_bX.o libatlas-obj/ATL_cNCmmNT_aX_b0.o libatlas-obj/ATL_cNCmmNT_aX_b1.o libatlas-obj/ATL_cNCmmNT_aX_bX.o libatlas-obj/ATL_cNCmmTN_a1_b0.o libatlas-obj/ATL_cNCmmTN_a1_b1.o libatlas-obj/ATL_cNCmmTN_a1_bX.o libatlas-obj/ATL_cNCmmTN_aX_b0.o libatlas-obj/ATL_cNCmmTN_aX_b1.o libatlas-obj/ATL_cNCmmTN_aX_bX.o libatlas-obj/ATL_cNCmmTT_a1_b0.o libatlas-obj/ATL_cNCmmTT_a1_b1.o libatlas-obj/ATL_cNCmmTT_a1_bX.o libatlas-obj/ATL_cNCmmTT_aX_b0.o libatlas-obj/ATL_cNCmmTT_aX_b1.o libatlas-obj/ATL_cNCmmTT_aX_bX.o libatlas-obj/ATL_caliased_gemm.o libatlas-obj/ATL_casum.o libatlas-obj/ATL_casum_xp0yp0aXbX.o libatlas-obj/ATL_caxpby.o libatlas-obj/ATL_caxpbyConj.o libatlas-obj/ATL_caxpbyConj_a0_b0.o libatlas-obj/ATL_caxpbyConj_a0_b1.o libatlas-obj/ATL_caxpbyConj_a0_bX.o libatlas-obj/ATL_caxpbyConj_a0_bXi0.o libatlas-obj/ATL_caxpbyConj_a1_b0.o libatlas-obj/ATL_caxpbyConj_a1_b1.o libatlas-obj/ATL_caxpbyConj_a1_bX.o libatlas-obj/ATL_caxpbyConj_a1_bXi0.o libatlas-obj/ATL_caxpbyConj_aX_b0.o libatlas-obj/ATL_caxpbyConj_aX_b1.o libatlas-obj/ATL_caxpbyConj_aX_bX.o libatlas-obj/ATL_caxpbyConj_aX_bXi0.o libatlas-obj/ATL_caxpbyConj_aXi0_b0.o libatlas-obj/ATL_caxpbyConj_aXi0_b1.o libatlas-obj/ATL_caxpbyConj_aXi0_bX.o libatlas-obj/ATL_caxpbyConj_aXi0_bXi0.o libatlas-obj/ATL_caxpby_a0_b0.o libatlas-obj/ATL_caxpby_a0_b1.o libatlas-obj/ATL_caxpby_a0_bX.o libatlas-obj/ATL_caxpby_a0_bXi0.o libatlas-obj/ATL_caxpby_a1_b0.o libatlas-obj/ATL_caxpby_a1_b1.o libatlas-obj/ATL_caxpby_a1_bX.o libatlas-obj/ATL_caxpby_a1_bXi0.o libatlas-obj/ATL_caxpby_aX_b0.o libatlas-obj/ATL_caxpby_aX_b1.o libatlas-obj/ATL_caxpby_aX_bX.o libatlas-obj/ATL_caxpby_aX_bXi0.o libatlas-obj/ATL_caxpby_aXi0_b0.o libatlas-obj/ATL_caxpby_aXi0_b1.o libatlas-obj/ATL_caxpby_aXi0_bX.o libatlas-obj/ATL_caxpby_aXi0_bXi0.o libatlas-obj/ATL_caxpby_xp0yp0aXbX.o libatlas-obj/ATL_caxpy.o libatlas-obj/ATL_caxpyConj.o libatlas-obj/ATL_caxpyConj_x1_y1.o libatlas-obj/ATL_caxpy_xp0yp0aXbX.o libatlas-obj/ATL_caxpy_xp1yp1aXbX.o libatlas-obj/ATL_ccol2blkConj_a1.o libatlas-obj/ATL_ccol2blkConj_aX.o libatlas-obj/ATL_ccol2blkConj_aXi0.o libatlas-obj/ATL_ccol2blk_a1.o libatlas-obj/ATL_ccol2blk_aX.o libatlas-obj/ATL_ccol2blk_aXi0.o libatlas-obj/ATL_ccopy.o libatlas-obj/ATL_ccopyConj.o libatlas-obj/ATL_ccopy_xp0yp0aXbX.o libatlas-obj/ATL_ccplxdivide.o libatlas-obj/ATL_ccplxinvert.o libatlas-obj/ATL_ccpsc.o libatlas-obj/ATL_ccpsc_xp0yp0aXbX.o libatlas-obj/ATL_cctrsmKL_rk2.o libatlas-obj/ATL_cctrsmKR_rk2.o libatlas-obj/ATL_cdot.o libatlas-obj/ATL_cdot_xp0yp0aXbX.o libatlas-obj/ATL_cdot_xp1yp1aXbX.o libatlas-obj/ATL_cdotc.o libatlas-obj/ATL_cdotc_xp0yp0aXbX.o libatlas-obj/ATL_cdotc_xp1yp1aXbX.o libatlas-obj/ATL_cgbmv.o libatlas-obj/ATL_cgeApBc_NB.o libatlas-obj/ATL_cgeApBt_NB.o libatlas-obj/ATL_cgeadd.o libatlas-obj/ATL_cgeadd_a0_b0.o libatlas-obj/ATL_cgeadd_a0_b1.o libatlas-obj/ATL_cgeadd_a0_bX.o libatlas-obj/ATL_cgeadd_a0_bXi0.o libatlas-obj/ATL_cgeadd_a1_b0.o libatlas-obj/ATL_cgeadd_a1_b1.o libatlas-obj/ATL_cgeadd_a1_bX.o libatlas-obj/ATL_cgeadd_a1_bXi0.o libatlas-obj/ATL_cgeadd_aX_b0.o libatlas-obj/ATL_cgeadd_aX_b1.o libatlas-obj/ATL_cgeadd_aX_bX.o libatlas-obj/ATL_cgeadd_aX_bXi0.o libatlas-obj/ATL_cgeadd_aXi0_b0.o libatlas-obj/ATL_cgeadd_aXi0_b1.o libatlas-obj/ATL_cgeadd_aXi0_bX.o libatlas-obj/ATL_cgeadd_aXi0_bXi0.o libatlas-obj/ATL_cgecollapse.o libatlas-obj/ATL_cgecopy.o libatlas-obj/ATL_cgemaxnrm.o libatlas-obj/ATL_cgemm.o libatlas-obj/ATL_cgemmCC.o libatlas-obj/ATL_cgemmCN.o libatlas-obj/ATL_cgemmCT.o libatlas-obj/ATL_cgemmNC.o libatlas-obj/ATL_cgemmNN.o libatlas-obj/ATL_cgemmNT.o libatlas-obj/ATL_cgemmRB.o libatlas-obj/ATL_cgemmTC.o libatlas-obj/ATL_cgemmTN.o libatlas-obj/ATL_cgemmTT.o libatlas-obj/ATL_cgemove.o libatlas-obj/ATL_cgemoveC.o libatlas-obj/ATL_cgemoveT.o libatlas-obj/ATL_cgemove_a0.o libatlas-obj/ATL_cgemove_a1.o libatlas-obj/ATL_cgemove_aX.o libatlas-obj/ATL_cgemove_aXi0.o libatlas-obj/ATL_cgemv.o libatlas-obj/ATL_cgemvCN.o libatlas-obj/ATL_cgemvCN_L1.o libatlas-obj/ATL_cgemvCN_L2.o libatlas-obj/ATL_cgemvCT.o libatlas-obj/ATL_cgemvCT_L1.o libatlas-obj/ATL_cgemvCT_L2.o libatlas-obj/ATL_cgemvN.o libatlas-obj/ATL_cgemvN_L1.o libatlas-obj/ATL_cgemvN_L2.o libatlas-obj/ATL_cgemvT.o libatlas-obj/ATL_cgemvT_L1.o libatlas-obj/ATL_cgemvT_L2.o libatlas-obj/ATL_cger2c.o libatlas-obj/ATL_cger2c_L1.o libatlas-obj/ATL_cger2c_L2.o libatlas-obj/ATL_cger2c_OOC.o libatlas-obj/ATL_cger2ck_Mlt16.o libatlas-obj/ATL_cger2ck_Nlt8.o libatlas-obj/ATL_cger2k_Mlt16.o libatlas-obj/ATL_cger2k_Nlt8.o libatlas-obj/ATL_cger2k__900002.o libatlas-obj/ATL_cger2k__900003.o libatlas-obj/ATL_cger2u.o libatlas-obj/ATL_cger2u_L1.o libatlas-obj/ATL_cger2u_L2.o libatlas-obj/ATL_cger2u_OOC.o libatlas-obj/ATL_cgerc.o libatlas-obj/ATL_cgerc_L1.o libatlas-obj/ATL_cgerc_L2.o libatlas-obj/ATL_cgerc_OOC.o libatlas-obj/ATL_cgerck_Mlt16.o libatlas-obj/ATL_cgerck_axpy.o libatlas-obj/ATL_cgereal2cplx.o 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libatlas-obj/ATL_ztrmmRLTU.o libatlas-obj/ATL_ztrmmRUCN.o libatlas-obj/ATL_ztrmmRUCU.o libatlas-obj/ATL_ztrmmRUNN.o libatlas-obj/ATL_ztrmmRUNU.o libatlas-obj/ATL_ztrmmRUTN.o libatlas-obj/ATL_ztrmmRUTU.o libatlas-obj/ATL_ztrmv.o libatlas-obj/ATL_ztrmv_scalLNN_aX.o libatlas-obj/ATL_ztrmv_scalLNU_an1.o libatlas-obj/ATL_ztrmv_scalUNN_aX.o libatlas-obj/ATL_ztrmv_scalUNU_an1.o libatlas-obj/ATL_ztrputL_b0.o libatlas-obj/ATL_ztrputL_b1.o libatlas-obj/ATL_ztrputL_bX.o libatlas-obj/ATL_ztrputL_bXi0.o libatlas-obj/ATL_ztrputL_bn1.o libatlas-obj/ATL_ztrputU_b0.o libatlas-obj/ATL_ztrputU_b1.o libatlas-obj/ATL_ztrputU_bX.o libatlas-obj/ATL_ztrputU_bXi0.o libatlas-obj/ATL_ztrputU_bn1.o libatlas-obj/ATL_ztrscal.o libatlas-obj/ATL_ztrsetL.o libatlas-obj/ATL_ztrsetU.o libatlas-obj/ATL_ztrsm.o libatlas-obj/ATL_ztrsmLLCN.o libatlas-obj/ATL_ztrsmLLCU.o libatlas-obj/ATL_ztrsmLLNN.o libatlas-obj/ATL_ztrsmLLNU.o libatlas-obj/ATL_ztrsmLLTN.o libatlas-obj/ATL_ztrsmLLTU.o libatlas-obj/ATL_ztrsmLUCN.o libatlas-obj/ATL_ztrsmLUCU.o libatlas-obj/ATL_ztrsmLUNN.o libatlas-obj/ATL_ztrsmLUNU.o libatlas-obj/ATL_ztrsmLUTN.o libatlas-obj/ATL_ztrsmLUTU.o libatlas-obj/ATL_ztrsmRLCN.o libatlas-obj/ATL_ztrsmRLCU.o libatlas-obj/ATL_ztrsmRLNN.o libatlas-obj/ATL_ztrsmRLNU.o libatlas-obj/ATL_ztrsmRLTN.o libatlas-obj/ATL_ztrsmRLTU.o libatlas-obj/ATL_ztrsmRUCN.o libatlas-obj/ATL_ztrsmRUCU.o libatlas-obj/ATL_ztrsmRUNN.o libatlas-obj/ATL_ztrsmRUNU.o libatlas-obj/ATL_ztrsmRUTN.o libatlas-obj/ATL_ztrsmRUTU.o libatlas-obj/ATL_ztrsv.o libatlas-obj/ATL_ztsymm.o libatlas-obj/ATL_ztsyr2k.o libatlas-obj/ATL_ztsyrk.o libatlas-obj/ATL_zttrmm.o libatlas-obj/ATL_zttrsm.o libatlas-obj/ATL_zupKBmm10_2_1_b0.o libatlas-obj/ATL_zupKBmm10_2_1_b1.o libatlas-obj/ATL_zupKBmm10_2_1_bX.o libatlas-obj/ATL_zupKBmm11_1_1_b0.o libatlas-obj/ATL_zupKBmm11_1_1_b1.o libatlas-obj/ATL_zupKBmm11_1_1_bX.o libatlas-obj/ATL_zupKBmm12_2_1_b0.o libatlas-obj/ATL_zupKBmm12_2_1_b1.o libatlas-obj/ATL_zupKBmm12_2_1_bX.o libatlas-obj/ATL_zupKBmm13_1_1_b0.o libatlas-obj/ATL_zupKBmm13_1_1_b1.o libatlas-obj/ATL_zupKBmm13_1_1_bX.o libatlas-obj/ATL_zupKBmm14_2_1_b0.o libatlas-obj/ATL_zupKBmm14_2_1_b1.o libatlas-obj/ATL_zupKBmm14_2_1_bX.o libatlas-obj/ATL_zupKBmm15_1_1_b0.o libatlas-obj/ATL_zupKBmm15_1_1_b1.o libatlas-obj/ATL_zupKBmm15_1_1_bX.o libatlas-obj/ATL_zupKBmm16_2_1_b0.o libatlas-obj/ATL_zupKBmm16_2_1_b1.o libatlas-obj/ATL_zupKBmm16_2_1_bX.o libatlas-obj/ATL_zupKBmm17_1_1_b0.o libatlas-obj/ATL_zupKBmm17_1_1_b1.o libatlas-obj/ATL_zupKBmm17_1_1_bX.o libatlas-obj/ATL_zupKBmm18_2_1_b0.o libatlas-obj/ATL_zupKBmm18_2_1_b1.o libatlas-obj/ATL_zupKBmm18_2_1_bX.o libatlas-obj/ATL_zupKBmm19_1_1_b0.o libatlas-obj/ATL_zupKBmm19_1_1_b1.o libatlas-obj/ATL_zupKBmm19_1_1_bX.o libatlas-obj/ATL_zupKBmm1_1_1_b0.o libatlas-obj/ATL_zupKBmm1_1_1_b1.o libatlas-obj/ATL_zupKBmm1_1_1_bX.o libatlas-obj/ATL_zupKBmm20_2_1_b0.o libatlas-obj/ATL_zupKBmm20_2_1_b1.o libatlas-obj/ATL_zupKBmm20_2_1_bX.o libatlas-obj/ATL_zupKBmm21_1_1_b0.o libatlas-obj/ATL_zupKBmm21_1_1_b1.o libatlas-obj/ATL_zupKBmm21_1_1_bX.o libatlas-obj/ATL_zupKBmm22_2_1_b0.o libatlas-obj/ATL_zupKBmm22_2_1_b1.o libatlas-obj/ATL_zupKBmm22_2_1_bX.o libatlas-obj/ATL_zupKBmm23_1_1_b0.o libatlas-obj/ATL_zupKBmm23_1_1_b1.o libatlas-obj/ATL_zupKBmm23_1_1_bX.o libatlas-obj/ATL_zupKBmm24_2_1_b0.o libatlas-obj/ATL_zupKBmm24_2_1_b1.o libatlas-obj/ATL_zupKBmm24_2_1_bX.o libatlas-obj/ATL_zupKBmm25_1_1_b0.o libatlas-obj/ATL_zupKBmm25_1_1_b1.o libatlas-obj/ATL_zupKBmm25_1_1_bX.o libatlas-obj/ATL_zupKBmm26_2_1_b0.o libatlas-obj/ATL_zupKBmm26_2_1_b1.o libatlas-obj/ATL_zupKBmm26_2_1_bX.o libatlas-obj/ATL_zupKBmm27_1_1_b0.o libatlas-obj/ATL_zupKBmm27_1_1_b1.o libatlas-obj/ATL_zupKBmm27_1_1_bX.o libatlas-obj/ATL_zupKBmm28_2_1_b0.o libatlas-obj/ATL_zupKBmm28_2_1_b1.o libatlas-obj/ATL_zupKBmm28_2_1_bX.o libatlas-obj/ATL_zupKBmm29_1_1_b0.o libatlas-obj/ATL_zupKBmm29_1_1_b1.o libatlas-obj/ATL_zupKBmm29_1_1_bX.o libatlas-obj/ATL_zupKBmm2_2_1_b0.o libatlas-obj/ATL_zupKBmm2_2_1_b1.o libatlas-obj/ATL_zupKBmm2_2_1_bX.o libatlas-obj/ATL_zupKBmm30_2_1_b0.o libatlas-obj/ATL_zupKBmm30_2_1_b1.o libatlas-obj/ATL_zupKBmm30_2_1_bX.o libatlas-obj/ATL_zupKBmm31_1_1_b0.o libatlas-obj/ATL_zupKBmm31_1_1_b1.o libatlas-obj/ATL_zupKBmm31_1_1_bX.o libatlas-obj/ATL_zupKBmm32_2_1_b0.o libatlas-obj/ATL_zupKBmm32_2_1_b1.o libatlas-obj/ATL_zupKBmm32_2_1_bX.o libatlas-obj/ATL_zupKBmm33_1_1_b0.o libatlas-obj/ATL_zupKBmm33_1_1_b1.o libatlas-obj/ATL_zupKBmm33_1_1_bX.o libatlas-obj/ATL_zupKBmm34_2_1_b0.o libatlas-obj/ATL_zupKBmm34_2_1_b1.o libatlas-obj/ATL_zupKBmm34_2_1_bX.o libatlas-obj/ATL_zupKBmm35_1_1_b0.o libatlas-obj/ATL_zupKBmm35_1_1_b1.o libatlas-obj/ATL_zupKBmm35_1_1_bX.o libatlas-obj/ATL_zupKBmm36_2_1_b0.o libatlas-obj/ATL_zupKBmm36_2_1_b1.o libatlas-obj/ATL_zupKBmm36_2_1_bX.o libatlas-obj/ATL_zupKBmm37_1_1_b0.o libatlas-obj/ATL_zupKBmm37_1_1_b1.o libatlas-obj/ATL_zupKBmm37_1_1_bX.o libatlas-obj/ATL_zupKBmm38_2_1_b0.o libatlas-obj/ATL_zupKBmm38_2_1_b1.o libatlas-obj/ATL_zupKBmm38_2_1_bX.o libatlas-obj/ATL_zupKBmm39_1_1_b0.o libatlas-obj/ATL_zupKBmm39_1_1_b1.o libatlas-obj/ATL_zupKBmm39_1_1_bX.o libatlas-obj/ATL_zupKBmm3_1_1_b0.o libatlas-obj/ATL_zupKBmm3_1_1_b1.o libatlas-obj/ATL_zupKBmm3_1_1_bX.o libatlas-obj/ATL_zupKBmm4_2_1_b0.o libatlas-obj/ATL_zupKBmm4_2_1_b1.o libatlas-obj/ATL_zupKBmm4_2_1_bX.o libatlas-obj/ATL_zupKBmm5_1_1_b0.o libatlas-obj/ATL_zupKBmm5_1_1_b1.o libatlas-obj/ATL_zupKBmm5_1_1_bX.o libatlas-obj/ATL_zupKBmm6_2_1_b0.o libatlas-obj/ATL_zupKBmm6_2_1_b1.o libatlas-obj/ATL_zupKBmm6_2_1_bX.o libatlas-obj/ATL_zupKBmm7_1_1_b0.o libatlas-obj/ATL_zupKBmm7_1_1_b1.o libatlas-obj/ATL_zupKBmm7_1_1_bX.o libatlas-obj/ATL_zupKBmm8_2_1_b0.o libatlas-obj/ATL_zupKBmm8_2_1_b1.o libatlas-obj/ATL_zupKBmm8_2_1_bX.o libatlas-obj/ATL_zupKBmm9_1_1_b0.o libatlas-obj/ATL_zupKBmm9_1_1_b1.o libatlas-obj/ATL_zupKBmm9_1_1_bX.o libatlas-obj/ATL_zupKBmm_b0.o libatlas-obj/ATL_zupKBmm_b1.o libatlas-obj/ATL_zupKBmm_bX.o libatlas-obj/ATL_zupMBmm0_2_0_b0.o libatlas-obj/ATL_zupMBmm0_2_0_b1.o libatlas-obj/ATL_zupMBmm0_2_0_bX.o libatlas-obj/ATL_zupMBmm0_4_0_b0.o libatlas-obj/ATL_zupMBmm0_4_0_b1.o libatlas-obj/ATL_zupMBmm0_4_0_bX.o libatlas-obj/ATL_zupMBmm0_6_0_b0.o libatlas-obj/ATL_zupMBmm0_6_0_b1.o libatlas-obj/ATL_zupMBmm0_6_0_bX.o libatlas-obj/ATL_zupMBmm_b0.o libatlas-obj/ATL_zupMBmm_b1.o libatlas-obj/ATL_zupMBmm_bX.o libatlas-obj/ATL_zupNBmm0_1_0_b0.o libatlas-obj/ATL_zupNBmm0_1_0_b1.o libatlas-obj/ATL_zupNBmm0_1_0_bX.o libatlas-obj/ATL_zupNBmm0_2_0_b0.o libatlas-obj/ATL_zupNBmm0_2_0_b1.o libatlas-obj/ATL_zupNBmm0_2_0_bX.o libatlas-obj/ATL_zupNBmm_b0.o libatlas-obj/ATL_zupNBmm_b1.o libatlas-obj/ATL_zupNBmm_bX.o   -lpthread -lm    -Wl,-soname -Wl,libatlas.so.2 -o .libs/libatlas.so.2.1.0
libatlas-obj/ATL_DecAtomicCount_mut.o: In function `ATL_DecAtomicCount':
ATL_DecAtomicCount_mut.c:(.text+0x0): multiple definition of `ATL_DecAtomicCount'
libatlas-obj/ATL_DecAtomicCount_amd64.o:(.text+0x0): first defined here
libatlas-obj/ATL_FreeAtomicCount_mut.o: In function `ATL_FreeAtomicCount':
ATL_FreeAtomicCount_mut.c:(.text+0x0): multiple definition of `ATL_FreeAtomicCount'
libatlas-obj/ATL_FreeAtomicCount_arch.o:ATL_FreeAtomicCount_arch.c:(.text+0x0): first defined here
libatlas-obj/ATL_ResetAtomicCount_mut.o: In function `ATL_ResetAtomicCount':
ATL_ResetAtomicCount_mut.c:(.text+0x0): multiple definition of `ATL_ResetAtomicCount'
libatlas-obj/ATL_ResetAtomicCount_amd64.o:(.text+0x0): first defined here
libatlas-obj/ATL_SetAtomicCount_mut.o: In function `ATL_SetAtomicCount':
ATL_SetAtomicCount_mut.c:(.text+0x0): multiple definition of `ATL_SetAtomicCount'
libatlas-obj/ATL_SetAtomicCount_arch.o:ATL_SetAtomicCount_arch.c:(.text+0x0): first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [libatlas.la] Error 1
make[3]: Target `all' not remade because of errors.
make[3]: Leaving directory `/home/buildbot/build/sage/lena-1/lena_full/build/sage-5.10.beta1/spkg/build/atlas-3.10.1.p0/ATLAS-lib'
Failed to build serial+parallel shared libraries, possibly because your
system does not support both. Trying to build serial libraries only.

Full log here

comment:439 Changed 6 years ago by jdemeyer

The build failure on lena went away after a rebuild.

comment:440 Changed 6 years ago by jdemeyer

  • Status changed from needs_review to needs_work
  • Work issues set to linker errors

New build on lena, again the same failure...

comment:442 Changed 6 years ago by jdemeyer

  • Dependencies changed from #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415, #14344 to #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415, #14344, #14465
  • Work issues changed from linker errors to linker errors, rebase

Documentation needs to be rebased to #14465.

Changed 6 years ago by jpflori

comment:443 Changed 6 years ago by jpflori

  • Description modified (diff)
  • Work issues changed from linker errors, rebase to linker errors

It seems somehow your last failures are caused by the fact that ATLAS finds out the generic implementation of thread related functions is as fast as the assembly one (whence the random failures I guess), and in the end both implementaitons end up in the archive, and wen Volker's code tries to make a shared library of this archive, it fails... I'll investigate more on that later, as 'm not sure upstream which does not really use shared libraries will care.

comment:444 Changed 6 years ago by jdemeyer

compilers.patch looks good.

I guess the only remaining problem now is the intermittent linker failure.

comment:445 follow-up: Changed 6 years ago by jpflori

I got why this is failing: basically it seems that atlas builds the thread stuff using an assembly version and a mutex version suffixed with _mut, put everything in the static libatlas.a, and then tests if the assembly version is actually faster. Usually it is and every thing is fine, but if not, then it rebuilds the mutex versions without the mut suffix and adds it to the static libatlas.a. So when we turn it into a shared library the linker fails because these symbols are available in two different objects we extracted from the static archive.

Now the solution is to modify ATLAS build system which is non-trivial without upstream support but might be feasible, I'll have a look. At first I wonder why the static archive produced for tuning is just modified (running "ar r") in the "build" phase, and not wiped out and then rebuilt from scratch.

comment:446 in reply to: ↑ 445 ; follow-up: Changed 6 years ago by leif

Replying to jpflori:

I got why this is failing: basically it seems that atlas builds the thread stuff using an assembly version and a mutex version suffixed with _mut, put everything in the static libatlas.a, and then tests if the assembly version is actually faster. Usually it is and every thing is fine, but if not, then it rebuilds the mutex versions without the mut suffix and adds it to the static libatlas.a. So when we turn it into a shared library the linker fails because these symbols are available in two different objects we extracted from the static archive.

Now the solution is to modify ATLAS build system which is non-trivial without upstream support but might be feasible, I'll have a look.

Or just build the shared library from the static one properly ;-), i.e., don't add both (or three?) "versions" of object files to the shared library if they define the same function(s)...


At first I wonder why the static archive produced for tuning is just modified (running "ar r") in the "build" phase, and not wiped out and then rebuilt from scratch.

Presumably because that's faster. (There are 3200+ object files in the archive.)

comment:447 follow-up: Changed 6 years ago by Snark

I find the idea of modifying ATLAS build system just for sage worrying: we'll end up once again with basically an incompatible fork of upstream... and headaches for packagers.

Please report and fix upstream problems upstream!

comment:448 follow-up: Changed 6 years ago by vbraun

How about we just delete the *_mut.o object files when building the shared library? This means some performance loss on ancient/barely supported architectures, but who cares?

comment:449 in reply to: ↑ 447 Changed 6 years ago by jpflori

Replying to Snark:

I find the idea of modifying ATLAS build system just for sage worrying: we'll end up once again with basically an incompatible fork of upstream... and headaches for packagers.

Please report and fix upstream problems upstream!

Its been reported upstream (at least variations of these thread related problems) for a couple of months now, but not so much reaction there: https://sourceforge.net/p/math-atlas/support-requests/895/. So my plan is patching here and then propose the patch upstream. We won't keep a broken lib or prevent integrating a newer version of a lib in Sage because upstream is not reacting or dead, that would be stupid.

comment:450 in reply to: ↑ 448 Changed 6 years ago by jpflori

Replying to vbraun:

How about we just delete the *_mut.o object files when building the shared library? This means some performance loss on ancient/barely supported architectures, but who cares?

That would be an easy solution. Anyway, as I'm now trying to understand ATLAS magical build system, I'll try to solve the other thread related problems as well (not hitting Sage at the moment, but if we plan on supporting FreeBSD that will be a problem, or debian/sparc).

Also note that taurus and lena do not look that obsolete and exotic.

comment:451 in reply to: ↑ 446 ; follow-up: Changed 6 years ago by jpflori

Replying to leif:

Replying to jpflori:

I got why this is failing: basically it seems that atlas builds the thread stuff using an assembly version and a mutex version suffixed with _mut, put everything in the static libatlas.a, and then tests if the assembly version is actually faster. Usually it is and every thing is fine, but if not, then it rebuilds the mutex versions without the mut suffix and adds it to the static libatlas.a. So when we turn it into a shared library the linker fails because these symbols are available in two different objects we extracted from the static archive.

Now the solution is to modify ATLAS build system which is non-trivial without upstream support but might be feasible, I'll have a look.

Or just build the shared library from the static one properly ;-), i.e., don't add both (or three?) "versions" of object files to the shared library if they define the same function(s)...

I don't see a really easy way to do that in full generality. I don't even know what will happen (of course I know what should happen) when linking to the static library, which object file will be picked up to resolve the function call? Volker's solution is not the right way to go but at least it will easily workaround the problem.


At first I wonder why the static archive produced for tuning is just modified (running "ar r") in the "build" phase, and not wiped out and then rebuilt from scratch.

Presumably because that's faster. (There are 3200+ object files in the archive.)

Good point.

comment:452 Changed 6 years ago by jpflori

Note than when I meant from scratch, I did not mean rebuild every object files, but only repacking them into a static archive.

comment:453 in reply to: ↑ 451 ; follow-up: Changed 6 years ago by leif

Replying to jpflori:

Replying to leif:

Or just build the shared library from the static one properly ;-), i.e., don't add both (or three?) "versions" of object files to the shared library if they define the same function(s)...

I don't see a really easy way to do that in full generality.

Well, if you don't want to mess with nm, you could just try to build some dummy program using ATL_<foo>AtomicCount() with *_mut.o to figure out whether the latter defines the function, just like autotools usually do. (And for each of those four modules, remove/don't include the object file with the alternate implementation in case the corresponding *_mut.o supplies one [with the same name].)

comment:454 Changed 6 years ago by vbraun

The right solution (TM) is to abstract away the blas/cblas/lapack/clapack compiler switches in a pkgconfig-like script. Then we could just switch to the new shared libraries that ATLAS recently introduced, or OpenBLAS, or a vendor blas... But thats for another ticket. For now, I think its a waste of time to try to change the ATLAS build system.

comment:455 in reply to: ↑ 453 ; follow-up: Changed 6 years ago by leif

Replying to leif:

[...] mess with nm [...]

Something along

# Works with all nm output formats (BSD/POSIX/System V):
if [ `nm -g /path/to/libatlas.a | egrep -w 'ATL_(Set|Reset|Free|Dec)AtomicCount' | grep -w T | wc -l` -gt 4 ]; then
    # Multiple definitions, use the ones from *_mut.o
    rm `ls -1 ATL_{Set,Reset,Free,Dec}AtomicCount_*.o | grep -v '_mut.o$'`
fi

Or similarly run nm individually on the *_mut.o files, removing the corresponding other object file if appropriate (e.g. if nm -g $MUT_OBJECT | grep -w $FUNCTION >/dev/null; then rm $ALTERNATE_OBJECT; fi).

comment:456 in reply to: ↑ 455 Changed 6 years ago by leif

Replying to leif:

Replying to leif:

[...] mess with nm [...]

Something along

# Works with all nm output formats (BSD/POSIX/System V):
if [ `nm -g /path/to/libatlas.a | egrep -w 'ATL_(Set|Reset|Free|Dec)AtomicCount' | grep -w T | wc -l` -gt 4 ]; then
    # Multiple definitions, use the ones from *_mut.o
    rm `ls -1 ATL_{Set,Reset,Free,Dec}AtomicCount_*.o | grep -v '_mut.o$'`
fi

Or similarly run nm individually on the *_mut.o files, removing the corresponding other object file if appropriate (e.g. if nm -g $MUT_OBJECT | grep -w $FUNCTION >/dev/null; then rm $ALTERNATE_OBJECT; fi).

Of courseTM, on Solaris / with Sun's nm, you have to use nm -g -p ..., but you can use that with GNU nm as well (despite that to the latter, it has a different meaning! :-) )

comment:457 follow-up: Changed 6 years ago by jpflori

Yup, that was I was thinking of when saying not simple :)

Anyway, lets go with Volker's solution and indeed in the future being able to use any blas implementation would be a killer feature.

comment:458 Changed 6 years ago by jpflori

And fyi in the taurus/lena situation, ATLAS cannot build its own version of the shared libraries, for the exact same reason...

comment:459 in reply to: ↑ 457 Changed 6 years ago by leif

Replying to jpflori:

Yup, that was I was thinking of when saying not simple :)

NOT SIMPLE?!1??!11!?

It even works on MacOS X! XD

comment:460 Changed 6 years ago by jdemeyer

  • Work issues changed from linker errors to linker errors, HTTP 404

comment:461 Changed 6 years ago by jpflori

  • Description modified (diff)

Yeah I was actually modifying that but you posted and prevented my modification!

comment:462 follow-up: Changed 6 years ago by jdemeyer

  • Work issues changed from linker errors, HTTP 404 to linker errors, cvxopt SPKG.txt

In the cvxopt spkg, the order of the Changelog entries is wrong (p0 seems to come after p1).

Does it make sense to add this BLAS fix to cvxopt without upgrading ATLAS? If yes, I propose to deal with the cvxopt spkg at #12832 instead of #10508.

comment:463 in reply to: ↑ 462 Changed 6 years ago by jpflori

Replying to jdemeyer:

In the cvxopt spkg, the order of the Changelog entries is wrong (p0 seems to come after p1).

Does it make sense to add this BLAS fix to cvxopt without upgrading ATLAS? If yes, I propose to deal with the cvxopt spkg at #12832 instead of #10508.

I'd say so, so feel free to include the fix at #12832 and remove the spkg from here.

comment:464 Changed 6 years ago by jdemeyer

  • Dependencies changed from #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415, #14344, #14465 to #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415, #14344, #14465, #12832
  • Description modified (diff)

Changed 6 years ago by jpflori

Use leif's fix.

comment:465 Changed 6 years ago by jdemeyer

  • Description modified (diff)

comment:466 Changed 6 years ago by jpflori

I've updated the spkg with an autotoolized version of leif's fix (this should automatically use proper flags for nm, even on Solaris) and flattened the three last commits (update/compilers/threads). thread.patch only reflects the last new commit where I've also modified .hgignre so that configure.ac in Volker's build system is tracked.

Hopefully this will now work on all supported platforms.

comment:467 Changed 6 years ago by jpflori

  • Status changed from needs_work to needs_review

Changed 6 years ago by jdemeyer

spkg diff 3.8.4.p1 -> 3.10.1.p0, except for the removal of old patches

comment:468 Changed 6 years ago by vbraun

I'm getting

Cannot find '/home/vbraun/opt/sage-5.10.beta2/spkg/build/atlas-3.10.1.p0/lapack-3.4.2.tar'

comment:469 Changed 6 years ago by jpflori

Oops, indded, forgot to add back the lapack tarfile. Reupped a fixed spkg.

comment:470 Changed 6 years ago by jpflori

I've reported the multiple definition problem at https://sourceforge.net/p/math-atlas/support-requests/907/

comment:471 Changed 6 years ago by jdemeyer

  • Work issues linker errors, cvxopt SPKG.txt deleted

comment:472 Changed 6 years ago by vbraun

Now fails with

ATLAS install complete.  Examine 
ATLAS/bin/<arch>/INSTALL_LOG/SUMMARY.LOG for details.
make[1]: Leaving directory `/home/vbraun/opt/sage-5.10.beta2/spkg/build/atlas-3.10.1.p0/ATLAS-build'
make -j10 -j1 clean
make[1]: Entering directory `/home/vbraun/opt/sage-5.10.beta2/spkg/build/atlas-3.10.1.p0/ATLAS-build'
rm -rf *.o x* config?.out *core*
make[1]: Leaving directory `/home/vbraun/opt/sage-5.10.beta2/spkg/build/atlas-3.10.1.p0/ATLAS-build'
Finished building ATLAS core.
Running ./configure --prefix=/home/vbraun/opt/sage-5.10.beta2/local --libdir=/home/vbraun/opt/sage-5.10.beta2/local/lib --disable-static
/bin/sh: ./configure: No such file or directory
------------------------------------------------------------
  File "./spkg-install", line 544, in <module>
    good='Finished configuring shared ATLAS library.')
  File "./spkg-install", line 75, in assert_success
    traceback.print_stack(file=sys.stdout)
------------------------------------------------------------
Error:  Configuring shared ATLAS library failed.

Thats because the auto-generated files are missing from patches/ATLAS-lib

Last edited 6 years ago by vbraun (previous) (diff)

comment:473 Changed 6 years ago by jpflori

Indeed, not a good morning for packaging today. Sorry about that, updated spkg coming in a few minutes.

comment:474 follow-up: Changed 6 years ago by vbraun

I can email you a coffee if necessary ;-)

comment:475 Changed 6 years ago by jpflori

I even broke the files permission in the previous upload, not such a good idea to untar and repack on an NTFS usb key.

This time I've at least tested the uploaded spkg builds on Linux.

comment:476 in reply to: ↑ 474 Changed 6 years ago by leif

Replying to vbraun:

I can email you a coffee if necessary ;-)

If you instead attach instant coffee to the ticket, we'll all benefit from it...

Not sure whether that should later get merged into Sage as well.

comment:477 Changed 6 years ago by vbraun

  • Reviewers changed from Benjamin Jones, Karl-Dieter Crisman, Dmitrii Pasechnik, Georg Weber, François Bissey, John Palmieri to Benjamin Jones, Karl-Dieter Crisman, Dmitrii Pasechnik, Georg Weber, François Bissey, John Palmieri, Volker Braun
  • Status changed from needs_review to positive_review

Changes look good to me.

comment:478 Changed 6 years ago by jdemeyer

  • Merged in set to sage-5.10.beta4
  • Resolution set to fixed
  • Status changed from positive_review to closed

comment:479 follow-up: Changed 6 years ago by jpflori

Is this actually working on any computer with a single core cpu?

comment:480 Changed 6 years ago by jpflori

(and no hyperthreading or similar stuff)

comment:481 in reply to: ↑ 479 Changed 6 years ago by jdemeyer

Replying to jpflori:

Is this actually working on any computer with a single core cpu?

Yes (this one has hyperthreading, but it's disabled):

buildbot@cicero:~$ cat /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 15
model           : 2
model name      : Intel(R) Pentium(R) 4 CPU 2.66GHz
stepping        : 7
microcode       : 0x37
cpu MHz         : 2666.600
cache size      : 512 KB
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 2
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe up pebs bts
bogomips        : 5332.27
clflush size    : 64
cache_alignment : 128
address sizes   : 36 bits physical, 32 bits virtual
power management:

comment:482 Changed 6 years ago by jpflori

Strange (but nice anyway). Could you provide a link to the buildlog of ATLAS?

comment:484 follow-up: Changed 6 years ago by jpflori

I see, scipy was updated at some point as well. Could you try running "from numpy.linalg import lapack_lite" in a sage shell?

comment:485 in reply to: ↑ 283 ; follow-up: Changed 6 years ago by jpflori

Replying to vbraun:

The "base" and "fast" targets are my invention. Of course they are only implemented when I know a working configuration ;-)

At least the SAGE_ATLAS_ARCH=ARMv7,NEON version seems to get a little bit further. But it fails to detect the clock rate and then dies: "Clock rate configured as 0Mhz"

This is not what makes it fail, but rather the same problem as on the qemu one:

cd /home/jpuydt/sage-5.4/spkg/build/atlas-3.10.0.p1/ATLAS-build ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 46 -Si nof77 0 -V 1024  -C ic '/usr/bin/gcc' -Fa ic '-fPIC' -C sm '/usr/bin/gcc' -Fa sm '-fPIC' -C dm '/usr/bin/gcc' -Fa dm '-fPIC' -C sk '/usr/bin/gcc' -Fa sk '-fPIC' -C dk '/usr/bin/gcc' -Fa dk '-fPIC' -C xc '/usr/bin/gcc' -Fa xc '-fPIC' -C gc '/usr/bin/gcc' -Fa gc '-fPIC' -C if '/home/jpuydt/sage-5.4/local/bin/sage_fortran' -Fa if '-fPIC' -b 32 -d b /home/jpuydt/sage-5.4/spkg/build/atlas-3.10.0.p1/ATLAS-build > config1.out
/usr/bin/ld: erreur: xctest passe les paramÚtres dans un registre VFP alors que /tmp/cccugGVu.o ne le fait pas

(error message is in frecnh this time :))

comment:486 Changed 6 years ago by jpflori

Julien, could you provide the output of cat /proc/cupinfo to at least solve the 0MHz issue?

comment:487 Changed 6 years ago by vbraun

Looks like a hardfp/softfp mismatch, most likely your toolchain is busted. Which gcc and which gfortran are you using?

comment:488 in reply to: ↑ 484 Changed 6 years ago by jpflori

Replying to jpflori:

I see, scipy was updated at some point as well. Could you try running "from numpy.linalg import lapack_lite" in a sage shell?

In fact it should work because the bad thread related functions are not built at all because:

make[7]: *** [IRun_aff] Aborted (core dumped)

whereas on other CPUs it can fail in a different way (that what i had on FreeBSD with a single thread CPU) and let bad functions be built, or on a CPU with multiple threads this will succeeds and build some bad functions even if you passed "-t 0" when configuring ATLAS.

comment:489 Changed 6 years ago by jpflori

Anyway, I got it now and should even be able to build non-threaded libraries correctly. I'll put that in #14605.

comment:490 Changed 6 years ago by jdemeyer

  • Merged in sage-5.10.beta4 deleted
  • Resolution fixed deleted
  • Status changed from closed to new

On hawk (OpenSolaris i386):

sage -t --long devel/sage/sage/numerical/test.py
**********************************************************************
File "devel/sage/sage/numerical/test.py", line 27, in sage.numerical.test
Failed example:
    e,v=arpack.eigs(A,k=6,which='SM')  # long time (4s on sage.math, 2012)
Exception raised:
    Traceback (most recent call last):
      File "/export/home/buildbot/build/sage/hawk-1/hawk_suncc/build/sage-5.10.beta4/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 466, in _run
        self.execute(example, compiled, test.globs)
      File "/export/home/buildbot/build/sage/hawk-1/hawk_suncc/build/sage-5.10.beta4/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 825, in execute
        exec compiled in globs
      File "<doctest sage.numerical.test[17]>", line 1, in <module>
        e,v=arpack.eigs(A,k=Integer(6),which='SM')  # long time (4s on sage.math, 2012)
      File "/export/home/buildbot/build/sage/hawk-1/hawk_suncc/build/sage-5.10.beta4/local/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 1276, in eigs
        params.iterate()
      File "/export/home/buildbot/build/sage/hawk-1/hawk_suncc/build/sage-5.10.beta4/local/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py", line 762, in iterate
        raise ArpackError(self.info, infodict=self.iterate_infodict)
    ArpackError: ARPACK error -9999: Could not build an Arnoldi factorization. IPARAM(5) returns the size of the current Arnoldi factorization. The user is advised to check that enough workspace and array storage has been allocated.
**********************************************************************

comment:492 Changed 6 years ago by jpflori

and http://mathema.tician.de/node/373

Not sure what scipy includes.

comment:493 Changed 6 years ago by jpflori

And it seems scipy recently switched to a fixed ARPACK-NG: https://github.com/scipy/scipy/commit/475a5d46653ad95ead37ccac445ca590db692a58

So hopefully, updating scipy to 0.12 should fix this!

Last edited 6 years ago by jpflori (previous) (diff)

comment:494 Changed 6 years ago by jpflori

  • Dependencies changed from #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415, #14344, #14465, #12832 to #13160, #13395, #13392, #13416, #12994, #9906, #12883, #13123, #13415, #14344, #14465, #12832, #14617
  • Status changed from new to needs_review

Updating scipy to 0.12 is now #14617. And hopefully the seemingly related problem I linked above should be fixed by this release which replaced legacy ARPACK by Arpack-NG (which changed the problematic second funciton to arpsnd (modulo spelling errors)).

comment:495 follow-up: Changed 6 years ago by jpflori

Jeroen, did you remove the blas and lapack spkg when concepting 5.10.beta4? I seem to remember when I was looking at the single core computer log that they were still there.

comment:496 Changed 6 years ago by jpflori

  • Status changed from needs_review to positive_review

scipy update was straightforward, so this should be tested again!

comment:497 in reply to: ↑ 495 Changed 6 years ago by jdemeyer

Replying to jpflori:

Jeroen, did you remove the blas and lapack spkg when concepting 5.10.beta4?

When merging this new ATLAS spkg, yes I did.

comment:498 Changed 6 years ago by jpflori

I just realized I've been commiting stuff with a typo in my work email address on one on my computers, so I've fixed it in this spkg before it's definitely merged.

comment:499 Changed 6 years ago by jdemeyer

HTTP 404 on the spkg...

comment:500 follow-up: Changed 6 years ago by jpflori

It's there now, I was messing things up a few moments ago and you must have tried to dwonload it at that time.

comment:501 in reply to: ↑ 500 Changed 6 years ago by jdemeyer

Replying to jpflori:

you must have tried to dwonload it at that time.

It seems at good at that, see also 461 :-)

comment:502 Changed 6 years ago by jdemeyer

Please make the lapack file inside the spkg world-readable (chmod 644 lapack-3.4.2.tar).

comment:503 Changed 6 years ago by jpflori

Done.

comment:504 in reply to: ↑ 485 Changed 6 years ago by jpflori

Replying to jpflori:

Replying to vbraun:

The "base" and "fast" targets are my invention. Of course they are only implemented when I know a working configuration ;-)

At least the SAGE_ATLAS_ARCH=ARMv7,NEON version seems to get a little bit further. But it fails to detect the clock rate and then dies: "Clock rate configured as 0Mhz"

This is not what makes it fail, but rather the same problem as on the qemu one:

cd /home/jpuydt/sage-5.4/spkg/build/atlas-3.10.0.p1/ATLAS-build ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 46 -Si nof77 0 -V 1024  -C ic '/usr/bin/gcc' -Fa ic '-fPIC' -C sm '/usr/bin/gcc' -Fa sm '-fPIC' -C dm '/usr/bin/gcc' -Fa dm '-fPIC' -C sk '/usr/bin/gcc' -Fa sk '-fPIC' -C dk '/usr/bin/gcc' -Fa dk '-fPIC' -C xc '/usr/bin/gcc' -Fa xc '-fPIC' -C gc '/usr/bin/gcc' -Fa gc '-fPIC' -C if '/home/jpuydt/sage-5.4/local/bin/sage_fortran' -Fa if '-fPIC' -b 32 -d b /home/jpuydt/sage-5.4/spkg/build/atlas-3.10.0.p1/ATLAS-build > config1.out
/usr/bin/ld: erreur: xctest passe les paramÚtres dans un registre VFP alors que /tmp/cccugGVu.o ne le fait pas

(error message is in frecnh this time :))

I guess http://math-atlas.sourceforge.net/errata.html#armhardfp could help... I now have a Raspberry Pi and a Tegra3 available, so I will be able to test ATLAS on ARM now. But note I currently have no idea of this soft/hard ABI stuff.

comment:505 Changed 6 years ago by vbraun

I would prefer to wait until upstream has sorted out the hard/softfp mess instead of trying to implement the workaround in the errata in the spkg-install. You can always use the host OS atlas library...

comment:506 Changed 6 years ago by Snark

I agree the problem should be dealt with upstream: if they know how that should work, then they'll probably publish a fixed version soon, won't they?

comment:507 Changed 6 years ago by jpflori

Yeah, anyway I was absolutely not planning to deal with it in this ticket, neither #14605 nor #14410.

comment:508 Changed 6 years ago by jpflori

And there is at least one upstream ticket for the Linux/ARM issues: https://sourceforge.net/p/math-atlas/support-requests/890/

comment:510 Changed 6 years ago by jdemeyer

  • Merged in set to sage-5.10.beta5
  • Resolution set to fixed
  • Status changed from positive_review to closed

comment:511 Changed 6 years ago by leif

With SAGE_ATLAS_LIB, the messages w.r.t. symlinking are still wrong (symlink and target swapped).

comment:512 in reply to: ↑ 64 Changed 6 years ago by leif

Replying to leif:

Replying to jdemeyer:

Timing on x86_64 with SAGE_FAT_BINARY=yes on sage.math:

real    139m50.733s
user    134m30.710s
sys     7m12.390s
Successfully installed atlas-3.8.4.p1
real    350m5.662s
user    330m23.460s
sys     22m1.010s
Successfully installed atlas-3.10.0

Why does the new ATLAS take so much longer to build than the old one?

I can beat that:

Finished installing shared ATLAS library.

real	821m14.881s
user	739m58.560s
sys	58m23.440s
Successfully installed atlas-3.10.0

(That's with sage -f ... on an otherwise idle machine, an AMD Fusion E-450 running Ubuntu 10.04.4 LTS x86_64.)

Same machine, 3.10.1.p0, SAGE_ATLAS_ARCH not set (this time with GCC 4.8.0, FWIW):

real	1244m45.739s
user	998m42.830s
sys	92m27.150s
Successfully installed atlas-3.10.1.p0

So now seems to take even longer than 3.10.0 did (although the sysload was occasionally above the number of cores).

It took far more time than building all of Sage [in parallel, on that dual-core CPU], including the old ATLAS spkg. I currently have no figures for a separate ATLAS 3.8.4 build, but the timings from previous parallel Sage builds on that machine vary between

real	214m52.096s
user	175m5.390s
sys	9m56.210s
Successfully installed atlas-3.8.4.p1

and

real	256m32.949s
user	217m30.760s
sys	10m31.050s
Successfully installed atlas-3.8.4.p1

(The LAPACK and BLAS spkg build times in these builds are a few minutes and less than one minute [wall time], respectively.)

I was actually hoping ATLAS 3.9.x / 3.10 meanwhile "knows" these AMD CPUs and therefore builds at least a bit faster...

comment:513 follow-ups: Changed 6 years ago by jdemeyer

I don't like the fact that this ticket adds 17 hours to the Sage build time on the slowest buildbot machine (cicero, Linux Pentium 4).

comment:514 in reply to: ↑ 513 ; follow-up: Changed 6 years ago by leif

Replying to jdemeyer:

I don't like the fact that this ticket adds 17 hours to the Sage build time on the slowest buildbot machine (cicero, Linux Pentium 4).

Interestingly, I haven't seen (or at least noticed) such a regression on a Pentium 4 Prescott.

comment:515 in reply to: ↑ 514 Changed 6 years ago by leif

Replying to leif:

Replying to jdemeyer:

I don't like the fact that this ticket adds 17 hours to the Sage build time on the slowest buildbot machine (cicero, Linux Pentium 4).

Interestingly, I haven't seen (or at least noticed) such a regression on a Pentium 4 Prescott.

3.8.4.p1: ~22-27 min user/cpu time ([also] varying GCC versions)

3.10.1.p0: ~25 min user/cpu time (only one figure)

(2.8 GHz, single-core / w/o HT, FWIW; without setting SAGE_ATLAS_ARCH)

Last edited 6 years ago by leif (previous) (diff)

comment:516 in reply to: ↑ 513 Changed 6 years ago by jpflori

Replying to jdemeyer:

I don't like the fact that this ticket adds 17 hours to the Sage build time on the slowest buildbot machine (cicero, Linux Pentium 4).

Could you try generating archdefs for this architecture? (unless there are already some, but in that case I don't know what to do... maybe Volker can help) Then we can package them in the spkg. Instruction are here: http://math-atlas.sourceforge.net/devel/atlas_devel/node26.html Basically keep the ATLAS build dir and run make ArchNew?.

comment:517 follow-up: Changed 6 years ago by jhpalmieri

I think this causes iml to fail its self test on sage.math. Log here.

comment:518 in reply to: ↑ 517 Changed 6 years ago by leif

Replying to jhpalmieri:

I think this causes iml to fail its self test on sage.math. Log here.

This looks suspicious:

checking whether GMP is 4.0 or greater... yes
checking for ATLAS >= 3.0... configure: creating ./config.status
config.status: creating Makefile

while it should be

checking whether GMP is 4.0 or greater... yes
checking for ATLAS >= 3.0... found
configure: creating ./config.status
config.status: creating Makefile

(I always get a syntax error in configure, so it's likely there's even more broken crap in it; see #748.)

comment:519 Changed 6 years ago by leif

Hahahahaha

  • iml-1.0.1.p14/

    diff -Nau iml-1.0.1.p14/src/configure iml-1.0.1.p14/patches/configure
    old new  
    2008420084elif test -n "$atlas_problem"; then
    2008520085        echo "$as_me:$LINENO: result: problem" >&5
    2008620086echo "${ECHO_T}problem" >&6
    20087         { { echo "$as_me:$LINENO: error: ATLAS not found!
    20088 ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.
    20089 " >&5
    20090 echo "$as_me: error: ATLAS not found!
    20091 ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.
    20092 " >&2;}
    20093    { (exit 1); exit 1; }; }
    20094 elif test "x$atlas_found" = "xno" ; then
    20095         echo "$as_me:$LINENO: result: not found" >&5
    20096 echo "${ECHO_T}not found" >&6
    20097         { { echo "$as_me:$LINENO: error: ATLAS not found!
    20098 ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.
    20099 " >&5
    20100 echo "$as_me: error: ATLAS not found!
    20101 ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.
    20102 " >&2;}
    20103    { (exit 1); exit 1; }; }
     20087#       { { echo "$as_me:$LINENO: error: ATLAS not found!
     20088#ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.
     20089#" >&5
     20090#echo "$as_me: error: ATLAS not found!
     20091#ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.
     20092#" >&2;}
     20093#   { (exit 1); exit 1; }; }
     20094#elif test "x$atlas_found" = "xno" ; then
     20095#       echo "$as_me:$LINENO: result: not found" >&5
     20096#echo "${ECHO_T}not found" >&6
     20097#       { { echo "$as_me:$LINENO: error: ATLAS not found!
     20098#ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.
     20099#" >&5
     20100#echo "$as_me: error: ATLAS not found!
     20101#ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.
     20102#" >&2;}
     20103#   { (exit 1); exit 1; }; }
    2010420104fi
    2010520105
    2010620106CFLAGS=${BACKUP_CFLAGS}

comment:520 follow-up: Changed 6 years ago by jhpalmieri

config.log for iml.

comment:521 Changed 6 years ago by vbraun

Maybe open a new ticket for the iml issue?

comment:522 in reply to: ↑ 520 ; follow-up: Changed 6 years ago by leif

Replying to jhpalmieri:

config.log for iml.

Could you "unapply" our weird "patch" to IML's configure and reinstall it with SAGE_CHECK=yes?

comment:523 in reply to: ↑ 522 Changed 6 years ago by leif

Replying to leif:

Replying to jhpalmieri:

config.log for iml.

Could you "unapply" our weird "patch" to IML's configure and reinstall it with SAGE_CHECK=yes?

(... and post the config.log from that.)

comment:524 Changed 6 years ago by jpflori

I tried that and it does not give any details (except that ir says that it did not find ATLAS). Looking at configure, it searches for cblas.h that our ATLAS spkg does not install.

comment:525 Changed 6 years ago by jhpalmieri

config.log for iml with its original ./configure file (or at least with the appropriate line in spkg-install commented out). Note, by the way, that there is a "new" version of iml, 1.0.3, dating from 2008. I haven't tried using that one instead, but I don't expect it to help.

Does all of this mean that iml is completely untested in the Sage library?

comment:526 Changed 6 years ago by jpflori

Putting the header from <atlas>/src/include/cblas.h in <sage>/local/lib fixes the problem.

I guess leif was lucky because he had a system-wide cblas.h? And in previous Sage versions we must have gotten one from the reference BLAS?

And the IML install script looks quite messy...

comment:527 Changed 6 years ago by Koen

In the Atlas spkg-install script, there is a function configure_atlas_library which does not specify --incdir to the configure of Atlas. That is why the header files of Atlas are not installed in sage 5.10.rc1.

comment:528 Changed 6 years ago by fbissey

Depends what you mean by untested. There are various problems with iml. I use 1.0.3 in sage-on-gentoo but the fix we have for BLAS detection is not applicable to the sage spkg. The install script is messy because there is quite some cruft in the source and patching will require running autotools on it. IML is definitely used in the sage library and it is at least indirectly called in some doctest.

comment:529 Changed 6 years ago by jpflori

I'd also say we don't call ATLAS's Makefile install target. Volker crafted an autotools stub to pack shared libraries and we install from there.

The easiest solution is to call ATLAS Makefile install target. That will install headers (maybe requiring the incdir option) and static libraries which IMHO is a good idea.

comment:530 Changed 6 years ago by jhpalmieri

I've created #14699 to discuss this issue with iml and ATLAS. We should move the discussion there.

comment:531 follow-up: Changed 6 years ago by leif

Putting the header from <atlas>/src/include/cblas.h in <sage>/local/lib fixes the problem.

I guess leif was lucky because he had a system-wide cblas.h?

Of course I have it, as does sage.math (which I had checked, also for system-wide libs). I guess John was actually testing on boxen.math, which does not have it.


And the IML install script looks quite messy...

The whole [s]package is a mess, see #748.

comment:532 in reply to: ↑ 531 Changed 6 years ago by fbissey

Replying to leif:

Putting the header from <atlas>/src/include/cblas.h in <sage>/local/lib fixes the problem.

I guess leif was lucky because he had a system-wide cblas.h?

Of course I have it, as does sage.math (which I had checked, also for system-wide libs). I guess John was actually testing on boxen.math, which does not have it.


And the IML install script looks quite messy...

The whole [s]package is a mess, see #748.

Ticket on which I meant to work for more than a year :(

comment:533 Changed 6 years ago by Koen

jpflori, the static libraries are already installed for me (this is done through an shutil.copy in configure_atlas_library). I'm unsure if the header files should be copied in a similar way, or if giving an extra option to configure will be enough.

comment:534 Changed 6 years ago by jdemeyer

  • Merged in sage-5.10.beta5 deleted
  • Milestone changed from sage-5.10 to sage-5.11
  • Resolution fixed deleted
  • Status changed from closed to new

Reverting this ticket: #14753.

comment:535 Changed 6 years ago by jdemeyer

  • Merged in set to sage-5.10.beta5
  • Milestone changed from sage-5.11 to sage-5.10
  • Resolution set to fixed
  • Status changed from new to closed

comment:536 Changed 6 years ago by jdemeyer

Keeping "merged in" information for future reference, we should not change this ticket further.

comment:537 Changed 6 years ago by jdemeyer

Upgrading ATLAS (again) is now #14754.

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