Opened 7 years ago

Closed 20 months ago

#19719 closed defect (invalid)

Upgrade ATLAS to version 3.11.38

Reported by: jdemeyer Owned by:
Priority: major Milestone: sage-duplicate/invalid/wontfix
Component: packages: standard Keywords: BLAS, LAPACK, --with-blas
Cc: vbraun, jpflori, leif, dimpase, jhpalmieri Merged in:
Authors: Reviewers: Dima Pasechnik
Report Upstream: Reported upstream. Developers acknowledge bug. Work issues:
Branch: u/jdemeyer/upgrade_atlas (Commits, GitHub, GitLab) Commit: c19635ff199c0a7e4e4aa66c2c7c7ac1e9347884
Dependencies: Stopgaps:

Status badges

Change History (84)

comment:1 Changed 7 years ago by fbissey

You need to update to a more recent ATLAS (3.11.something), upstream worked hard to make it build on power8 relatively recently.

comment:3 Changed 7 years ago by jdemeyer

Thanks for the info, I will check it out.

So far, I managed to build all packages except ATLAS and packages depending on it.

comment:4 Changed 7 years ago by jdemeyer

  • Authors set to Jeroen Demeyer
  • Description modified (diff)

comment:5 Changed 7 years ago by jdemeyer

  • Description modified (diff)

comment:6 Changed 7 years ago by jdemeyer

  • Branch set to u/jdemeyer/upgrade_atlas

comment:7 Changed 7 years ago by jdemeyer

  • Commit set to 2b458deaf2e6f89b81b136edc3098f3de98eb57c

Can anyone get this branch working? On my Linux Core i7 system, I get

./xgmmsearch -p s -f 4
xgmmsearch: /usr/local/src/sage-config/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//tune/blas/gemm/gmmsearch.c:233: FullSrchMUNU: Assertion `mfB > 0
.0' failed.
TIMING BCAST VS SPLAT MVEC WITH: B=(120,120,120) U=(2,4,1)
   BCAST = -nan MFLOP
   SPLAT = -nan MFLOP
VBCAST PROVIDES -nan SPEEDUP
Full search on MUxNU for nb=120, NREG=16, VLEN=4, KVEC=0
   MU= 1, NU= 1, MFLOP=-nan
   MU= 1, NU= 2, MFLOP=-nan
   MU= 1, NU= 3, MFLOP=-nan
   MU= 1, NU= 4, MFLOP=-nan
   MU= 1, NU= 5, MFLOP=-nan
[...]
Makefile:445: recipe for target 'res/snreg' failed
make[6]: *** [res/snreg] Aborted
[...]
ERROR 539 DURING CACHESIZE SEARCH!!.  CHECK INSTALL_LOG/Stage1.log FOR DETAILS.
[...]

New commits:

2b458deUpgrade ATLAS to version 3.11.38

comment:8 follow-up: Changed 7 years ago by fbissey

Haven't tried the branch yet but I have built it from ebuild on my machine. That being said my first attempt failed in the same way at the exact same point.

It got past once I set the ebuild to use threads which would have added -t -1 -Si omp 0 to the build options. I also had --use-ifko enabled, it took ~3h30mn to build on my 12 cores machine.

comment:9 in reply to: ↑ 8 ; follow-up: Changed 7 years ago by jdemeyer

Replying to fbissey:

Haven't tried the branch yet but I have built it from ebuild on my machine.

Do you know exactly which version that was?

comment:10 Changed 7 years ago by git

  • Commit changed from 2b458deaf2e6f89b81b136edc3098f3de98eb57c to 9f29a30e07b7823b0163dfe51df198f94ef745e0

Branch pushed to git repo; I updated commit sha1. New commits:

9f29a30Really override ATLAS throttling check

comment:11 Changed 7 years ago by git

  • Commit changed from 9f29a30e07b7823b0163dfe51df198f94ef745e0 to c0da5dd5d3ae67ead9b00fa98445a6924d131f47

Branch pushed to git repo; I updated commit sha1. New commits:

c0da5ddFix string overflow in case >= 100 threads

comment:12 Changed 7 years ago by jdemeyer

  • Description modified (diff)
  • Report Upstream changed from N/A to Reported upstream. No feedback yet.

comment:13 in reply to: ↑ 9 ; follow-up: Changed 7 years ago by fbissey

Replying to jdemeyer:

Replying to fbissey:

Haven't tried the branch yet but I have built it from ebuild on my machine.

Do you know exactly which version that was?

3.11.38 the same one.

How many cores does your machine have?

comment:14 in reply to: ↑ 13 Changed 7 years ago by jdemeyer

Replying to fbissey:

How many cores does your machine have?

Depends how you count... there are 24 cores, but it has multi-threading, so ATLAS detects 192 processors.

comment:15 Changed 7 years ago by jdemeyer

ATLAS is finally building now...

comment:16 Changed 7 years ago by git

  • Commit changed from c0da5dd5d3ae67ead9b00fa98445a6924d131f47 to 852a87496926114449061eee9aadece26a9b58a7

Branch pushed to git repo; I updated commit sha1. New commits:

852a874Skip throttling check with patch

comment:17 Changed 7 years ago by jdemeyer

  • Description modified (diff)

comment:18 Changed 7 years ago by git

  • Commit changed from 852a87496926114449061eee9aadece26a9b58a7 to 5c9ac1e0d7e5c0d7c3ea88d57460bca52b973157

Branch pushed to git repo; I updated commit sha1. New commits:

5c9ac1eDowngrade to LAPACK 3.5.0 for SciPy

comment:19 follow-up: Changed 7 years ago by fbissey

I see that you have meet scipy's use of lapack deprecated function https://archives.gentoo.org/gentoo-science/message/e5cb5f1117bc956cd829a667918026f4 and after. The good news is there is already a commit removing them from the unreleased 0.17 https://github.com/scipy/scipy/pull/5518 and it can be otherwise solved by telling lapack to build with deprecated functions. According to the Gentoo ebuild after running configure you can do

echo "BUILD_DEPRECATED=1" >> src/lapack/reference/make.inc.example

in your build directory and it will add back the deprecated functions in lapack-3.6.0.


New commits:

5c9ac1eDowngrade to LAPACK 3.5.0 for SciPy

comment:20 in reply to: ↑ 19 Changed 7 years ago by jdemeyer

Replying to fbissey:

I see that you have meet scipy's use of lapack deprecated function

I guess you mean removed functions, despite what LAPACK calls them. If they are not built by default, they are de facto removed, not deprecated.

I am going for the easy way out, which is using LAPACK 3.5.0 and SciPy 0.16.1 clean from upstream.

comment:21 Changed 7 years ago by jdemeyer

I any case, I needed to make a new ATLAS tarball, because there were some mistakes with the ARCHS directory.

comment:22 Changed 7 years ago by git

  • Commit changed from 5c9ac1e0d7e5c0d7c3ea88d57460bca52b973157 to bcb3dc466a1c75f9ad923591a02443651ea0040c

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

bcb3dc4Upgrade ATLAS to version 3.11.38

comment:23 Changed 7 years ago by jdemeyer

  • Status changed from new to needs_review
  • Summary changed from Port ATLAS to ppc64le to Upgrade ATLAS to version 3.11.38

comment:24 Changed 7 years ago by jdemeyer

  • Status changed from needs_review to needs_work

ATLAS works fine on my x86_64 laptop and the previous version built fine on POWER8. Unfortunately, the latest version of this branch failed on POWER8. I'm trying again to see if this a reproducible problem.

comment:25 Changed 7 years ago by jdemeyer

It succeeded the second time (without changes). I don't know how common this failure is or why it happened, but I do have a working ATLAS now.

comment:26 Changed 7 years ago by fbissey

That's very curious. It is probably a bug in ATLAS's build system that's a bit random. I am somewhat worried about the randomness. I may have to test on more hardware.

comment:27 Changed 7 years ago by jdemeyer

I reported the random build failure at http://sourceforge.net/p/math-atlas/support-requests/1013/

comment:28 Changed 7 years ago by git

  • Commit changed from bcb3dc466a1c75f9ad923591a02443651ea0040c to 615875b6c7a8a433b2840da7881c14700448b311

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

615875bUpgrade ATLAS to version 3.11.38

comment:29 Changed 7 years ago by jdemeyer

  • Cc vbraun added
  • Status changed from needs_work to needs_review

Rebased to 7.0.beta0. Volker, can you test this on the buildbot?

comment:30 Changed 7 years ago by vbraun

  • Reviewers set to Volker Braun
  • Status changed from needs_review to positive_review

comment:31 Changed 7 years ago by jdemeyer

Sage 7.0.beta0 is causing new problems: #19767

comment:32 follow-up: Changed 7 years ago by vbraun

On Arando it dies with

make -f Make.top time
make[4]: Entering directory `/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build'
./xatlbench -dc /home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/bin/INSTALL_LOG -dp 
Error around argument 4 (Out of args)!
USAGE: ./xatlbench [flags]
   -dp <prior benchmark directory>
   -dc <current benchmark directory>
   -f <filename w/o prefix>
   -o <outfile> : default=stdout
make[4]: *** [time] Error 4
make[4]: Leaving directory `/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build'
make[3]: *** [time] Error 2
make[3]: Leaving directory `/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build'
The ATLAS timing data failed to be collected.

see http://build.sagedev.org/release/builders/%20%20fast%20Oxford%20arando%20%28Ubuntu%2013.04%20i686%29%20incremental/builds/731/steps/compile/logs/atlas

comment:33 follow-up: Changed 7 years ago by vbraun

A different failure on http://build.sagedev.org/release/builders/%20%20slow%20AIMS%20bu14_32s02%20%28Ubuntu%2014.04%2032%20bit%29%20incremental/builds/279/steps/compile/logs/atlas possibly because of

/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//tune/blas/gemm/gmmsearch.c:1:0: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default]
 /*
 ^
./xgmmsearch -p s -f 4
ERROR IN COMMAND: make xsammtime_pt mb=120 nb=120 kb=120 mmrout=ATL_samm120_4m_4x4x1.c mu=4 nu=4 ku=1 mvA=1 mvB=1 mvC=0 kmoves=" -DATL_MOVEA -DATL_MOVEB" beta=1 outF="-f res/tmpout.ktim" > /dev/null 2>&1
   PROPOSED FILENAME: res/tmpout.ktim
   GENSTR='make gen_amm pre=s rt=ATL_samm120_4m_4x4x1.c vec=mdim vlen=4 mu=4 nu=4 ku=1 bcast=1'
TIMING BCAST VS SPLAT MVEC WITH: B=(120,120,120) U=(1,4,1)
make[9]: *** [res/snreg] Error 255
make[9]: Leaving directory `/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/blas/gemm'
make[8]: *** [res/snreg] Error 2
make[8]: Leaving directory `/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/sysinfo'
xsyssum: /mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//tune/sysinfo/GetSysSum.c:129: getmmnreg: Assertion `system(fnam) == 0' failed.

comment:34 follow-up: Changed 7 years ago by vbraun

On the Ubuntu 15.10 64-bit machine ATLAS builds but then runs into an assertion in the Sage doctests:

sage: import sage.matrix.benchmark as b ## line 724 ##
sage: ts = b.matrix_multiply_GF(100, p=19) ## line 725 ##
assertion K > 2 && K <= 96 failed, line 23 of file /mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//src/blas/ammm/ATL_GetRankKInfo.c

See http://build.sagedev.org/release/builders/%20%20slow%20AIMS%20bu1510_64s02%20%28Ubuntu%2015.10%2064%20bit%29%20incremental/builds/12/steps/shell_4/logs/stdio

comment:35 in reply to: ↑ 32 Changed 7 years ago by jdemeyer

Replying to vbraun:

On Arando it dies with

make -f Make.top time
make[4]: Entering directory `/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build'
./xatlbench -dc /home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/bin/INSTALL_LOG -dp 
Error around argument 4 (Out of args)!
USAGE: ./xatlbench [flags]
   -dp <prior benchmark directory>
   -dc <current benchmark directory>
   -f <filename w/o prefix>
   -o <outfile> : default=stdout
make[4]: *** [time] Error 4
make[4]: Leaving directory `/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build'
make[3]: *** [time] Error 2
make[3]: Leaving directory `/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build'
The ATLAS timing data failed to be collected.

see http://build.sagedev.org/release/builders/%20%20fast%20Oxford%20arando%20%28Ubuntu%2013.04%20i686%29%20incremental/builds/731/steps/compile/logs/atlas

That's not actually considered to be an error (because I made it so).

comment:36 in reply to: ↑ 33 ; follow-up: Changed 7 years ago by jdemeyer

Replying to vbraun:

A different failure on http://build.sagedev.org/release/builders/%20%20slow%20AIMS%20bu14_32s02%20%28Ubuntu%2014.04%2032%20bit%29%20incremental/builds/279/steps/compile/logs/atlas possibly because of

/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//tune/blas/gemm/gmmsearch.c:1:0: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default]
 /*
 ^
./xgmmsearch -p s -f 4
ERROR IN COMMAND: make xsammtime_pt mb=120 nb=120 kb=120 mmrout=ATL_samm120_4m_4x4x1.c mu=4 nu=4 ku=1 mvA=1 mvB=1 mvC=0 kmoves=" -DATL_MOVEA -DATL_MOVEB" beta=1 outF="-f res/tmpout.ktim" > /dev/null 2>&1
   PROPOSED FILENAME: res/tmpout.ktim
   GENSTR='make gen_amm pre=s rt=ATL_samm120_4m_4x4x1.c vec=mdim vlen=4 mu=4 nu=4 ku=1 bcast=1'
TIMING BCAST VS SPLAT MVEC WITH: B=(120,120,120) U=(1,4,1)
make[9]: *** [res/snreg] Error 255
make[9]: Leaving directory `/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/blas/gemm'
make[8]: *** [res/snreg] Error 2
make[8]: Leaving directory `/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/sysinfo'
xsyssum: /mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//tune/sysinfo/GetSysSum.c:129: getmmnreg: Assertion `system(fnam) == 0' failed.

For this one, could you try a different GCC version?

comment:37 in reply to: ↑ 34 Changed 7 years ago by jdemeyer

Replying to vbraun:

On the Ubuntu 15.10 64-bit machine ATLAS builds but then runs into an assertion in the Sage doctests:

sage: import sage.matrix.benchmark as b ## line 724 ##
sage: ts = b.matrix_multiply_GF(100, p=19) ## line 725 ##
assertion K > 2 && K <= 96 failed, line 23 of file /mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//src/blas/ammm/ATL_GetRankKInfo.c

See http://build.sagedev.org/release/builders/%20%20slow%20AIMS%20bu1510_64s02%20%28Ubuntu%2015.10%2064%20bit%29%20incremental/builds/12/steps/shell_4/logs/stdio

Hmm, for this one a traceback would be nice.

comment:38 Changed 7 years ago by vbraun

You do have an account on the AIMS buildbot slaves, right?

comment:39 Changed 7 years ago by jdemeyer

I forgot, but it seems I do.

comment:40 Changed 7 years ago by jdemeyer

On ppc64le, I built this successfully (that's 2 out of 3) on 7.0.beta0 after adding an LD_LIBRARY_PATH workaround for #19767.

comment:41 Changed 7 years ago by vbraun

  • Status changed from positive_review to needs_work

comment:42 Changed 7 years ago by jpflori

  • Cc jpflori added

comment:43 Changed 7 years ago by jdemeyer

On my ppc64le machine, the score is now 2 successful builds out of 4 tries. The last time it failed with:

if [ -s "/home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/src/blas/gemv/Make_dmvn" ]; then \
           cd  /home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/src/blas/gemv ; make -j1 -f Make_dmvn killall ; \
           rm -f /home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/src/blas/gemv/Make_dmvn ; \
        fi
./xmvnhgen -p d -F res/dMVNK.sum -d dmvnoutd
xmvnhgen: /home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//include/atlas_genparse.h:239: GetDoubleArr: Assertion `sscanf(str, "%le",
 d+i) == 1' failed.
Makefile:682: recipe for target 'dmvninstall' failed
make[7]: *** [dmvninstall] Aborted
make[7]: Leaving directory '/home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/blas/gemv'
Makefile:422: recipe for target 'res/dMVNK.sum' failed
make[6]: *** [res/dMVNK.sum] Error 2
make[6]: Leaving directory '/home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/blas/gemv'
Makefile:334: recipe for target '/home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/blas/gemv/res/dMVNK.sum' failed
make[5]: *** [/home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/blas/gemv/res/dMVNK.sum] Error 2
make[5]: Leaving directory '/home/jdemeyer/sage/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/bin'
ERROR 626 DURING MVNTUNE!!.  CHECK INSTALL_LOG/dMVNTUNE.LOG FOR DETAILS.

I'm afraid that this new ATLAS is full of random failures...

comment:44 Changed 7 years ago by vbraun

My experience with atlas unstable releases was similar...

comment:45 Changed 7 years ago by jdemeyer

  • Description modified (diff)

comment:46 Changed 7 years ago by jdemeyer

Failed twice more with the same error as 43. It turns out there is a buffer overflow somewhere because the command line is too long.

Yet another "WTF??? Implementing a build system in C"

comment:47 Changed 7 years ago by vbraun

Yep, I remember fixing buffer overflows in the ATLAS build system before...

comment:48 Changed 7 years ago by jdemeyer

At least it's good to know that it's not a random error.

comment:49 Changed 7 years ago by jdemeyer

It's not a buffer overflow, it is somehow choking on the commas in -Wl,rpath,...

comment:50 Changed 7 years ago by git

  • Commit changed from 615875b6c7a8a433b2840da7881c14700448b311 to 69bf336774c9e8e1f0dea4b49174abefcae7807e

Branch pushed to git repo; I updated commit sha1. New commits:

deda1bcMerge commit '54ff55f9f7569850caa4eb68ddc0aced74b72d44' into t/19719/upgrade_atlas
69bf336Fix misparsing of double array in case CFLAGS contains commas

comment:51 Changed 7 years ago by git

  • Commit changed from 69bf336774c9e8e1f0dea4b49174abefcae7807e to 6607e28d3a35cd6d54cd3d0a2eb81912a11a89cb

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

6607e28Fix misparsing of double array in case CFLAGS contains commas

comment:52 Changed 7 years ago by jdemeyer

  • Description modified (diff)

comment:53 Changed 7 years ago by jdemeyer

After fixing the comma issue, I tried twice more to build ATLAS on ppc64le. There was 1 success, 1 failure (the same as the first time). So the score is now 3/5.

comment:54 Changed 7 years ago by git

  • Commit changed from 6607e28d3a35cd6d54cd3d0a2eb81912a11a89cb to f21cc5000fb2930ca2e8cff2bb90340489a73ee5

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

f21cc50Upgrade ATLAS to version 3.11.38

comment:55 Changed 7 years ago by jdemeyer

The buildbot failure on sagebu1510_64s02 is a random failure.

On sagebu14_32s02, I got the same failure as the buildbot.

comment:56 Changed 7 years ago by jdemeyer

  • Description modified (diff)

comment:57 Changed 7 years ago by jdemeyer

The reproducible build problem on sagebu14_32s02 is fixed by using GCC 4.9.x instead of GCC 4.8.4.

Unfortunately, there are still doctest failures:

sage -t --long --warn-long 90.7 src/sage/matrix/matrix_modn_dense_template.pxi
**********************************************************************
File "src/sage/matrix/matrix_modn_dense_template.pxi", line 1037, in sage.matrix.matrix_modn_dense_template.Matrix_modn_dense_template._matrix_times_matrix_
Failed example:
    (MS(0) * A) == 0
Expected:
    True
Got:
    False
**********************************************************************
File "src/sage/matrix/matrix_modn_dense_template.pxi", line 1040, in sage.matrix.matrix_modn_dense_template.Matrix_modn_dense_template._matrix_times_matrix_
Failed example:
    (MS(1) * A) == A
Expected:
    True
Got:
    False
**********************************************************************
File "src/sage/matrix/matrix_modn_dense_template.pxi", line 1082, in sage.matrix.matrix_modn_dense_template.Matrix_modn_dense_template._matrix_times_matrix_
Failed example:
    (MS(0) * A) == 0
Expected:
    True
Got:
    False
**********************************************************************
File "src/sage/matrix/matrix_modn_dense_template.pxi", line 1085, in sage.matrix.matrix_modn_dense_template.Matrix_modn_dense_template._matrix_times_matrix_
Failed example:
    (MS(1) * A) == A
Expected:
    True
Got:
    False
**********************************************************************

These are testing that multiplying a matrix over a finite field with the zero or identity matrix work as expected.

comment:58 Changed 7 years ago by jdemeyer

  • Description modified (diff)

comment:59 Changed 7 years ago by jdemeyer

  • Report Upstream changed from Reported upstream. No feedback yet. to Reported upstream. Developers acknowledge bug.

comment:60 Changed 6 years ago by git

  • Commit changed from f21cc5000fb2930ca2e8cff2bb90340489a73ee5 to e79da1ffebc490b2e6ced066290f735fc1f9d463

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

e79da1fUpgrade ATLAS to version 3.11.38

comment:61 Changed 6 years ago by jpflori

@jeroen: From what you wrote on #19701, I understand there are no doctests failures anymore?

comment:62 Changed 6 years ago by jdemeyer

There are no reproducible doctest failures anymore. However, there seem to be some pexpect problems with GAP which are hard to reproduce and therefore debug.

comment:63 Changed 6 years ago by jpflori

Ok, I saw the GAP issue, I was just wondering about ATLAS, I'm building it right now.

comment:64 Changed 6 years ago by jdemeyer

I also get "Bad exit: 2" sometimes, for example

sage -t --long --warn-long 92.8 src/sage/homology/simplicial_complex.py
    Bad exit: 2
**********************************************************************
Tests run before process (pid=88791) failed:
sage: SimplicialComplex([[1], [3, 7]]) ## line 76 ##
[...]
sage: SimplicialComplex([[]]).connected_component() ## line 3119 ##
sage: sig_on_count() # check sig_on/off pairings (virtual doctest) ## line 3123 ##
0
sage: S1 = simplicial_complexes.Sphere(1) ## line 3162 ##
sage: S1.fundamental_group() ## line 3163 ##

**********************************************************************

See #19845.

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

comment:65 in reply to: ↑ 36 Changed 6 years ago by jpflori

Replying to jdemeyer:

Replying to vbraun:

A different failure on http://build.sagedev.org/release/builders/%20%20slow%20AIMS%20bu14_32s02%20%28Ubuntu%2014.04%2032%20bit%29%20incremental/builds/279/steps/compile/logs/atlas possibly because of

/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//tune/blas/gemm/gmmsearch.c:1:0: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default]
 /*
 ^
./xgmmsearch -p s -f 4
ERROR IN COMMAND: make xsammtime_pt mb=120 nb=120 kb=120 mmrout=ATL_samm120_4m_4x4x1.c mu=4 nu=4 ku=1 mvA=1 mvB=1 mvC=0 kmoves=" -DATL_MOVEA -DATL_MOVEB" beta=1 outF="-f res/tmpout.ktim" > /dev/null 2>&1
   PROPOSED FILENAME: res/tmpout.ktim
   GENSTR='make gen_amm pre=s rt=ATL_samm120_4m_4x4x1.c vec=mdim vlen=4 mu=4 nu=4 ku=1 bcast=1'
TIMING BCAST VS SPLAT MVEC WITH: B=(120,120,120) U=(1,4,1)
make[9]: *** [res/snreg] Error 255
make[9]: Leaving directory `/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/blas/gemm'
make[8]: *** [res/snreg] Error 2
make[8]: Leaving directory `/mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/tune/sysinfo'
xsyssum: /mnt/highperf/buildbot/slave/sage_git/build/local/var/tmp/sage/build/atlas-3.11.38/src/ATLAS-build/../ATLAS//tune/sysinfo/GetSysSum.c:129: getmmnreg: Assertion `system(fnam) == 0' failed.

For this one, could you try a different GCC version?

Also got hit by that one on POWER8. Presumably because of the system GCC 4.9.2. Fixed by installing Sage's GCC 4.9.3.

comment:66 Changed 6 years ago by git

  • Commit changed from e79da1ffebc490b2e6ced066290f735fc1f9d463 to 2872a8018f1d83ba9f4fd4057294cc6612e6d47e

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

2872a80Upgrade ATLAS to version 3.11.38

comment:67 Changed 6 years ago by cpernet

In case porting ATLAS to Power8 gets too painfull, I just wanted to remind that in a hopefully not too distant future, OpenBLAS should replace ATLAS (#20096) and OpenBLAS compiles cleanly on Power8.

comment:68 Changed 6 years ago by git

  • Commit changed from 2872a8018f1d83ba9f4fd4057294cc6612e6d47e to 13388a53dabb28bee4355360e4797f184b60a9a5

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

13388a5Upgrade ATLAS to version 3.11.38

comment:69 Changed 6 years ago by git

  • Commit changed from 13388a53dabb28bee4355360e4797f184b60a9a5 to c19635ff199c0a7e4e4aa66c2c7c7ac1e9347884

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

c19635fUpgrade ATLAS to version 3.11.38

comment:70 Changed 6 years ago by leif

  • Cc leif added
  • Keywords BLAS LAPACK --with-blas added
  • Milestone changed from sage-7.0 to sage-7.4

comment:71 Changed 3 years ago by slelievre

  • Milestone changed from sage-7.4 to sage-8.7

Note: ATLAS 3.11.40 was released on 2018-10-02.

comment:72 Changed 3 years ago by slelievre

And apparently ATLAS 3.11.41 a couple of days later.

No announcement but listed in the "Developer" folder at

comment:73 Changed 3 years ago by embray

  • Milestone changed from sage-8.7 to sage-8.8

Ticket retargeted after milestone closed (if you don't believe this ticket is appropriate for the Sage 8.8 release please retarget manually)

comment:74 Changed 3 years ago by embray

  • Milestone changed from sage-8.8 to sage-8.9

Tickets still needing working or clarification should be moved to the next release milestone at the soonest (please feel free to revert if you think the ticket is close to being resolved).

comment:75 Changed 2 years ago by embray

  • Milestone changed from sage-8.9 to sage-9.1

Ticket retargeted after milestone closed

comment:76 Changed 2 years ago by mkoeppe

  • Milestone changed from sage-9.1 to sage-9.2

comment:77 Changed 23 months ago by mkoeppe

  • Cc dimpase jhpalmieri added

Latest as of 2020-08-13 is 3.11.40, released 2018-10-02, see https://github.com/math-atlas/math-atlas/releases

Do we want to make the upgrade, or downgrade atlas to experimental, or remove the spkg altogether?

comment:78 Changed 23 months ago by jhpalmieri

Any way of knowing if anyone uses it with Sage, short of just removing it and see who complains?

comment:79 Changed 23 months ago by jhpalmieri

Oh, also, with the most recent release almost two years old, I don't see any reason for us to put much work into it. So I vote for either downgrading to experimental or removing.

comment:80 Changed 23 months ago by mkoeppe

My preferred approach would be to just remove it. Making it experimental is too complicated.

comment:81 Changed 23 months ago by mkoeppe

But if we remove it, let's still keep the makefile variable BLAS (used in the dependencies) and configure variable SAGE_BLAS, rather than hardcoding openblas. It will make it easier to plug in another BLAS implementation if one comes along, and I also need it for #29387.

comment:82 Changed 23 months ago by mkoeppe

  • Authors Jeroen Demeyer deleted
  • Milestone changed from sage-9.2 to sage-duplicate/invalid/wontfix
  • Reviewers Volker Braun deleted
  • Status changed from needs_work to needs_review

I've opened #30350 (Remove ATLAS).

Let's close the present ticket.

comment:83 Changed 23 months ago by dimpase

  • Reviewers set to Dima Pasechnik
  • Status changed from needs_review to positive_review

ok

comment:84 Changed 20 months ago by chapoton

  • Resolution set to invalid
  • Status changed from positive_review to closed
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