#9896 closed defect (fixed)
Upgrading from 4.5.3 to 4.6.alpha* can fail (not limited to MacOS X)
Reported by:  jhpalmieri  Owned by:  leif 

Priority:  blocker  Milestone:  sage4.6 
Component:  build  Keywords:  upgrade update dependencies PARI NewPARI 
Cc:  cremona, drkirkby, jdemeyer, leif, justin, mhansen  Merged in:  sage4.6.rc0 
Authors:  Leif Leonhardy  Reviewers:  John Palmieri, Mitesh Patel 
Report Upstream:  N/A  Work issues:  
Branch:  Commit:  
Dependencies:  Stopgaps: 
Description (last modified by )
On two separate machines running OS X 10.6, upgrading from 4.5.3 to 4.6.alpha0 seemed to work  no errors were reported  but Sage fails to start:
  Sage Version 4.6.alpha0, Release Date: 20100910   Type notebook() for the GUI, and license() for information.   ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** *** bug in PARI/GP (Segmentation Fault), please report *** bug in PARI/GP (Segmentation Fault), please report
(Building from scratch works fine.)
How to test:
Upgrade path for testing the fixes: http://sage.math.washington.edu/home/release/sage4.6.rc0/sage4.6.rc0/
Note that noninplace upgrades had been broken in Sage 4.6.alpha3, due to the inclusion of matplotlib 1.0.0 (#9221) into that version. To temporarily work around this, it is sufficient to trigger a rebuild of freetype during the upgrade when upgrading from a moved (copied or renamed) Sage installation to alpha3:
$ rm spkg/installed/freetype*
This is not required for the rc0 upgrade path.
If you want to speed up the upgrade (i.e., reduce the number of packages that get rebuilt) on systems other than Cygwin, HPUX and Solaris, do the following before starting the upgrade:
$ touch spkg/installed/iconv1.13.1.p3 # fake it was already installed
(This package is only used on the above systems, but upgrading it triggers the rebuild of MPIR on any platform, which in turn causes rebuilding all packages that directly or indirectly depend on MPIR, the GMP replacement package.)
Do the upgrade:
$ ./sage upgrade http://sage.math.washington.edu/home/release/sage4.6.rc0/sage4.6.rc0/
Note that you'll be prompted to confirm upgrading (by typing "y" followed by carriage return), so be careful when tee
ing the output, since currently the script's output isn't flushed s.t. you won't see the prompt in that case and perhaps wait forever... ;) (this has been fixed in #10011.)
To the release manager / How to merge this ticket:
 Replace
spkg/install
by http://trac.sagemath.org/sage_trac/rawattachment/ticket/9896/trac_9896SAGE_ROOT__spkg__install.v2b  Replace
spkg/standard/deps
by http://trac.sagemath.org/sage_trac/rawattachment/ticket/9896/trac_9896SAGE_ROOT__spkg__standard__deps.v3  Apply http://trac.sagemath.org/sage_trac/rawattachment/ticket/9896/9896_scripts_hgignore.patch to the Sage scripts repository (Not mandatory, but helpful.)
 Apply http://trac.sagemath.org/sage_trac/rawattachment/ticket/9896/trac_9896propagate_upgrading_to_install_scriptscripts_repo.patch to the Sage scripts repository
 Apply http://trac.sagemath.org/sage_trac/rawattachment/ticket/9896/trac_9896fix_extension_module_depssagelib.patch to the Sage library repository
 Apply http://trac.sagemath.org/sage_trac/rawattachment/ticket/9896/trac_9896fix_hardcoded_libdirs_in_extmod_linker_cmdsagelib.patch to the Sage library repository
 Run
./sage sdist ...
Attachments (14)
Change History (197)
comment:1 Changed 9 years ago by
 Cc leif added
comment:2 followup: ↓ 3 Changed 9 years ago by
 Cc jdemeyer added
comment:3 in reply to: ↑ 2 Changed 9 years ago by
Replying to mpatel:
Can we somehow trace the PARI calls that lead to this?
Running sage gdb
could help, but on bsd.math, I get
[...] We need authorization from an admin user to run the debugger. This will only happen once per login session. Admin username (mpatel):
comment:4 Changed 9 years ago by
My problem is I don't know how to use gdb. After running "sage gdb", I see a ton of message like
Reading symbols for shared libraries . done
and warnings like
warning: Could not find object file "/Applications/sage_builds/sage4.5.3/spkg/build/gsl1.14/src/.libs/libgsl.lax/libgslcdf.a/weibull.o"  no debug information available for "weibull.c".
Then
Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x0000000000000000 0x000000010285aadc in err_leave () (gdb)
Now what should I type to provide meaningful information?
comment:5 Changed 9 years ago by
 Cc drkirkby added
What happens if you type bt
(for a backtrace)? I'm not very familiar with GDB, but perhaps this or David can help?
comment:6 Changed 9 years ago by
bt
(backtrace)?
Btw, the segfault happens somewhere in pari_init()
, because Sage afterwards disables PARI's signal handlers.
comment:7 Changed 9 years ago by
Perhaps also first rebuild PARI with CFLAGS=fnoomitframepointer
, and less optimization (O1
or O0
).
comment:8 Changed 9 years ago by
Well, I tried to rebuild PARI by setting CFLAGS="fnoomitframepointer O0" and then "sage f pari...". (I also tried running PARI's ./Configure with the "g" debugging option, but it failed with
ld: symbol(s) not found for inferred architecture x86_64
so I gave up on that.) When I ran "bt", I got this:
(gdb) bt #0 0x000000010285aadc in err_leave () #1 0x0000000102a72b5d in __pyx_pf_4sage_4libs_4pari_3gen_12PariInstance___init__ (__pyx_v_self=0x10211a4f0, __pyx_args=<value temporarily unavailable, due to optimizations>, __pyx_kwds=0x101f573b0) at sage/libs/pari/gen.c:36951 #2 0x000000010006d8c5 in type_call () #3 0x000000010000bcd2 in PyObject_Call () #4 0x0000000102a424fc in initgen () at sage/libs/pari/gen.c:46847 #5 0x00000001000d2e11 in _PyImport_LoadDynamicModule () #6 0x00000001000d10bf in import_submodule () #7 0x00000001000d15da in load_next () #8 0x00000001000d1932 in PyImport_ImportModuleLevel () #9 0x00000001000aeef3 in builtin___import__ () #10 0x000000010000bcd2 in PyObject_Call () #11 0x000000010000f825 in PyObject_CallFunction () #12 0x00000001000d209b in PyImport_Import () #13 0x000000010238cfeb in __Pyx_ImportModule [inlined] () at /Applications/sage_builds/sage4.6.alpha0upgrade/devel/sagemain/sage/rings/complex_double.c:15716 #14 0x000000010238cfeb in __Pyx_ImportType (module_name=0x1023a8eb2 "sage.libs.pari.gen", class_name=0x1023a825b "gen", size=56, strict=1) at sage/rings/complex_double.c:15660 #15 0x00000001023a3463 in initcomplex_double () at sage/rings/complex_double.c:14241 #16 0x00000001000d2e11 in _PyImport_LoadDynamicModule () #17 0x00000001000d10bf in import_submodule () #18 0x00000001000d15da in load_next () #19 0x00000001000d1932 in PyImport_ImportModuleLevel () #20 0x00000001000aeef3 in builtin___import__ () #21 0x000000010000bcd2 in PyObject_Call () #22 0x00000001000b0147 in PyEval_CallObjectWithKeywords () #23 0x00000001000b440e in PyEval_EvalFrameEx () #24 0x00000001000b9010 in PyEval_EvalCodeEx () #25 0x00000001000b90f6 in PyEval_EvalCode () #26 0x00000001000cdfb0 in PyImport_ExecCodeModuleEx () #27 0x00000001000cf212 in load_source_module () #28 0x00000001000d10bf in import_submodule () #29 0x00000001000d15da in load_next () #30 0x00000001000d1932 in PyImport_ImportModuleLevel () #31 0x00000001000aeef3 in builtin___import__ () #32 0x000000010000bcd2 in PyObject_Call () #33 0x00000001000b0147 in PyEval_CallObjectWithKeywords () #34 0x00000001000b440e in PyEval_EvalFrameEx () #35 0x00000001000b9010 in PyEval_EvalCodeEx () #36 0x00000001000b90f6 in PyEval_EvalCode () #37 0x00000001000cdfb0 in PyImport_ExecCodeModuleEx () #38 0x00000001000cf212 in load_source_module () #39 0x00000001000d10bf in import_submodule () #40 0x00000001000d15da in load_next () #41 0x00000001000d18ec in PyImport_ImportModuleLevel () #42 0x00000001000aeef3 in builtin___import__ () #43 0x000000010000bcd2 in PyObject_Call () #44 0x00000001000b0147 in PyEval_CallObjectWithKeywords () #45 0x00000001000b440e in PyEval_EvalFrameEx () #46 0x00000001000b9010 in PyEval_EvalCodeEx () #47 0x00000001000b90f6 in PyEval_EvalCode () #48 0x00000001000cdfb0 in PyImport_ExecCodeModuleEx () #49 0x00000001000cf212 in load_source_module () #50 0x00000001000d10bf in import_submodule () #51 0x00000001000d15da in load_next () #52 0x00000001000d1932 in PyImport_ImportModuleLevel () #53 0x00000001000aeef3 in builtin___import__ () #54 0x000000010000bcd2 in PyObject_Call () #55 0x00000001000b0147 in PyEval_CallObjectWithKeywords () #56 0x00000001000b440e in PyEval_EvalFrameEx () #57 0x00000001000b9010 in PyEval_EvalCodeEx () #58 0x00000001000b90f6 in PyEval_EvalCode () #59 0x00000001000cdfb0 in PyImport_ExecCodeModuleEx () #60 0x00000001000cf212 in load_source_module () #61 0x00000001000d10bf in import_submodule () #62 0x00000001000d15da in load_next () #63 0x00000001000d1932 in PyImport_ImportModuleLevel () #64 0x00000001000aeef3 in builtin___import__ () #65 0x000000010000bcd2 in PyObject_Call () #66 0x00000001000b0147 in PyEval_CallObjectWithKeywords () #67 0x00000001000b440e in PyEval_EvalFrameEx () #68 0x00000001000b9010 in PyEval_EvalCodeEx () #69 0x00000001000b90f6 in PyEval_EvalCode () #70 0x00000001000cdfb0 in PyImport_ExecCodeModuleEx () #71 0x00000001000cf212 in load_source_module () #72 0x00000001000d10bf in import_submodule () #73 0x00000001000d15da in load_next () #74 0x00000001000d1932 in PyImport_ImportModuleLevel () #75 0x00000001000aeef3 in builtin___import__ () #76 0x000000010000bcd2 in PyObject_Call () #77 0x00000001000b0147 in PyEval_CallObjectWithKeywords () #78 0x00000001000b440e in PyEval_EvalFrameEx () #79 0x00000001000b9010 in PyEval_EvalCodeEx () #80 0x00000001000b90f6 in PyEval_EvalCode () #81 0x00000001000cdfb0 in PyImport_ExecCodeModuleEx () #82 0x00000001000cf212 in load_source_module () #83 0x00000001000d10bf in import_submodule () #84 0x00000001000d15da in load_next () #85 0x00000001000d18ec in PyImport_ImportModuleLevel () #86 0x00000001000aeef3 in builtin___import__ () #87 0x00000001000b82b8 in PyEval_EvalFrameEx () #88 0x00000001000b745a in PyEval_EvalFrameEx () #89 0x00000001000b9010 in PyEval_EvalCodeEx () #90 0x00000001000b6ffd in PyEval_EvalFrameEx () #91 0x00000001000b9010 in PyEval_EvalCodeEx () #92 0x000000010003b0ad in function_call () #93 0x000000010000bcd2 in PyObject_Call () #94 0x000000010001dd0d in instancemethod_call () #95 0x000000010000bcd2 in PyObject_Call () #96 0x00000001000b0147 in PyEval_CallObjectWithKeywords () #97 0x0000000100020d0e in PyInstance_New () #98 0x000000010000bcd2 in PyObject_Call () #99 0x00000001000b457e in PyEval_EvalFrameEx () #100 0x00000001000b9010 in PyEval_EvalCodeEx () #101 0x00000001000b6ffd in PyEval_EvalFrameEx () #102 0x00000001000b9010 in PyEval_EvalCodeEx () #103 0x00000001000b90f6 in PyEval_EvalCode () #104 0x00000001000dde0e in PyRun_FileExFlags () #105 0x00000001000de0c9 in PyRun_SimpleFileExFlags () #106 0x00000001000eb5eb in Py_Main () #107 0x0000000100000f14 in start ()
comment:9 Changed 9 years ago by
John, can you provide a link to the full PARI spkg install log?
I also wonder if somehow PARI uses parts of its old installation (in $SAGE_LOCAL/{lib,include/pari}/
) during the build (which one would not necessarily see in the log though). It would be safer to delete all these files prior to upgrading...
Does the standalone interpreter work?
comment:10 Changed 9 years ago by
I found the problem, I think, thanks to one of your questions on sagerelease: in local/lib, I have
rwxrxrx 1 palmieri admin 5249848 Sep 11 18:39 libparigmp2.4.dylib rwxrxrx 1 palmieri admin 3487624 Sep 8 21:53 libparigmp.dylib rwrr 1 palmieri admin 21398976 Sep 11 18:39 libpari.a rwxrxrx 1 palmieri admin 5249848 Sep 11 18:39 libpari.dylib
Note the timestamp on the file libparigmp.dylib: this is from the old PARI installation. If I get rid of this file and then link libparigmp2.4.dylib to libparigmp.dylib, then Sage starts with no trouble. If I just delete the file, then Sage complains
ImportError: dlopen(/Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage/rings/complex_double.so, 2): Library not loaded: libparigmp.dylib
I also get the complaint after running "sage ba". I don't see anything in the PARI install log about libparigmp.dylib, just libparigmp2.4.dylib, so I'm a little confused about whether this link should be here. Two things I might try next: running tests with the link, or deleting the old dylib file and then running "sage upgrade ..." to see if that helps.
comment:11 followup: ↓ 49 Changed 9 years ago by
The time stamps on pariport.h, paritype.h, and paripriv.h are all old, too.
comment:12 Changed 9 years ago by
Some part in John's build must have been linked against libpari.*
when this still was a copy of / symbolic link to the old libparigmp.*
, s.t. the old soname got recorded, and all PARI symbols were resolved from there before libparigmp2.4.*
was considered.
libcsage.*
is IMHO a good candidate... Did this really get updated in local/lib
, i.e. got devel/sage/c_lib/libcsage.*
rebuilt?
comment:13 Changed 9 years ago by
Two things I might try next: running tests with the link, or deleting the old dylib file and then running "sage upgrade ..." to see if that helps.
I did these on two different machines. With the link, all tests passed. Deleting the old dylib file (and the old include files, just for kicks) and then upgrading caused problems: ImportError
as above.
libcsage.* is IMHO a good candidate... Did this really get updated in local/lib, i.e. got devel/sage/c_lib/libcsage.* rebuilt?
Yes, it did. After taking a clean 4.5.3 install and upgrading, here are the recent files in local/lib:
lrwxrxrx 1 palmieri admin 37 Sep 11 21:32 libcsage.dylib > ../../devel/sage/c_lib/libcsage.dylib rwxrxrx 1 palmieri admin 77488 Sep 11 21:32 libLfunction.so rwxrxrx 1 palmieri admin 5249848 Sep 11 21:31 libparigmp2.4.dylib rwrr 1 palmieri admin 21398976 Sep 11 21:31 libpari.a rwxrxrx 1 palmieri admin 5249848 Sep 11 21:31 libpari.dylib
Here is the file to which libcsage.dylib links:
rwxrxrx 1 palmieri admin 83864 Sep 11 21:32 libcsage.dylib
The rest of the libraries in local/lib are old enough that they must have come from 4.5.3.
comment:14 followup: ↓ 15 Changed 9 years ago by
 Cc justin added
Justin reported successful upgrade from 4.5.3 on MacOS X 10.5.8 on sagerelease, though some doctests fail.
comment:15 in reply to: ↑ 14 Changed 9 years ago by
Replying to leif:
Justin reported successful upgrade from 4.5.3 on MacOS X 10.5.8 on sagerelease, though some doctests fail.
(... due to eclib
not getting rebuilt.)
comment:16 Changed 9 years ago by
Necessary steps to properly upgrade (from Sage 4.5.3) to Sage 4.6.alpha0:
 Build Sage 4.5.3 from scratch ;)
 Run
./sage upgrade http://sage.math.washington.edu/home/release/sage4.6.alpha0/sage4.6.alpha0/
(Unfortunately, modifyingspkg/standard/deps
before doing so doesn't help since this file gets overwritten during upgrade.)  Run
./sage f eclib20100711
(just to record the new PARI shared library name in its various shared libraries).  Touch the Sage library files that have to be rebuilt for the same reason:
(Three command invocations just to make it readable without horizontal scrolling.)
touch devel/sage/sage/libs/cremona/homspace.pyx touch devel/sage/sage/libs/cremona/newforms.pyx touch devel/sage/sage/libs/mwrank/mwrank.pyx
 Run
./sage b
to rebuild them (i.e., their respective Python modules / shared libraries).
Deleting the old PARI shared library files (local/lib/libparigmp.*
) is not necessary, but will trigger Sage import errors if you omit one of the above steps... (unless you have a systemwide PARI library installed which matches the old version, i.e. 2.3.*)
comment:17 followup: ↓ 19 Changed 9 years ago by
Necessary steps to properly upgrade (from Sage 4.5.3) to Sage 4.6.alpha0:
This didn't work for me; I get the same segmentation fault message. (I think that when I tried "sage ba" before, that would have rebuilt the files from all the pyx files, so I guess it's not a surprise that this failed.)
comment:18 followup: ↓ 42 Changed 9 years ago by
 Cc mhansen added
 Status changed from new to needs_info
I consider the "touch
issue" a bug in module_list.py
, since PARI is not directly used by those extension modules (but listed in their libraries
, and therefore gets recorded in the list of needed libraries).
Explicitly linking against PARI would then only be necessary if we built some statically linked executable. Or is this also required on some systems like Cygwin? If so, we should make use of uname_specific()
there, too.
comment:19 in reply to: ↑ 17 Changed 9 years ago by
Replying to jhpalmieri:
Necessary steps to properly upgrade (from Sage 4.5.3) to Sage 4.6.alpha0:
This didn't work for me; I get the same segmentation fault message. (I think that when I tried "sage ba" before, that would have rebuilt the files from all the pyx files, so I guess it's not a surprise that this failed.)
Must be some bad environment... ;)
Does gp
work (after upgrading)?
comment:20 Changed 9 years ago by
Does gp work (after upgrading)?
./sage gp
starts up and can execute simple calculations. No segfault.
comment:21 Changed 9 years ago by
And what import errors do you now get after deleting the old PARI's dylibs (libparigmp.*
)?
comment:22 Changed 9 years ago by
For me (Ubuntu 10.04 x86_64), upgrading with the above steps passes ptestlong
with the original module_list.py
, and also after deleting "pari"
from the library lists of the mentioned extension modules, then again touching the .pyx
files and running ./sage b
.
comment:23 Changed 9 years ago by
After going through the above steps, if I also delete the old libparigmp, then I get
ImportError: dlopen(/Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage/rings/complex_double.so, 2): Library not loaded: libparigmp.dylib Referenced from: /Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage/rings/complex_double.so Reason: image not found
If I touch complex_double.pyx and "sage b", there is no change. Touching all of the py, pyx, and pxd files in the libs/pari directory also triggers a rebuild of complex_double.pyx, and also doesn't help.
comment:24 followup: ↓ 25 Changed 9 years ago by
And the files in .../local/lib/python2.6/sitepackages/...
got properly updated?!?
Can you attach a log of the ./sage b
run?
The only (other) thing I could imagine is some old PARI library in the linker/loader search path during linking, but not at runtime (i.e. dynamic loader search path). (Really) Environment issue?
comment:25 in reply to: ↑ 24 Changed 9 years ago by
Replying to leif:
And the files in
.../local/lib/python2.6/sitepackages/...
got properly updated?!?
According to the time stamps, yes.
Can you attach a log of the
./sage b
run?
Which one? Here's what happens if I follow your instructions, delete libparigmp.dylib, and touch complex_double.pyx:
$ ./sage b  sage: Building and installing modified Sage library files. Installing c_lib scons: `install' is up to date. Updating Cython code.... Building modified file sage/rings/complex_double.pyx. Execute 1 commands (using 1 threads) python `which cython` embedpositions directive cdivision=True I/Applications/sage_builds/sage4.6.alpha0upgrade/devel/sagemain o sage/rings/complex_double.c sage/rings/complex_double.pyx sage/rings/complex_double.pyx > /Applications/sage_builds/sage4.6.alpha0upgrade/local//lib/python/sitepackages//sage/rings/complex_double.pyx Time to execute 1 commands: 4.32504701614 seconds Finished compiling Cython code (time = 4.87559199333 seconds) running install running build running build_py running build_ext building 'sage.rings.complex_double' extension gcc fnostrictaliasing g O2 DNDEBUG g fwrapv O3 Wall Wstrictprototypes I/Applications/sage_builds/sage4.6.alpha0upgrade/local//include I/Applications/sage_builds/sage4.6.alpha0upgrade/local//include/csage I/Applications/sage_builds/sage4.6.alpha0upgrade/devel//sage/sage/ext I/Applications/sage_builds/sage4.6.alpha0upgrade/local/include/python2.6 c sage/rings/complex_double.c o build/temp.macosx10.6i3862.6/sage/rings/complex_double.o std=c99 D_XPG6 w gcc L/Applications/sage_builds/sage4.5.3/local/lib bundle undefined dynamic_lookup build/temp.macosx10.6i3862.6/sage/rings/complex_double.o L/Applications/sage_builds/sage4.6.alpha0upgrade/local//lib lcsage lgsl lcblas latlas lpari lgmp lm lstdc++ lntl o build/lib.macosx10.6i3862.6/sage/rings/complex_double.so Total time spent compiling C/C++ extensions: 7.72538805008 seconds. running install_lib copying build/lib.macosx10.6i3862.6/sage/rings/complex_double.so > /Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage/rings running install_egg_info Removing /Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage0.0.0py2.6.egginfo Writing /Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage0.0.0py2.6.egginfo real 0m13.963s user 0m12.678s sys 0m1.095s
The only (other) thing I could imagine is some old PARI library in the linker/loader search path during linking, but not at runtime (i.e. dynamic loader search path). (Really) Environment issue?
Well, I see it on two different machines. I don't have LD_LIBRARY_PATH or DYLD_LIBRARY_PATH set, and when I run "./sage sh", I don't see anything odd in those variables. I've posted what I get from "export" ordinarily and also after running "./sage sh" at http://sage.math.washington.edu/home/palmieri/misc/env.txt. I'm going to try this all on bsd.math, which involves building sage 4.5.3 first, so it will take a while. I've hardly used that machine, so my environment there is pretty vanilla.
comment:26 followup: ↓ 27 Changed 9 years ago by
gcc L/Applications/sage_builds/sage4.5.3/local/lib bundle undefined dynamic_lookup build/temp.macosx10.6i3862.6/sage/rings/complex_double.o L/Applications/sage_builds/sage4.6.alpha0upgrade/local//lib lcsage lgsl lcblas latlas lpari lgmp lm lstdc++ lntl o build/lib.macosx10.6i3862.6/sage/rings/complex_double.so
That's what I was thinking of. Looks as if the linker also (first!) searches the old lib dir.
You renamed the directory of the upgrade / copied the Sage tree to a new directory...
Could you temporarily rename the 4.5.3 directory and rerun ./sage b
(after again touching Cython files)?
(I assume /Applications/sage_builds/sage4.5.3
still exists.)
comment:27 in reply to: ↑ 26 ; followup: ↓ 28 Changed 9 years ago by
Replying to leif:
You renamed the directory of the upgrade / copied the Sage tree to a new directory...
Yes, I copied it. I always do this so if the upgrade screws up, I still have a working copy of Sage.
Could you temporarily rename the 4.5.3 directory and rerun
./sage b
(after again touching Cython files)?
Okay, I did that. Here's part of the log from "./sage b". Note the warning, since I renamed the directory:
gcc L/Applications/sage_builds/sage4.5.3/local/lib bundle undefined dynamic_lookup build/temp.macosx10.6i3862.6/sage/rings/complex_double.o L/Applications/sage_builds/sage4.6.alpha0upgrade/local//lib lcsage lgsl lcblas latlas lpari lgmp lm lstdc++ lntl o build/lib.macosx10.6i3862.6/sage/rings/complex_double.so ld: warning: directory '/Applications/sage_builds/sage4.5.3/local/lib' following L not found Total time spent compiling C/C++ extensions: 9.04102396965 seconds. running install_lib copying build/lib.macosx10.6i3862.6/sage/rings/complex_double.so > /Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage/rings running install_egg_info Removing /Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage0.0.0py2.6.egginfo Writing /Applications/sage_builds/sage4.6.alpha0upgrade/local/lib/python2.6/sitepackages/sage0.0.0py2.6.egginfo
I still get the import error, unfortunately.
comment:28 in reply to: ↑ 27 Changed 9 years ago by
Replying to jhpalmieri:
I still get the import error, unfortunately.
Hopefully now from a different import?
comment:29 Changed 9 years ago by
Ah, if I touch libs/pari/gen.pxd and then do "./sage b", it starts without an error. That seems to clear up all of the dependencies.
comment:30 followup: ↓ 32 Changed 9 years ago by
So I think I need to delete the old libparigmp library, move the old Sage directory, touch
 devel/sage/sage/libs/cremona/homspace.pyx
 devel/sage/sage/libs/cremona/newforms.pyx
 devel/sage/sage/libs/mwrank/mwrank.pyx
 devel/sage/sage/libs/pari/gen.pxd
and then run "./sage b". Simple.
comment:31 Changed 9 years ago by
I still hate trac...
Hmmm, the preprocessor supports I
, unfortunately the linker not L
, so we have to modify the dumb Python default compiler settings to get rid of obsolete directories...
comment:32 in reply to: ↑ 30 Changed 9 years ago by
Replying to jhpalmieri:
So I think I need to delete the old libparigmp library, move the old Sage directory, touch
...
 devel/sage/sage/libs/pari/gen.pxd
The latter shouldn't be necessary.
Simple.
;) How many users will agree on that?
comment:33 Changed 9 years ago by
Also looks like a Python on Darwin bug; I have the opposite order of linker search directories.
comment:34 followup: ↓ 35 Changed 9 years ago by
The latter shouldn't be necessary.
I guess you're right.
Wouldn't it be easier for upgrading to see if libparigmp.dylib exists, and if so, delete it and then link libparigmp2.4.dylib to it?
By the way, on a linux box I see libparigmp.so.2 and libparigmp.so.2.3.5 lying around from the old install. They don't seem to cause any trouble, but should they be removed also?
comment:35 in reply to: ↑ 34 ; followup: ↓ 36 Changed 9 years ago by
Replying to jhpalmieri:
Wouldn't it be easier for upgrading to see if libparigmp.dylib exists, and if so, delete it and then link libparigmp2.4.dylib to it?
I was thinking of fixing this in general, not a specific workaround limited to updating to this release.
By the way, on a linux box I see libparigmp.so.2 and libparigmp.so.2.3.5 lying around from the old install. They don't seem to cause any trouble, but should they be removed also?
As I said, on Linux we seem to have the correct order of library search dirs, so if all necessary files actually get rebuilt, the old libs shouldn't cause problems. In fact, you can use both versions "at the same time" (on Linux), i.e. some Sage modules using the old, and some the new version. The Darwin loader doesn't support this, at least with how the modules are currently built on Darwin.
For the directory renaming issue (perhaps typical for upgrades, but not limited to):
distutils.sysconfig.get_config_vars()["LDFLAGS"]="" # remove potentially obsolete "L$SAGE_LOCAL/lib"
(To be added to devel/sage/setup.py
; doesn't hurt on normal installations where it is redundant anyway.)
comment:36 in reply to: ↑ 35 Changed 9 years ago by
Replying to leif:
distutils.sysconfig.get_config_vars()["LDFLAGS"]="" # remove potentially obsolete "L$SAGE_LOCAL/lib"
In theory... We have to recustomize the compiler.
comment:37 Changed 9 years ago by
I'm not sure where the 4.5.3 is coming from. If I do ./sage ipython
:
In [1]: import distutils.sysconfig In [2]: s=''.join([str(x) for x in distutils.sysconfig.get_config_vars().values()]) In [3]: s.find('4.5') Out[3]: 1
So the string '4.5' is not in any value of any variable listed by get_config_vars
. (By inspection it wasn't in LDFLAGS.) I'm assuming that running ./sage ipython
sets all of the variables the same way as during the ./sage b
process, but I suppose this could be wrong.
So where does 4.5.3 come from? Is there some file which stores it which needs to be rebuilt? I notice that devel/sage/module_list.pyc is old and seems to refer to the absolute path, but rebuilding it didn't help. Any other ideas?
comment:38 Changed 9 years ago by
I'm sorry, that's wrong, I was running it on the wrong machine. 4.5.3 appears in lots of places:
'BINDIR': '/Applications/sage_builds/sage4.5.3/local/bin', 'BINLIBDEST': '/Applications/sage_builds/sage4.5.3/local/lib/python2.6', 'BLDSHARED': 'gcc L/Applications/sage_builds/sage4.5.3/local/lib bundle undefined dynamic_lookup', 'CONFIG_ARGS': "'enableshared' 'prefix=/Applications/sage_builds/sage4.5.3/local' 'enableunicode=ucs4' 'disabletoolboxglue' 'CC=gcc' 'LDFLAGS=L/Applications/sage_builds/sage4.5.3/local/lib ' 'CPPFLAGS=I/Applications/sage_builds/sage4.5.3/local/include '", 'CONFINCLUDEDIR': '/Applications/sage_builds/sage4.5.3/local/include', 'CONFINCLUDEPY': '/Applications/sage_builds/sage4.5.3/local/include/python2.6', 'CPPFLAGS': 'I. IInclude I./Include I/Applications/sage_builds/sage4.5.3/local/include', 'DESTDIRS': '/Applications/sage_builds/sage4.5.3/local /Applications/sage_builds/sage4.5.3/local/lib /Applications/sage_builds/sage4.5.3/local/lib/python2.6 /Applications/sage_builds/sage4.5.3/local/lib/python2.6/libdynload', 'DESTLIB': '/Applications/sage_builds/sage4.5.3/local/lib/python2.6', 'DESTSHARED': '/Applications/sage_builds/sage4.5.3/local/lib/python2.6/libdynload' 'INCLDIRSTOMAKE': '/Applications/sage_builds/sage4.5.3/local/include /Applications/sage_builds/sage4.5.3/local/include /Applications/sage_builds/sage4.5.3/local/include/python2.6 /Applications/sage_builds/sage4.5.3/local/include/python2.6', 'INCLUDEDIR': '/Applications/sage_builds/sage4.5.3/local/include', 'INCLUDEPY': '/Applications/sage_builds/sage4.5.3/local/include/python2.6', 'LDFLAGS': 'L/Applications/sage_builds/sage4.5.3/local/lib', 'LDSHARED': 'gcc L/Applications/sage_builds/sage4.5.3/local/lib bundle undefined dynamic_lookup', 'LIBDEST': '/Applications/sage_builds/sage4.5.3/local/lib/python2.6' 'LIBDIR': '/Applications/sage_builds/sage4.5.3/local/lib' 'LIBP': '/Applications/sage_builds/sage4.5.3/local/lib/python2.6' 'LIBPL': '/Applications/sage_builds/sage4.5.3/local/lib/python2.6/config' 'MACHDESTLIB': '/Applications/sage_builds/sage4.5.3/local/lib/python2.6' 'MANDIR': '/Applications/sage_builds/sage4.5.3/local/share/man' 'PY_CFLAGS': 'fnostrictaliasing g O2 DNDEBUG g fwrapv O3 Wall Wstrictprototypes I. IInclude I./Include I/Applications/sage_builds/sage4.5.3/local/include DPy_BUILD_CORE' 'SCRIPTDIR': '/Applications/sage_builds/sage4.5.3/local/lib'
comment:39 Changed 9 years ago by
I can get rid of the second dir by adding the following line in devel/sage/setup.py
:
self.compiler.set_library_dirs([]) # may have contained obsolete ones self.compiler.link_shared_object( ...
But your LDSHARED
looks bad; mine is just
'gcc march=native O3 fnostrictaliasing fomitframepointer DHONORS_CFLAGS pthread shared'
or simply (the relevant part)
'gcc pthread shared'
comment:40 Changed 9 years ago by
You can also replace or modify the linker command (for shared libraries) in setup.py
by e.g.
self.compiler.linker_so=["gcc","shared","pthread"] # Linux self.compiler.link_shared_object( ...
In your case, perhaps just delete the second list element ("L/..."
).
Similar things have perhaps to be done for other commands and args / parameters.
comment:41 Changed 9 years ago by
Maybe doing the equivalent of export LDSHARED='gcc bundle undefined dynamic_lookup'
will do it. Actually running that in the shell, then touching a bunch of pyx files and typing "./sage b", produces a version of sage which starts up without an import error. It seems to use the correct command when building the Sage library files, and in distutils.sysconfig.customize_compiler, it says
if 'LDSHARED' in os.environ: ldshared = os.environ['LDSHARED']
I wish we knew why this is getting set wrong...
comment:42 in reply to: ↑ 18 Changed 9 years ago by
Replying to leif:
I consider the "
touch
issue" a bug inmodule_list.py
, since PARI is not directly used by those extension modules (but listed in theirlibraries
, and therefore gets recorded in the list of needed libraries).
I've opened #9914 to fix this; minimal patch up there, needs review.
(Note that these extension modules also did not get rebuilt because they don't [directly] depend on PARI, despite that fact linked against it. Unless one links with asneeded
, which isn't very portable, the  potentially later obsolete  PARI library unnecessarily gets recorded as a prerequisite for those extension modules.)
comment:43 Changed 9 years ago by
I have another possible data point. I upgraded to 4.6.alpha1 (not alpha0) from 4.5.3 on OS X 10.6, and all seems well, except for failing doctests in schemes/elliptic_curves/ell_rational_field.py
and libs/mwrank/interface.py
. Both errors are in mwrank.
I have an updated Pynac (which would be timeconsuming to revert) on this installation, which I suppose could have something to do with this. But this seems fairly unlikely to me, so I thought I'd ask if anyone had tried the new upgrade possibility and seen something similar.
comment:44 followup: ↓ 45 Changed 9 years ago by
I should point out that the errors look like the ones here, segmentation fault in Pari and all that. It's not the computer I'm on right now, so I won't laboriously type it all out.
For what it's worth, I get
sage t "devel/sage/sage/libs/mwrank/interface.py" The doctested process was killed by signal 4 [199.7 s] sage t "devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py" The doctested process was killed by signal 4 [337.5 s]
on OS X 10.4 with this same upgrade pattern, and without the new Pynac. Also curious.
comment:45 in reply to: ↑ 44 ; followups: ↓ 46 ↓ 53 Changed 9 years ago by
Replying to kcrisman:
I should point out that the errors look like the ones here, segmentation fault in Pari and all that. It's not the computer I'm on right now, so I won't laboriously type it all out.
For what it's worth, I get
sage t "devel/sage/sage/libs/mwrank/interface.py" The doctested process was killed by signal 4 [199.7 s] sage t "devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py" The doctested process was killed by signal 4 [337.5 s]
on OS X 10.4 with this same upgrade pattern, and without the new Pynac. Also curious.
Hmmm, not that surprising, except that signal 4 is "illegal instruction", not a segmentation fault (but perhaps Apple uses different numbers on Darwin 8).
Did you
 rebuild ECLIB (with
./sage f ...
) (depends on PARI)  rename or copy the 4.5.3 directory?
As mentioned above, three extension modules do not get rebuilt though they link against PARI (and depend on ECLIB).
In case you copied the directory to keep the 4.5.3 installation, the linker on Darwin will first search $SAGE_LOCAL/lib
of the old Sage installation, and therefore link against the wrong PARI library. You can export LDSHARED
to prevent this (see above).
I'm not sure if the setting differs on MacOS X 10.4, so you could do:
sage: import distutils.sysconfig sage: distutils.sysconfig.get_config_var("LDSHARED") ' (current setting) '
and set LDSHARED
to what you see except the first L...
(and export it).
Then force rebuilding ECLIB, touch the three Cython files listed above and do ./sage b
.
I  hate  trac ... 8 (once again just logged me off when replying s.t. my whole comment went to /dev/null)
comment:46 in reply to: ↑ 45 ; followup: ↓ 47 Changed 9 years ago by
Did you
 rebuild ECLIB (with
./sage f ...
) (depends on PARI) rename or copy the 4.5.3 directory?
Nope  like I said, it was a data point.
Then force rebuilding ECLIB, touch the three Cython files listed above and do
./sage b
.
I'll try this.
comment:47 in reply to: ↑ 46 Changed 9 years ago by
Then force rebuilding ECLIB, touch the three Cython files listed above and do
./sage b
.I'll try this.
Yup, this fixed it. I hope you figure out how to fix this before 4.6 is released! A lot of our clientele is likely to have precisely this platform.
comment:48 followup: ↓ 52 Changed 9 years ago by
KarlDieter, could you add another data point, the output of
distutils.sysconfig.get_config_var("LDSHARED")
on your MacOS X 10.4 box? (Just to make sure it doesn't differ much from the settings on 10.5 and 10.6.)
Btw, "illegal instruction" errors (signal 4) are also reasonable when the wrong PARI library is used, since memory might get corrupted and function pointers may point to some arbitrary location.
This upgrade problem isn't that hard to fix (since we now know the two rather unrelated causes), but I think I'll open a followup ticket for the necessary patches.
comment:49 in reply to: ↑ 11 ; followup: ↓ 50 Changed 9 years ago by
Replying to jhpalmieri:
The time stamps on pariport.h, paritype.h, and paripriv.h are all old, too.
Just for the record: paripriv.h
is a patched Sage version which is copied with p
on Darwin, but that's in general ok (though we don't preserve the file attributes, including the modification time, on others systems).
comment:50 in reply to: ↑ 49 ; followup: ↓ 51 Changed 9 years ago by
Replying to leif:
Replying to jhpalmieri:
The time stamps on pariport.h, paritype.h, and paripriv.h are all old, too.
Just for the record:
paripriv.h
is a patched Sage version which is copied withp
on Darwin, but that's in general ok (though we don't preserve the file attributes, including the modification time, on others systems).
The file paripriv.h
is also patched on Solaris.
Note William told me the file should be private to Pari (hence the "priv" in the name), so he is not surprised it needs patching for OS X and Solaris.
I don't actually understand what this file does, but I rather get the feeling it is a hack of some sort.
comment:51 in reply to: ↑ 50 Changed 9 years ago by
Replying to drkirkby:
The file
paripriv.h
is also patched on Solaris.
The patched version only avoids a single name clash on MacOS X and Solaris.
I don't actually understand what this file does, but I rather get the feeling it is a hack of some sort.
It defines more lowerlevel structures and functions of PARI that we use in sage/libs/pari/gen.pyx
, the Python/Cython? PARI library interface.
comment:52 in reply to: ↑ 48 Changed 9 years ago by
Replying to leif:
KarlDieter, could you add another data point, the output of
distutils.sysconfig.get_config_var("LDSHARED")on your MacOS X 10.4 box? (Just to make sure it doesn't differ much from the settings on 10.5 and 10.6.)
sage: import distutils sage: distutils.sysconfig.get_config_var("LDSHARED") 'gcc L/Users/crisman/Desktop/sage4.5.3/local/lib bundle undefined dynamic_lookup'
Incidentally, I already changed the name of that folder to sage4.6.alpha1, so that by itself is a little unsettling...
comment:53 in reply to: ↑ 45 Changed 9 years ago by
Replying to leif:
Replying to kcrisman:
I should point out that the errors look like the ones here, segmentation fault in Pari and all that. It's not the computer I'm on right now, so I won't laboriously type it all out.
For what it's worth, I get
sage t "devel/sage/sage/libs/mwrank/interface.py" The doctested process was killed by signal 4 [199.7 s] sage t "devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py" The doctested process was killed by signal 4 [337.5 s]
Ok, did everything right and
sage t "devel/sage/sage/libs/mwrank/interface.py" [50.8 s] sage t "devel/sage/sage/schemes/elliptic_curves/ell_rational_field.py" [279.7 s]  All tests passed!
Thanks!
Changed 9 years ago by
Sage library patch. Fixes the relevant extension module dependencies. Based on Sage 4.6.alpha1.
Changed 9 years ago by
New spkg/standard/deps
. Based on Sage 4.6.alpha1. (Not under revision control.)
comment:54 followups: ↓ 55 ↓ 59 Changed 9 years ago by
 Keywords upgrade update dependencies PARI NewPARI added
 Status changed from needs_info to needs_review
I've attached a few patches / files and their diffs that make upgrading from Sage < 4.6 (i.e. to the new PARI) work.
I think this is a general improvement (not limited to PARI upgrade), though for e.g. the GMP/MPIR 2.1.2 upgrade (see #8664), more dependencies (or some other mechanism) have to be added to module_list.py
to properly rebuild the Sage library (i.e. all extension modules that depend on MPIR). Sage packages depending on an upgraded spkg will now get rebuilt without the need to download unmodified "new" versions (with just the patch level bumped in order to get them rebuilt).
I'm setting this to "needs review", though I've not yet uploaded a patch to get around the specific Darwin linker problem (but I'll provide one later).
When doing an "inplace" upgrade (i.e. keeping the old directory name), the current patches should also fully work on MacOS X. A workaround to the linker problem (i.e. when the Sage to be upgraded is located in a new directory) is manually setting (and exporting) LDSHARED
to the output of distutils.sysconfig.get_config_var("LDSHARED")
with the second "word" (L...
) either dropped or replaced by L
immediately followed by $SAGE_ROOT/local/lib
(with $SAGE_ROOT
the actual directory name, not the environment variable; see also comments above for more details).
Unfortunately we'll have to set up a Sage package server (or a special directory on e.g. www.sagemath.org
) to "fully" test this, i.e. by really running sage upgrade
.
On the other hand, the changes are quite small such that they should easily be reviewed. The behavior can be tested by e.g. running make
with SAGE_UPGRADING
set to "yes", faking some spkg was new (to see that all dependent spkgs really get rebuilt) etc. .
One can also test it by doing a real upgrade from some vanilla version to 4.6.alpha1, after that applying the patch to module_list.py
and copying over the new spkg/install
and spkg/standard/deps
, then exporting SAGE_UPGRADE=yes
and running make
. Then everything should be properly [re]built.
comment:55 in reply to: ↑ 54 Changed 9 years ago by
Replying to leif:
Unfortunately we'll have to set up a Sage package server (or a special directory on e.g.
www.sagemath.org
) to "fully" test this, i.e. by really runningsage upgrade
.
I could probably do this.
comment:56 followup: ↓ 60 Changed 9 years ago by
 Status changed from needs_review to needs_work
Your spkg/install
file gives trouble:
cd spkg && ./install all 2>&1  tee a ../install.log ./install: line 90: syntax error near unexpected token `' ./install: line 90: `  ([ f "$SAGE_LOCAL/bin/sageupgrade" ] &&'
comment:57 Changed 9 years ago by
This is on a Gentoo Linux x86_64 system, with
GNU bash, version 3.2.39(1)release (x86_64pclinuxgnu) Copyright (C) 2007 Free Software Foundation, Inc.
comment:58 followup: ↓ 69 Changed 9 years ago by
I looks like lines 90 and 91 need a \
at the end of the line.
comment:59 in reply to: ↑ 54 Changed 9 years ago by
 Status changed from needs_work to needs_review
Replying to leif:
One can also test it by doing a real upgrade from some vanilla version to 4.6.alpha1, after that applying the patch to
module_list.py
and copying over the newspkg/install
andspkg/standard/deps
, then exportingSAGE_UPGRADE=yes
and runningmake
. Then everything should be properly [re]built.
s/SAGE_UPGRADE
/SAGE_UPGRADING
/
comment:60 in reply to: ↑ 56 Changed 9 years ago by
comment:61 followup: ↓ 62 Changed 9 years ago by
I created a Sage distribution for testing this.
Please test:
sage upgrade http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/
comment:62 in reply to: ↑ 61 ; followup: ↓ 63 Changed 9 years ago by
 Description modified (diff)
 Summary changed from upgrading from 4.5.3 to 4.6.alpha0 fails on OS X 10.6 to Upgrading from 4.5.3 to 4.6.alpha* can fail (not limited to MacOS X)
Replying to jdemeyer:
I created a Sage distribution for testing this.
Please test:
sage upgrade http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/
Thanks!
Upgrade path: http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/
On MacOS X, one should at the moment either do an "inplace" upgrade (without renaming the directory / copying the original installation) or follow the instructions given above (regarding LDSHARED
).
comment:63 in reply to: ↑ 62 Changed 9 years ago by
Replying to leif:
On MacOS X, one should at the moment either do an "inplace" upgrade (without renaming the directory / copying the original installation) or follow the instructions given above (regarding
LDSHARED
).
If one tests upgrading in a new directory (renamed or copied) on MacOS X, it should be suffient to do
export LDSHARED="gcc bundle undefined dynamic_lookup"
before running ./sage upgrade ...
(with the upgrade path provided by Jeroen).
comment:64 Changed 9 years ago by
 Description modified (diff)
comment:65 followup: ↓ 66 Changed 9 years ago by
As is often the case with upgrading, I'm puzzled by the logic here. How can any patches help an upgrade from 4.5.3 (for example) to 4.6?
 Upgrading won't affect files like
spkg/standard/deps
orspkg/install
as long as those files aren't tracked anywhere  see #9433.  Upgrading will change scripts like
sageupgrade
, but of course it has to be running the old versions during the upgrade process.
I can understand that patches to these files might help in future versions, but is there any way to deal with 4.5.3 to 4.6?
(Meanwhile, I'm building a vanilla 4.5.3 to test the new upgrade path.)
comment:66 in reply to: ↑ 65 Changed 9 years ago by
Replying to jhpalmieri:
As is often the case with upgrading, I'm puzzled by the logic here. How can any patches help an upgrade from 4.5.3 (for example) to 4.6?
 Upgrading won't affect files like
spkg/standard/deps
orspkg/install
as long as those files aren't tracked anywhere  see #9433.
sageupgrade.py
also copies these two files (cf. the pipestatus
issue with upgrading to 4.5[.1]).
 Upgrading will change scripts like
sageupgrade
, but of course it has to be running the old versions during the upgrade process.
The new spkg/install
is aware of that, i.e. deals with an old sageupgrade
, too. (See comments in the patch to the former.)
I can understand that patches to these files might help in future versions, but is there any way to deal with 4.5.3 to 4.6?
The patches are intended to especially deal with this (and should ease future upgrades as well).
(Meanwhile, I'm building a vanilla 4.5.3 to test the new upgrade path.)
Fine. I've copied a 4.5.3 installation (of course^{TM} first running out of disk space) on Ubuntu 9.04 x86 and am currently running the upgrade.
Note that when teeing the output it appears to hang, since the user is prompted, but the output isn't flushed. (One has to type "y" and hit return to start upgrading.) I'll open a ticket for that.
comment:67 Changed 9 years ago by
Ooops, it's not sageupgrade.py
, its name is sageupdate
(a Python script though).
comment:68 followup: ↓ 70 Changed 9 years ago by
Ouch!
Jeroen, you forgot to put the new spkg/install
into the upgrade path.
(http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/spkg/install is still the old one, which doesn't work.)
comment:69 in reply to: ↑ 58 Changed 9 years ago by
Replying to jdemeyer:
I looks like lines 90 and 91 need a
\
at the end of the line.
I shouldn't have moved the 
to the next line (which I later found more readable). ;)
The \
currently on line 90 (following &&
) is superfluous, at least for POSIXconformant shells.
comment:70 in reply to: ↑ 68 Changed 9 years ago by
Replying to leif:
Ouch!
Jeroen, you forgot to put the new
spkg/install
into the upgrade path.(http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/spkg/install is still the old one, which doesn't work.)
Should be fixed (let's hope I didn't mess up anything else).
comment:71 Changed 9 years ago by
Hmmm, this is really odd:
Since the sage_scripts
spkg has been updated, and is part of $(BASE)
, and all standard packages depend on $(BASE)
, all packages were rebuilt during upgrade.
(This is "correct", but except for the number of packages that have to be downloaded, this isn't better than rebuilding the new Sage version from source. Unfortunately, for this release. I wonder if we can improve spkg/standard/deps
, or avoid updating sage_scripts
[to often] in the future.)
comment:72 Changed 9 years ago by
Which packages do really depend on sage_scripts
?
(I currently have no idea, except perhaps those depending on Python? Fortran?)
comment:73 followup: ↓ 74 Changed 9 years ago by
First, after doing
$ export LDSHARED="gcc bundle undefined dynamic_lookup" $ ./sage upgrade ...
Sage starts without segfaulting. However, it wasn't totally successful because eclib didn't get rebuilt (nor did most of the packages). Every log file gets touched, typically with a message like sage: eclib20100711 is already installed
, but that's it. It looks to me as though the upgrade path still doesn't have the right version of "install", either in SAGE_ROOT/spkg or in the scripts spkg (which I don't think matters for upgrading).
Second, of course every package depends on sage_scripts because the script sagespkg (for example) must be present. But for upgrading, I don't know which ones really might depend on changes made to it.
comment:74 in reply to: ↑ 73 ; followup: ↓ 77 Changed 9 years ago by
Replying to jhpalmieri:
[...] it wasn't totally successful because eclib didn't get rebuilt (nor did most of the packages). Every log file gets touched, typically with a message like
sage: eclib20100711 is already installed
, but that's it. It looks to me as though the upgrade path still doesn't have the right version of "install", either in SAGE_ROOT/spkg or in the scripts spkg (which I don't think matters for upgrading).
Hmmm, did you upgrade to early? Or a cache issue? Worked for me (see above, the machine was completely "clean", i.e. lacking any new version of spkg/install
, and that got properly updated by sageupdate
.
Second, of course every package depends on sage_scripts because the script sagespkg (for example) must be present.
But a copy of that is already present (in spkg/base/
), so it doesn't have to be extracted from an spkg, and is just copied over to local/bin
(and later overwritten by the one from sage_scripts
).
But for upgrading, I don't know which ones really might depend on changes made to it.
I rather thought of dependencies on other scripts. I intentionally did not change sagespkg
. ;)
comment:75 Changed 9 years ago by
The copying is done in spkg/base/dir0.1install
:
... mymkdir "../local/bin" mymkdir "../local/include" mymkdir "../tmp/" mymkdir "$BUILD" mymkdir "installed/" cp base/sage* ../local/bin/ ...
comment:76 Changed 9 years ago by
... and the base packages are of course not installed with sagespkg
:
######################################## # Building the base system ######################################## $(INST)/$(DIR): $(INSTALL) "base/$(DIR)install 2>&1" "tee a $(SAGE_LOGS)/$(DIR).log"
comment:77 in reply to: ↑ 74 Changed 9 years ago by
Replying to leif:
I rather thought of dependencies on other scripts. I intentionally did not change
sagespkg
. ;)
An example is the (Pythonrelated) sagemake_relative
, but this could be run once at the end. (Or [also] integrated into sagespkg
, as suggested by Dave elsewhere.)
comment:78 followup: ↓ 79 Changed 9 years ago by
Hmmm, did you upgrade to early?
The file http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/spkg/install is still the old one. Or maybe with the activity on sage.math (with William working on /home, etc.), it got changed back to the old one?
comment:79 in reply to: ↑ 78 Changed 9 years ago by
Replying to jhpalmieri:
Hmmm, did you upgrade to early?
The file http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/spkg/install is still the old one. Or maybe with the activity on sage.math (with William working on /home, etc.), it got changed back to the old one?
That's a total mess. It's not still, it's again the old one!
Hopefully trac isn't affected by such...
I only wonder if spkg/install
gets somehow again overwritten during the upgrade process, since after the upgrade, I again have the old version, though I verified the new one was downloaded in the first place (and otherwise I wouldn't have run into the rebuild all issue; sagespkg
was definitely called with f
).
Perhaps it (i.e. the old version) got later again downloaded when doing the Doublechecking....
And perhaps William should follow Dave and enable the ZIL (on an SSD).
comment:80 followup: ↓ 81 Changed 9 years ago by
From sagesage
:
if [ "$1" = 'upgrade' o "$1" = "upgrade" ]; then # People often move the Sage install right before doing the upgrade, so it's # important to fix any path hardcoding issues first, or certain library # links will fail. "$SAGE_ROOT/local/bin/"sagelocation # Do it twice since when installing sagescripts and a running # script changes, it gets confused and exits with an error. # Running again (with the script replaced) then fixes the problem. # Run from a temporary copy of sagesage shift sageupgrade "$@" if [ $? = 2 ]; then # this exit codes means the user elected not to do the upgrade at all. exit $? fi echo "Double checking that all packages have been installed." sageupgrade "$@" exit $? fi
But sageupdate
won't download spkg/install
twice if "No new spkgs" are available, which should be the case after a successful (first) upgrade.
So it must get overwritten from somewhere else...
comment:81 in reply to: ↑ 80 ; followup: ↓ 86 Changed 9 years ago by
Replying to leif:
So it must get overwritten from somewhere else...
Yep, it's overwritten in sage_scripts*
's spkginstall
, and Jeroen (also) forgot to put the new one into the sage_scripts
spkg, s.t. after the upgrade, the old one is back.
(deps
and sageupgrade
are ok.)
comment:82 followup: ↓ 87 Changed 9 years ago by
I've successfully built and tested 4.6.alpha1 (from scratch) with a modified deps
file where only the Sage library spkg depends on the Sage scripts, with 32 jobs on an already 50% loaded system.
So as I expected, adding the scripts to $(BASE)
is obsolete.
I'll upload a ...deps.v2
later, which then avoids rebuilding all packages on every upgrade.
comment:83 Changed 9 years ago by
Apologies for the mess, I'm having a look what's going on...
comment:84 Changed 9 years ago by
Could it be that spkg/install
is overwritten by make
? I've patched spkg/install
and then built Sage.
comment:85 Changed 9 years ago by
Yes, make
overwrites spkg/install
some time in the very beginning of the installation. Anybody knows where this spkg/install
comes from?
comment:86 in reply to: ↑ 81 Changed 9 years ago by
comment:87 in reply to: ↑ 82 ; followup: ↓ 95 Changed 9 years ago by
Replying to leif:
I've successfully built and tested 4.6.alpha1 (from scratch) with a modified
deps
file where only the Sage library spkg depends on the Sage scripts, with 32 jobs on an already 50% loaded system.So as I expected, adding the scripts to
$(BASE)
is obsolete.
I added the scripts to $(BASE)
during the reorganization of deps
at #8306, because of the problem mentioned in this comment. This may well have been overkill.
I'll upload a
...deps.v2
later, which then avoids rebuilding all packages on every upgrade.
comment:88 Changed 9 years ago by
This morning, the upgrade procedure isn't working. I'm getting this in the termcap install log (?!), after the new sage_scripts has been installed successfully:
ar rc libtermcap.a termcap.o tparam.o version.o ranlib libtermcap.a /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install c m 644 libtermcap.a /Applications/sage_builds/sage4.6.alpha1upgrade/local/lib/libtermcap.a Creating pipestatus. cp: base/sage*: No such file or directory cp: base/testcc.sh: No such file or directory cp: base/testcxx.sh: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 105: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 108: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 111: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 120: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 123: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 126: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 129: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 132: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 135: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 138: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 141: standard/newest_version: No such file or directory /Applications/sage_builds/sage4.6.alpha1upgrade/local/bin/install: line 144: standard/newest_version: No such file or directory Error determining package name using spkg/standard/newest_version script. make[1]: *** [install] Error 1
Looks like a directory is not set correctly, because for example "install" is being run from local/bin/ rather than from spkg/.
comment:89 followup: ↓ 93 Changed 9 years ago by
LOL, we should in any case rename our install
which comes from sage_scripts
and is first copied to $SAGE_LOCAL/bin
(which is in the path!).
So it happened that the scripts spkg got installed during libtermcap
s installation / configure
, and that found our install
as a BSDcompatible install.
I'm happy removing sage_scripts
from $(BASE)
also solves this! :)
comment:90 Changed 9 years ago by
(Or libtermcap
simply ran the first install
[currently] in the path, which happened to be ours.)
I don't think testing with the upgrade (test) path currently makes sense, not to mention the filesystem trouble.
comment:91 followup: ↓ 94 Changed 9 years ago by
In any case, I think I fixed the issues with spkg/install
in my upgrade path
http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/
comment:92 Changed 9 years ago by
I've long since thought that we need a way of stopping people upgrade from incomatible versions. One stratergy might be to only allow upgrades of the same major version, then ensure that incomatible changes are not permitted in the same version.
I've personally given up tryig to use the upgrade option.
Dave
comment:93 in reply to: ↑ 89 Changed 9 years ago by
Replying to leif:
I'm happy removing
sage_scripts
from$(BASE)
also solves this! :)
That's not really true, but we definitely need a new sage_scripts
spkg.
I'll provide one later, together with a modified deps
.
@Dave: Nice attitude; I don't think many users will agree with you. If we can make upgrading work, we should IMHO do it.
comment:94 in reply to: ↑ 91 ; followup: ↓ 100 Changed 9 years ago by
Replying to jdemeyer:
In any case, I think I fixed the issues with
spkg/install
in my upgrade path http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/
Well, spkg/install
and spkg/standard/deps
are current again, but you've checked the (also current) install
in (s.t. it's now in the Sage scripts repo, and also ends up in $SAGE_ROOT/local/bin
where the scripts repo of the installation lives):
leif@quadriga:~/tmp/sage_scripts4.6.upgradetest_alpha1$ hg log v install changeset: 1582:876225f0dec8 tag: 4.6.upgradetest_alpha1 user: Jeroen Demeyer <jdemeyer@cage.ugent.be> date: Sat Sep 25 11:32:06 2010 +0200 files: install description: #9896: new spkg/install leif@quadriga:~/tmp/sage_scripts4.6.upgradetest_alpha1$
(The file should be in .hgignore
.)
I don't think the instance in the sage_scripts
spkg should be copied over spkg/install
during that spkg's installation; if at all (see below), we should do that after the running instance of spkg/install
has terminated, i.e. from the scripts that start it (sageupgrade
and the toplevel Makefile, perhaps some other scripts).
But in principle we don't have to copy it at all; we should just make sure that both are the same. If that's not the case, something went very wrong. This is true for both upgrades and builds from scratch.
comment:95 in reply to: ↑ 87 ; followup: ↓ 99 Changed 9 years ago by
Replying to mpatel:
Replying to leif:
So as I expected, adding the scripts to
$(BASE)
is obsolete.I added the scripts to
$(BASE)
during the reorganization ofdeps
at #8306, because of the problem mentioned in this comment. This may well have been overkill.
LOL (again), "good catch". That just happened because some !"#$%& decided to put the Rpy package into R's spkg and recursively call sagespkg
from R's spkginstall
. Perhaps #9906 should be a blocker... ;)
sagespkg
is copied over to $SAGE_LOCAL/bin
early, in dir0.1install
(and $SAGE_ROOT/sage
is also present), but not $SAGE_LOCAL/bin/sagesage
:
... echo "Now install rpy" cd "$CUR" RPY_VER=rpy22.0.8 sage f "$RPY_VER".spkg if [ ! f "$SAGE_ROOT"/spkg/installed/"$RPY_VER" ]; then echo "Error installing rpy." exit 1 fi ...
(From R's spkginstall
. If we as a first step call sagespkg
there directly, the error from #8306 won't happen.)
comment:96 followup: ↓ 97 Changed 9 years ago by
The programs "sagedownload_package", "sagelatestonlinepackage", "sagebuilddebian" could conceivably be called by sagespkg during installation, but they shouldn't for any standard packages. The script "sagecheck64" is called by sageenv, so perhaps it should be added to spkg/base?
The sagetex package should depend on the scripts package, since its spkgcheck file runs Sage, and so relies on the presence of the script sagesage.
comment:97 in reply to: ↑ 96 Changed 9 years ago by
Replying to jhpalmieri:
The programs "sagedownload_package", "sagelatestonlinepackage", "sagebuilddebian" could conceivably be called by sagespkg during installation, but they shouldn't for any standard packages.
Hopefully. ;)
The script "sagecheck64" is called by sageenv, so perhaps it should be added to spkg/base?
If we keep it at all (we already had that discussion), it should be and certainly should have earlier been included in base/
.
The sagetex package should depend on the scripts package, since its spkgcheck file runs Sage, and so relies on the presence of the script sagesage.
I intended to make the Sage library depend on the Sage scripts; sagetex
of course (also) depends on the former.
comment:98 Changed 9 years ago by
Analogous to SAGE_UPGRADING
, we should perhaps set SAGE_BUILDING
(or SAGE_IN_BUILD
) to "yes" to prevent undesired behavior like downloading in scripts.
comment:99 in reply to: ↑ 95 Changed 9 years ago by
comment:100 in reply to: ↑ 94 ; followup: ↓ 101 Changed 9 years ago by
Replying to leif:
Well,
spkg/install
andspkg/standard/deps
are current again, but you've checked the (also current)install
in (s.t. it's now in the Sage scripts repo, and also ends up in$SAGE_ROOT/local/bin
where the scripts repo of the installation lives):
But why is it copied to $SAGE_ROOT/local/bin
? Surely, putting the file under revision control should not have that as consequence?
comment:101 in reply to: ↑ 100 ; followup: ↓ 102 Changed 9 years ago by
Replying to jdemeyer:
Replying to leif:
Well,
spkg/install
andspkg/standard/deps
are current again, but you've checked the (also current)install
in (s.t. it's now in the Sage scripts repo, and also ends up in$SAGE_ROOT/local/bin
where the scripts repo of the installation lives):But why is it copied to
$SAGE_ROOT/local/bin
? Surely, putting the file under revision control should not have that as consequence?
sage_scripts*.spkg
contains the local/bin/.hg
repository (at the top level), and only that. If during installation of the spkg a repository already exists in $SAGE_LOCAL/bin
, it gets synchronized from that, so any file checked into the spkg's repo will be "copied" to $SAGE_LOCAL/bin
. Other files in the spkg's toplevel directory (i.e., in .hgignore
) won't.
It would perhaps be less confusing if that spkg had the same structure as almost all others, i.e. the files to be installed in src/
(including the local/bin
repo), and the files that manage the installation in the toplevel directory, sage_scripts*/
, along with their own, separate, Mercurial repository.
comment:102 in reply to: ↑ 101 ; followup: ↓ 103 Changed 9 years ago by
Replying to leif:
Replying to jdemeyer:
Replying to leif:
Well,
spkg/install
andspkg/standard/deps
are current again, but you've checked the (also current)install
in (s.t. it's now in the Sage scripts repo, and also ends up in$SAGE_ROOT/local/bin
where the scripts repo of the installation lives):But why is it copied to
$SAGE_ROOT/local/bin
? Surely, putting the file under revision control should not have that as consequence?
sage_scripts*.spkg
contains thelocal/bin/.hg
repository (at the top level), and only that. If during installation of the spkg a repository already exists in$SAGE_LOCAL/bin
, it gets synchronized from that, so any file checked into the spkg's repo will be "copied" to$SAGE_LOCAL/bin
. Other files in the spkg's toplevel directory (i.e., in.hgignore
) won't.
So, this means that install
should be put in .hgignore
, right?
It would perhaps be less confusing if that spkg had the same structure as almost all others, i.e. the files to be installed in
src/
(including thelocal/bin
repo), and the files that manage the installation in the toplevel directory,sage_scripts*/
, along with their own, separate, Mercurial repository.
Any volunteers to do this? :)
comment:103 in reply to: ↑ 102 ; followup: ↓ 104 Changed 9 years ago by
Replying to jdemeyer:
So, this means that
install
should be put in.hgignore
, right?
Yep. (Or one could hg rename
it to something else, s.t. it doesn't get confused with a BSD install
.)
It would perhaps be less confusing if that spkg had the same structure as almost all others, i.e. the files to be installed in
src/
(including thelocal/bin
repo), and the files that manage the installation in the toplevel directory,sage_scripts*/
, along with their own, separate, Mercurial repository.Any volunteers to do this? :)
You? But that should be done after this ticket and especially #9433, which adds a new root repository (and deals with files like install
currently not under revision control), have been merged.
comment:104 in reply to: ↑ 103 Changed 9 years ago by
Replying to leif:
Replying to jdemeyer:
So, this means that
install
should be put in.hgignore
, right?Yep. (Or one could
hg rename
it to something else, s.t. it doesn't get confused with a BSDinstall
.)
P.S.: In case you rename it, if its name starts with sage
, it will also be copied during an install/build from scratch (but then also wouldn't be confused with some system tool).
Changed 9 years ago by
Improved new spkg/standard/deps
. Based on Sage 4.6.alpha1. (Not under revision control.)
Changed 9 years ago by
Improved new spkg/install
. Based on Sage 4.6.alpha1. (Not under revision control.)
comment:105 Changed 9 years ago by
Updated upgrade path: http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha1/
comment:106 Changed 9 years ago by
 Description modified (diff)
comment:107 followup: ↓ 108 Changed 9 years ago by
Upgraded succesfully from 4.5.3 on a Mac OS X 10.4 PPC system.
comment:108 in reply to: ↑ 107 Changed 9 years ago by
Replying to jdemeyer:
Upgraded succesfully from 4.5.3 on a Mac OS X 10.4 PPC system.
I did so on Ubuntu 9.04 x86 (inplace), and on Ubuntu 10.04 x86_64 (in a renamed directory), too.
ptestlong
passed all tests, but Sphinx raises an exception related to linear_programming
on both systems:
... sphinxbuild b html d /home/leif/Sage/sage4.5.3forv2bupgraded/devel/sage/doc/output/doctrees/en/constructions /home/leif/Sage/sage4.5.3forv2bupgraded/devel/sage/doc/en/constructions /home/leif/Sage/sage4.5.3forv2bupgraded/devel/sage/doc/output/html/en/constructions Running Sphinx v0.6.3 loading pickled environment... done building [html]: targets for 18 source files that are out of date updating environment: [config changed] 17 added, 0 changed, 1 removed reading sources... [ 5%] algebraic_geometry reading sources... [ 11%] calculus reading sources... [ 17%] contributions reading sources... [ 23%] elliptic_curves reading sources... [ 29%] graph_theory reading sources... [ 35%] groups reading sources... [ 41%] index reading sources... [ 47%] interface_issues reading sources... [ 52%] linear_algebra reading sources... [ 58%] linear_codes reading sources... [ 64%] modular_forms reading sources... [ 70%] number_fields reading sources... [ 76%] number_theory reading sources... [ 82%] plotting reading sources... [ 88%] polynomials reading sources... [ 94%] rep_theory reading sources... [100%] rings looking for nowoutdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 5%] algebraic_geometry writing output... [ 11%] calculus writing output... [ 16%] contributions writing output... [ 22%] elliptic_curves writing output... [ 27%] graph_theory writing output... [ 33%] groups writing output... [ 38%] index writing output... [ 44%] interface_issues writing output... [ 50%] linear_algebra writing output... [ 55%] linear_codes writing output... [ 61%] linear_programming Exception occurred: File "/home/leif/Sage/sage4.5.3forv2bupgraded/local/lib/python2.6/sitepackages/Sphinx0.6.3py2.6.egg/sphinx/environment.py", line 934, in get_toc_for toc = self.tocs[docname].deepcopy() KeyError: 'linear_programming' The full traceback has been saved in /tmp/sphinxerrBbYhGC.log, if you want to report the issue to the author. Please also report this if it was a user error, so that a better error message can be provided next time. Send reports to sphinxdev@googlegroups.com. Thanks! Build finished. The built documents can be found in /home/leif/Sage/sage4.5.3forv2bupgraded/devel/sage/doc/output/html/en/constructions ...
After removing the doctrees and rebuilding the documentation, this doesn't happen; linear_programming
had been moved from Constructions to the Thematic Tutorials. (Note that Sage completely ignores any Sphinx errors, but that's just another bug.)
comment:109 followup: ↓ 112 Changed 9 years ago by
Btw, if somebody reviewed #10016 (and that got merged into Sage 4.6), we could drop the dependency of R on sage_scripts
, which would further decrease the number of packages that have to be rebuilt during an upgrade.
(The sage_scripts
spkg currently "changes" in any new Sage version, which is suboptimal anyway.)
comment:110 Changed 9 years ago by
 Description modified (diff)
New upgrade path based on sage4.6.alpha2: http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha2/
comment:111 followup: ↓ 114 Changed 9 years ago by
I'm confused again. On my mac, it seems like
$ export LDSHARED="gcc bundle undefined dynamic_lookup"
solves the problem: I did this and then upgraded from 4.5.3 to 4.6.alpha3, and did not have the reported problem and all tests pass in sage/libs/pari. So do we need the various patches? They may be good ideas, but are they necessary for this ticket? (I have only seen a problem on OS X, so I can't easily test what works and what doesn't on other systems.)
Also, do we need to advertise the need to set LDSHARED like this? Or can we set it automatically during the upgrade process?
comment:112 in reply to: ↑ 109 ; followup: ↓ 113 Changed 9 years ago by
comment:113 in reply to: ↑ 112 ; followup: ↓ 115 Changed 9 years ago by
Replying to mpatel:
Replying to leif:
Btw, if somebody reviewed #10016 (and that got merged into Sage 4.6), we could drop the dependency of R on
sage_scripts
, which would further decrease the number of packages that have to be rebuilt during an upgrade.With #10016 merged into 4.6.alpha2, should we update
deps
?
Yes, we can... ;)
(The modifications are already all in, but currently commented out, including the additions / changes we need once RPy becomes a standalone spkg. I can perhaps upload v3 versions tomorrow, or otherwise feel free to do it.)
comment:114 in reply to: ↑ 111 Changed 9 years ago by
Replying to jhpalmieri:
I'm confused again. On my mac, it seems like
$ export LDSHARED="gcc bundle undefined dynamic_lookup"
solves the problem: I did this and then upgraded from 4.5.3 to 4.6.alpha3, and did not have the reported problem and all tests pass in sage/libs/pari.
ptestlong
? Some extension modules should still refer to the old PARI shared library, which can cause trouble. Did you do anything else except export LDSHARED=...
and ./sage upgrade /path/to/alpha3
?
So do we need the various patches?
Currently just four IIRC... ;)
They may be good ideas, but are they necessary for this ticket? (I have only seen a problem on OS X, so I can't easily test what works and what doesn't on other systems.)
While setting LDSHARED
is not necessary on systems other than MacOS X (at least as far as I know / on the supported platforms), the patches make upgrading more "reliable". (I personally had to play a little to make upgrading fail on my Linux boxes I must admit, but without the patches it definitely can fail. Also, we'd run into similar problems when it comes to upgrading e.g. MPIR; to make that work, we'll in addition have to add some more dependencies to module_list.py
.)
Also, do we need to advertise the need to set LDSHARED like this? Or can we set it automatically during the upgrade process?
I intended to do so, there are just (too) many ways how one could do this. ;) (Basically e.g. adding a few Darwinspecific lines to devel/sage/setup.py
, which is part of the sagex.y.z.spkg
, which "of course" gets updated upon every upgrade, regardless if there are any changes to the Sage library at all  besides version.py
which is or will become redundant anyway.)
comment:115 in reply to: ↑ 113 Changed 9 years ago by
 Status changed from needs_review to needs_work
Replying to leif:
(The modifications are already all in, but currently commented out, including the additions / changes we need once RPy becomes a standalone spkg. I can perhaps upload v3 versions tomorrow, or otherwise feel free to do it.)
Setting status to "needs_work" because of this comment.
comment:116 Changed 9 years ago by
 Work issues set to Perhaps rebase module_list patch on alpha3; remove sage_scripts from R's deps
Changed 9 years ago by
Improved new spkg/standard/deps
. Based on Sage 4.6.alpha3, removes sage_scripts
from R's deps. (Not under revision control.)
comment:117 Changed 9 years ago by
 Work issues changed from Perhaps rebase module_list patch on alpha3; remove sage_scripts from R's deps to Provide a patch (to setup.py) which fixes the Darwin linker issue.
Since #10016 has been merged into Sage 4.6.alpha2, I've attached a new version (v3) of spkg/standard/deps
, which just removes the dependency of R on sage_scripts
.
Here's a diff between v2b and v3:

trac_9896SAGE_ROOT__spkg__standard__deps.
old new 21 21 # Rather than making *all* standard packages depend on SAGE_SCRIPTS (which 22 22 # triggers the rebuild of *every* package on an upgrade), add SAGE_SCRIPTS 23 23 # to the dependencies of only those packages that rely on them. 24 # These are: 25 #  R until #10016 is merged (replacing "sage f ..." by a call to sagespkg), 26 # or until #9906 is merged (which moves the RPy spkg out of R's) 24 # These are (as of Sage 4.6.alpha3): 27 25 #  The Sage library, $(SAGE) 28 26 #  sagetex, but this in turn depends on $(SAGE) 29 27 … … 368 366 $(INST)/$(MAXIMA): $(BASE) $(INST)/$(ECL) 369 367 $(INSTALL) "$(SAGE_SPKG) $(MAXIMA) 2>&1" "tee a $(SAGE_LOGS)/$(MAXIMA).log" 370 368 371 # Until #10016 (or #9906) gets merged, R depends on SAGE_SCRIPTS, because it 372 # installs the contained RPy spkg with "sage f", which also requires sagesage: 373 $(INST)/$(R): $(BASE) $(INST)/$(SAGE_SCRIPTS) \ 374 $(INST)/$(PYTHON) $(INST)/$(ATLAS) $(INST)/$(ICONV) $(INST)/$(FORTRAN) 369 # Note that even with a separate RPy spkg (#9906), Sage's R will still depend on 370 # Python (but does no longer on SAGE_SCRIPTS, #10016): 371 $(INST)/$(R): $(BASE) $(INST)/$(PYTHON) $(INST)/$(ATLAS) $(INST)/$(ICONV) $(INST)/$(FORTRAN) 375 372 $(INSTALL) "$(SAGE_SPKG) $(R) 2>&1" "tee a $(SAGE_LOGS)/$(R).log" 376 # Note that even with a separate RPy spkg (#9906), Sage's R still depends on377 # Python (but no longer on SAGE_SCRIPTS, see above):378 # $(INST)/$(R): $(BASE) $(INST)/$(PYTHON) $(INST)/$(ATLAS) $(INST)/$(ICONV) $(INST)/$(FORTRAN)379 # $(INSTALL) "$(SAGE_SPKG) $(R) 2>&1" "tee a $(SAGE_LOGS)/$(R).log"380 373 381 374 # Needed when #9906 gets merged (moving RPy out of R's spkg): 382 375 # $(INST)/$(RPY): $(BASE) $(INST)/$(PYTHON) $(INST)/$(R)
(Note that neither spkg/install
nor spkg/standard/deps
have changed between Sage 4.6.alpha1 and 4.6.alpha3, so there's no new v3 of the former, and the diffs apply to alpha1...alpha3. Also, although devel/sage/module_list.py
has changed, the current patch here still applies to Sage 4.6.alpha3 without rejects.)
comment:118 Changed 9 years ago by
 Description modified (diff)
comment:119 Changed 9 years ago by
 Description modified (diff)
Changed 9 years ago by
Sage library patch. Fixes Darwin linker issue (in setup.py
). Based on Sage 4.6.alpha3.
comment:120 followup: ↓ 121 Changed 9 years ago by
 Description modified (diff)
 Status changed from needs_work to needs_review
 Work issues changed from Provide a patch (to setup.py) which fixes the Darwin linker issue. to Update upgrade path for testing
I've attached a patch that avoids manually setting LDSHARED
on MacOS X.
Of course the upgrade path has yet to be updated for testing this, but the patch can be reviewed.
comment:121 in reply to: ↑ 120 Changed 9 years ago by
Replying to leif:
Of course the upgrade path has yet to be updated for testing this, but the patch can be reviewed.
One can also (partially) test the new patch by (optionally renaming the Sage directory of an installation to be upgraded, then) running ./sage upgrade ...
with the current upgrade path, and after that applying the new patch to the Sage library, then running ./sage ba
and make ptestlong
or alike. (Running just ./sage b
would though show that the obsolete hardcoded directory gets replaced, of course only if SAGE_ROOT
had been changed. Another way is to put fake directories into LDSHARED
, e.g. by setting it to "gcc bundle L/foo/bar/ undefined dynamic_lookup Lbaz"
on MacOS X, or e.g. "gcc L/foo/bar pthread Lbaz/ shared"
on Linux.)
comment:122 followup: ↓ 123 Changed 9 years ago by
I am preparing a new upgrade path with the patches.
comment:123 in reply to: ↑ 122 ; followup: ↓ 124 Changed 9 years ago by
Replying to jdemeyer:
I am preparing a new upgrade path with the patches.
Thanks again. Do you keep the alpha2 upgrade path? Incidentally, I was just going to test that on another machine...
comment:124 in reply to: ↑ 123 Changed 9 years ago by
comment:125 followup: ↓ 126 Changed 9 years ago by
 Description modified (diff)
 Work issues Update upgrade path for testing deleted
New upgrade path: http://sage.math.washington.edu/home/jdemeyer/dist/sage4.6.upgradetest_alpha3/
Leif: the stuff about LDSHARED in the description might be outdated, can you fix it?
comment:126 in reply to: ↑ 125 Changed 9 years ago by
 Description modified (diff)
Replying to jdemeyer:
Leif: the stuff about LDSHARED in the description might be outdated, can you fix it?
Done. Thanks.
comment:127 followup: ↓ 128 Changed 9 years ago by
Just for the record: I again did a fresh build of Sage 4.5.3, renamed the directory and then upgraded to Sage 4.6.alpha2 with the (previous) test upgrade path (on Ubuntu 10.04 x86_64).
The upgrade failed in the first place, I then "successfully" ran make
(all new packages are present) and now I get lots of doctest errors (ptestlong
).
More to come (still running); currently testing the new alpha3 test upgrade path on another machine.
comment:128 in reply to: ↑ 127 Changed 9 years ago by
Replying to leif:
Just for the record: I again did a fresh build of Sage 4.5.3, renamed the directory and then upgraded to Sage 4.6.alpha2 with the (previous) test upgrade path (on Ubuntu 10.04 x86_64).
Meaning: Did anybody test the alpha2 upgrade path? (I don't see reports here.)
The upgrade failed in the first place, I then "successfully" ran
make
(all new packages are present) and now I get lots of doctest errors (ptestlong
).More to come (still running)
The following tests failed: sage t long devel/sage/sage/plot/misc.py # 4 doctests failed sage t long devel/sage/sage/plot/plot.py # 12 doctests failed
At least some end like this:
File "/home/leif/Sage/sage4.5.34.6.alpha2/local/lib/python/sitepackages/matplotlib/mathtext.py", line 658, in __init__ self._stix_fallback = StixFonts(*args, **kwargs) File "/home/leif/Sage/sage4.5.34.6.alpha2/local/lib/python/sitepackages/matplotlib/mathtext.py", line 900, in __init__ fullpath = findfont(name) File "/home/leif/Sage/sage4.5.34.6.alpha2/local/lib/python/sitepackages/matplotlib/font_manager.py", line 1306, in findfont if not os.path.exists(font): File "/home/leif/Sage/sage4.5.34.6.alpha2/local/lib/python2.6/genericpath.py", line 18, in exists st = os.stat(path) TypeError: coercing to Unicode: need string or buffer, dict found
comment:129 Changed 9 years ago by
 Description modified (diff)
Updated instructions for testing w.r.t. upgrades not performed inplace.
comment:130 Changed 9 years ago by
 Description modified (diff)
comment:131 Changed 9 years ago by
 Description modified (diff)
comment:132 Changed 9 years ago by
I've now successfully upgraded to Sage 4.6.alpha3 (from fresh builds of Sage 4.5.3) and (with the exception of the 32bit system) ptestlong
passed without errors on:
 Ubuntu 9.04 x86 (inplace; after upgrading I now also get #10041, which doesn't occur when building from scratch)
 Ubuntu 9.04 x86_64 (Sage installation moved before upgrading, with the workaround given in the description, i.e. also forcing a rebuild of freetype)
 Ubuntu 10.04 x86_64 (inplace)
I also "repaired" a failed upgrade from a moved Sage installation on the latter system by forcing reinstallation of freetype and running make
afterwards; ptestlong
then also passed without errors.
Currently, the installation of matplotlib 1.0.0 (included in alpha3, #9221) breaks older versions of matplotlib in other Sage installations; this is now fixed by #6235.
Deleting or renaming $HOME/.matplotlib/
(probably each time) before running an older (or after running the new) version of Sage also avoids that problem (cf. traceback above, "TypeError: coercing to Unicode: need string or buffer, dict found").
comment:133 followup: ↓ 137 Changed 9 years ago by
 Merged in set to sage4.6.rc0
Following Jeroen's suggestion on sagedevel, I'm planning to merge this ticket into 4.6.rc0.
comment:134 Changed 9 years ago by
Upgraded succesfully on a PPC Mac OS X 10.4 from sage4.5.3 to sage4.6.alpha3 and ptestlong
passes. This upgrade was done in place.
comment:135 Changed 9 years ago by
Upgraded a copied directory on OS X 10.6 successfully. Also an inplace upgrade on OpenSolaris, just to try a different platform and also to test that setting SAGE_ATLAS_LIB before the initial build wouldn't interfere with anything.
comment:136 Changed 9 years ago by
 Description modified (diff)
comment:137 in reply to: ↑ 133 ; followup: ↓ 138 Changed 9 years ago by
Replying to mpatel:
Following Jeroen's suggestion on sagedevel, I'm planning to merge this ticket into 4.6.rc0.
I'll merge all of the patches and files in the description's current "How to merge this ticket" section.
comment:138 in reply to: ↑ 137 ; followup: ↓ 139 Changed 9 years ago by
Replying to mpatel:
Replying to mpatel:
Following Jeroen's suggestion on sagedevel, I'm planning to merge this ticket into 4.6.rc0.
I'll merge all of the patches and files in the description's current "How to merge this ticket" section.
Thanks!
Upgrading from Sage 4.4.4 in a renamed directory (with the official rc0 upgrade path) fully worked for me on Ubuntu 9.04 x86_64 (Core2, gcc 4.3.3; parallel build with 16 jobs).
Quite surprisingly, even ptestlong
passed without any doctest errors. ;) (Cf. sagerelease.)
Despite that, I guess there are still missing dependencies in module_list.py
that will come into play when e.g. updating MPIR (#8664). (I primarily addressed upgrading to the new PARI on this ticket; more changes should IMHO be made on other / the respective spkg tickets.)
comment:139 in reply to: ↑ 138 Changed 9 years ago by
Replying to leif:
Despite that, I guess there are still missing dependencies in
module_list.py
that will come into play when e.g. updating MPIR (#8664). (I primarily addressed upgrading to the new PARI on this ticket; more changes should IMHO be made on other / the respective spkg tickets.)
NumPy and SciPy (#9808) are other candidates.
comment:140 Changed 9 years ago by
 Description modified (diff)
 Owner changed from GeorgSWeber to leif
comment:141 Changed 9 years ago by
Also successfully upgraded a copied Sage 4.5.3 installation to 4.6.rc0 on Ubuntu 9.04 x86; ptestlong
passed without errors (cf. sagerelease).
comment:142 followup: ↓ 143 Changed 9 years ago by
As far as reviewing goes, I'm happy with all of the patches except for two.
 /trac_9896fix_hardcoded_libdirs_in_extmod_linker_cmdsagelib.patch. This seems fine, but the messages like "Library dir found in dynamic linker command..." don't actually appear in any log (unless you pipe the whole thing through tee, perhaps, but I haven't tried this yet). (I'm assuming that, since I upgraded from 4.5.3 on OS X, the situation dealt with in the loop would occur, and I searched through all of the logs without finding this string.) I was hoping that they would appear in the sage4.6.rc0 log, but no. Is there anything to be done about this?
 trac_9896fix_extension_module_depssagelib.patch. I just don't know enough about the Sage build process and the dependencies to be able to review this well, and I don't have the time to learn about it right now. I'm hoping that someone else can do this.
comment:143 in reply to: ↑ 142 Changed 9 years ago by
Replying to jhpalmieri:
As far as reviewing goes, I'm happy with all of the patches except for two.
 /trac_9896fix_hardcoded_libdirs_in_extmod_linker_cmdsagelib.patch. This seems fine, but the messages like "Library dir found in dynamic linker command..." don't actually appear in any log (unless you pipe the whole thing through tee, perhaps, but I haven't tried this yet). (I'm assuming that, since I upgraded from 4.5.3 on OS X, the situation dealt with in the loop would occur, and I searched through all of the logs without finding this string.) I was hoping that they would appear in the sage4.6.rc0 log, but no. Is there anything to be done about this?
if ldso_cmd[i][:2] == "L": libdir = os.path.normpath(ldso_cmd[i][2:]) self.debug_print( "Library dir found in dynamic linker command: " + "\"%s\"" % libdir) if libdir != sage_libdir: self.compiler.warn( "Replacing library search directory in linker " + "command:\n \"%s\" > \"%s\"\n" % (libdir, sage_libdir)) ldso_cmd[i] = "L"+sage_libdir
No, that's intentional. self.debug_print()
only produces output if DISTUTILS_DEBUG
is set.
In contrast, self.compiler.warn()
always prints a message, so you should find "warning: Replacing library search directory ..." in the logs of the installations you had moved:
$ grep "^warning: " install.log
or
$ grep "^warning: Replacing" spkg/logs/sage*
should show these.
comment:144 Changed 9 years ago by
Oh, sorry, that's what I meant by "messages like ...". I don't see "Replacing library" in any log file, either. (I copied my sage4.5.3 directory to sage4.6.rc0upgrade and ran "./sage upgrade".)
comment:145 Changed 9 years ago by
Hmmm, what does
$ ./sage b 2>&1  grep A2 "^warning"
give (in a moved Sage installation)?
You could also do
$ env DISTUTILS_DEBUG=yes ./sage b
but that produces a lot of output.
comment:146 Changed 9 years ago by
grep A2
is a GNUism  it will not work with Sun's grep. It would be better to stick to only the options mandated by the POSIX specification on the OpenGroup? web site. But I can say for sure that would break on Solaris.
Dave
comment:147 followup: ↓ 148 Changed 9 years ago by
I don't think John has Sun's grep
installed on MacOS X... ;)
On topic again:
There are two reasons you (John) can't find such messages:
./sage upgrade
doesn't log toinstall.log
(I usedscript
to log what happened, also because of #10011.)
 There's a less obvious indirect dependency of Python on iconv (via GNUTLS, libgpg_error), so the Python spkg got rebuilt, too, which of course also updated the library search path of distutils.
comment:148 in reply to: ↑ 147 ; followups: ↓ 149 ↓ 152 Changed 9 years ago by
Replying to leif:
I don't think John has Sun's
grep
installed on MacOS X... ;)
I was just about to install it, but I guess I'll wait a bit now.
 There's a less obvious indirect dependency of Python on iconv (via GNUTLS, libgpg_error), so the Python spkg got rebuilt, too, which of course also updated the library search path of distutils.
The python spkg did get rebuilt. I'm trying again, first touching spkg/installed/iconv1.13.1.p3.
comment:149 in reply to: ↑ 148 ; followup: ↓ 150 Changed 9 years ago by
Replying to jhpalmieri:
Replying to leif:
I don't think John has Sun's
grep
installed on MacOS X... ;)I was just about to install it, but I guess I'll wait a bit now.
 There's a less obvious indirect dependency of Python on iconv (via GNUTLS, libgpg_error), so the Python spkg got rebuilt, too, which of course also updated the library search path of distutils.
The python spkg did get rebuilt. I'm trying again, first touching spkg/installed/iconv1.13.1.p3.
Note that I've updated the description on that (you have to run make build
afterwards to make that work).
comment:150 in reply to: ↑ 149 ; followup: ↓ 151 Changed 9 years ago by
Replying to leif:
Replying to jhpalmieri:
Replying to leif:
I don't think John has Sun's
grep
installed on MacOS X... ;)I was just about to install it, but I guess I'll wait a bit now.
 There's a less obvious indirect dependency of Python on iconv (via GNUTLS, libgpg_error), so the Python spkg got rebuilt, too, which of course also updated the library search path of distutils.
The python spkg did get rebuilt. I'm trying again, first touching spkg/installed/iconv1.13.1.p3.
Note that I've updated the description on that (you have to run
make build
afterwards to make that work).
Ooops, weird. That doesn't seem to be necessary... (And just touching the new iconv worked for me, i.e. e.g. Python did not get rebuilt.)
comment:151 in reply to: ↑ 150 Changed 9 years ago by
 Description modified (diff)
Replying to leif:
Ooops, weird. That doesn't seem to be necessary... (And just touching the new iconv worked for me, i.e. e.g. Python did not get rebuilt.)
Funny, that's because newest_version
doesn't inspect spkg/installed/*
, but e.g. spkg/standard/*.spkg
(and therefore make
concludes all is uptodate).
So it works the way I originally described.
comment:152 in reply to: ↑ 148 Changed 9 years ago by
Replying to jhpalmieri:
Replying to leif:
I don't think John has Sun's
grep
installed on MacOS X... ;)I was just about to install it, but I guess I'll wait a bit now.
Given the title title had the "(not limited to OS X)" I assumed this needed a solution to work on any platform. But I've not been following this ticket closely, so I'll shut up.
If John does manage to install Sun's grep on his OS X machine, let me know how. I might even buy a Mac then!
Dave
comment:153 followup: ↓ 168 Changed 9 years ago by
Okay, after touching iconv, I see the warning in the sage spkg log. (And this was on a machine where I didn't run "make build" before upgrading, as Leif says.)
Given the title title had the "(not limited to OS X)" I assumed this needed a solution to work on any platform. But I've not been following this ticket closely, so I'll shut up.
At that point, Leif was just suggesting something for me to try on one machine, a mac, to troubleshoot something, not as an actual solution to any problem. So it was a safe suggestion.
Anyway, I guess now I'm happy with all but one of the patches (trac_9896fix_extension_module_depssagelib.patch), and someone else will have to help with that.
comment:154 followup: ↓ 155 Changed 9 years ago by
Oh, on another OS X machine I did "touch .../iconv..." and then "make build" and then "sage upgrade ...", and then during the upgrade, the linbox spkg failed to install.
comment:155 in reply to: ↑ 154 Changed 9 years ago by
Replying to jhpalmieri:
Oh, on another OS X machine I did "touch .../iconv..." and then "make build" and then "sage upgrade ...", and then during the upgrade, the linbox spkg failed to install.
Details? Perhaps just once again a race condition?
(The make build
should be a nop, i.e. have no influence, unless the installation hadn't been uptodate before.)
comment:156 followup: ↓ 160 Changed 9 years ago by
The linbox log has messages like this:
/bin/sh ../../libtool tag=CXX mode=link g++ g fPIC I"/Applications/sage_builds/sage4.6.rc0X/local/include" I"/Applications/sage_builds/sage4.6.rc0X/local/include/linbox" L"/Applications/sage_builds/sage4.6.rc0X/local/lib" I/Applications/sage_builds/sage4.6.rc0X/spkg/build/linbox1.1.6.p3/src I/Applications/sage_builds/sage4.6.rc0X/spkg/build/linbox1.1.6.p3/src/linbox I/Applications/sage_builds/sage4.6.rc0X/local/include I/Applications/sage_builds/sage4.6.rc0X/local/include D__LINBOX_HAVE_CBLAS o libutil.la timer.lo error.lo commentator.lo debug.lo /usr/lib/libcblas.dylib L/Applications/sage_builds/sage4.6.rc0X/local/lib lgmpxx lgmp L/Applications/sage_builds/sage4.6.rc0X/local/lib lgivaro libtool: link: warning: library `/Applications/sage_builds/sage4.6.rc0X/local/lib/libgmpxx.la' was moved. grep: /Applications/sage_builds/sage4.5.3/local/lib/libgmp.la: No such file or directory sed: /Applications/sage_builds/sage4.5.3/local/lib/libgmp.la: No such file or directory libtool: link: `/Applications/sage_builds/sage4.5.3/local/lib/libgmp.la' is not a valid libtool archive make[4]: *** [libutil.la] Error 1 make[3]: *** [installrecursive] Error 1 make[2]: *** [installrecursive] Error 1 make[1]: *** [installrecursive] Error 1 Error installing linbox
comment:157 Changed 9 years ago by
Update: on one OS X 10.6 machine, after touching spkg/installed/iconv1.13.1.p3, it doesn't matter whether I run "make build" or not before upgrading: I get the above error with linbox either way. On another OS X 10.6 machine, I didn't run "make build" and it seemed to complete successfully; I haven't tried with "make build". I'll run doctests to see if it's really successful.
I don't know what's different about the two machines. Maybe the 4.5.3 build got corrupted on the first one somehow? I can try rebuilding 4.5.3 and doing it again...
comment:158 Changed 9 years ago by
 Description modified (diff)
comment:159 Changed 9 years ago by
 Description modified (diff)
comment:160 in reply to: ↑ 156 Changed 9 years ago by
Replying to jhpalmieri:
The linbox log has messages like this:
/bin/sh ../../libtool tag=CXX mode=link g++ g fPIC I"/Applications/sage_builds/sage4.6.rc0X/local/include" I"/Applications/sage_builds/sage4.6.rc0X/local/include/linbox" L"/Applications/sage_builds/sage4.6.rc0X/local/lib" I/Applications/sage_builds/sage4.6.rc0X/spkg/build/linbox1.1.6.p3/src I/Applications/sage_builds/sage4.6.rc0X/spkg/build/linbox1.1.6.p3/src/linbox I/Applications/sage_builds/sage4.6.rc0X/local/include I/Applications/sage_builds/sage4.6.rc0X/local/include D__LINBOX_HAVE_CBLAS o libutil.la timer.lo error.lo commentator.lo debug.lo /usr/lib/libcblas.dylib L/Applications/sage_builds/sage4.6.rc0X/local/lib lgmpxx lgmp L/Applications/sage_builds/sage4.6.rc0X/local/lib lgivaro libtool: link: warning: library `/Applications/sage_builds/sage4.6.rc0X/local/lib/libgmpxx.la' was moved. grep: /Applications/sage_builds/sage4.5.3/local/lib/libgmp.la: No such file or directory sed: /Applications/sage_builds/sage4.5.3/local/lib/libgmp.la: No such file or directory libtool: link: `/Applications/sage_builds/sage4.5.3/local/lib/libgmp.la' is not a valid libtool archive make[4]: *** [libutil.la] Error 1 make[3]: *** [installrecursive] Error 1 make[2]: *** [installrecursive] Error 1 make[1]: *** [installrecursive] Error 1 Error installing linbox
I think this should have been fixed by local/bin/sagelocation
's
def update_library_files(R): LIB = '%s/local/lib/'%os.path.abspath(SAGE_ROOT) # The .a files should be reranlib'd os.system('cd "%s"; ranlib *.a 1>/dev/null 2>/dev/null'%LIB) # The .la files hardcode path info. Fix this. for F in os.listdir(LIB): if F[3:] == ".la": G = open(LIB + F).read() i = G.find('libdir=') j = i+8 + G[i+8:].find("'") z = G[i+8:j].strip().strip("'") i = z.rfind('local/') if i != 1: z = z[:i] H = G.replace(z, os.path.abspath(SAGE_ROOT) + '/') open(LIB + F,'w').write(H)
which is (also) called from sage upgrade
(i.e. sagesage
) if the installation has (newly) moved. (I'm not sure how robust that code is, it's at least less readable.)
Did you perhaps interrupt this in the first run?
comment:161 followup: ↓ 162 Changed 9 years ago by
Ah, I see. The above code fixes just one instance of a hardcoded path in libgmpxx.la
, namely libdir=...
, but not:
# Libraries that this one depends upon. dependency_libs=' /home/leif/Sage/sage4.6.rc0pre1/local/lib/libgmp.la'
I just wonder why this doesn't cause trouble on the other system.
comment:162 in reply to: ↑ 161 Changed 9 years ago by
Replying to leif:
Ah, I see. The above code fixes just one instance of a hardcoded path in
libgmpxx.la
, namelylibdir=...
, but not:
# Libraries that this one depends upon. dependency_libs=' /home/leif/Sage/sage4.6.rc0pre1/local/lib/libgmp.la'
Not true. The above reads the old path from libdir='...'
, but then replaces all occurrences of that (i.e. the old $SAGE_ROOT
) by the new one. So perhaps really this was interrupted on the machine where LINBOX failed to build.
comment:163 followup: ↓ 164 Changed 9 years ago by
Did you perhaps interrupt this in the first run?
It's possible. In any case, I can't repeat it now.
comment:164 in reply to: ↑ 163 Changed 9 years ago by
Replying to jhpalmieri:
Did you perhaps interrupt this in the first run?
It's possible. In any case, I can't repeat it now.
It would in any case be better to trap SIGINT
/ KeyboardInterrupt
while doing sagelocation
, or make backup copies first.
Also, it would be helpful for such situations to
 log
$SAGE_ROOT
changes / movement (in a history file) for debugging or even to get the previous one,  perhaps log what changes
sagelocation
made (to some file, perhaps a summary on the screen),  log the whole upgrade process as we do for builds / spkg installations (I'd suggest
$SAGE_ROOT/upgrade.log
, but only after #10011 and #10157 have been merged).
Do you still have the broken installation? If so, you could
$ ls rtl local/lib/*.la # see which were changed last / when $ cat local/lib/libgmpxx.la # to see the wrong paths
(libtool's .la
files are plain text files.
comment:165 Changed 9 years ago by
$ ls rtl local/lib/*.la
The only difference between the broken one and the working one is that the two linbox files have been updated more recently in the working one, presumably when the linbox spkg was installed. There are plenty of .la files with the wrong path in the working version. The output from the working version:
rwxrxrx@ 1 palmieri admin 779 Feb 23 2008 local/lib/libgfortran.la* rwxrxrx 1 palmieri admin 975 Sep 24 08:23 local/lib/libpng12.la* rwxrxrx 1 palmieri admin 832 Sep 24 08:24 local/lib/libgc.la* rwxrxrx 1 palmieri admin 902 Sep 24 08:24 local/lib/libcord.la* rwxrxrx 1 palmieri admin 983 Sep 24 08:27 local/lib/libm4ri.la* rwxrxrx 1 palmieri admin 827 Sep 24 08:28 local/lib/libmpir.la* rwxrxrx 1 palmieri admin 897 Sep 24 08:28 local/lib/libmpirxx.la* rwxrxrx 1 palmieri admin 890 Sep 24 08:28 local/lib/libgmpxx.la* rwxrxrx 1 palmieri admin 821 Sep 24 08:28 local/lib/libgmp.la* rwxrxrx 1 palmieri admin 857 Sep 24 08:30 local/lib/libsqlite3.la* rwxrxrx 1 palmieri admin 887 Sep 24 08:31 local/lib/libgpgerror.la* rwxrxrx 1 palmieri admin 879 Sep 24 08:37 local/lib/libecm.la* rwxrxrx 1 palmieri admin 1066 Sep 24 08:38 local/lib/libmpfr.la* rwxrxrx 1 palmieri admin 980 Sep 24 08:42 local/lib/libgivaro.la* rwxrxrx 1 palmieri admin 1068 Sep 24 08:44 local/lib/libglpk.la* rwxrxrx 1 palmieri admin 852 Sep 24 08:44 local/lib/libmpfi.la* rwxrxrx 1 palmieri admin 982 Sep 24 08:55 local/lib/libgcrypt.la* rwxrxrx 1 palmieri admin 1023 Sep 24 09:01 local/lib/libfplll.la* rwxrxrx 1 palmieri admin 1053 Sep 24 09:01 local/lib/libopencdk.la* rwxrxrx 1 palmieri admin 1084 Sep 24 09:02 local/lib/libgnutls.la* rwxrxrx 1 palmieri admin 1272 Sep 24 09:02 local/lib/libgnutlsopenssl.la* rwxrxrx 1 palmieri admin 1321 Sep 24 09:02 local/lib/libgnutlsextra.la* rwxrxrx 1 palmieri admin 945 Oct 23 10:46 local/lib/libcdd.la* rwxrxrx 1 palmieri admin 1075 Oct 23 10:46 local/lib/libcddgmp.la* rwxrxrx 1 palmieri admin 876 Oct 23 10:53 local/lib/libfreetype.la* rwxrxrx 1 palmieri admin 1087 Oct 23 10:54 local/lib/libgd.la* rwxrxrx 1 palmieri admin 979 Oct 23 10:59 local/lib/libgslcblas.la* rwxrxrx 1 palmieri admin 951 Oct 23 10:59 local/lib/libgsl.la* rwxrxrx 1 palmieri admin 1044 Oct 23 11:02 local/lib/libpynac.la* rwxrxrx 1 palmieri admin 951 Oct 23 11:37 local/lib/libiml.la* rwxrxrx 1 palmieri admin 1236 Oct 23 11:41 local/lib/liblinboxsage.la* rwxrxrx 1 palmieri admin 1206 Oct 23 11:41 local/lib/liblinbox.la*
I think this is the difference, although I haven't tested it: I had a directory "/Applications/sage_builds/sage4.5.3". In the broken one, I copied this to another directory, sage4.6.rc0, and then I moved the original directory (so that any references to it would fail). When upgrading the working version, I left the old directory in place.
comment:166 Changed 9 years ago by
So it appears to be a bug in sagelocation
?
Can you track this further down on a followup ticket? Works for me on Linuces...
Perhaps copy all .la
files to a temporary directory, move Sage (and run ./sage c quit
to invoke sagelocation
), and then compare them.
comment:167 Changed 9 years ago by
Okay, the problem is this: if you build Sage but never run it, then the script sagelocation doesn't get run, so the file SAGE_ROOT/local/lib/sagelocation.txt doesn't get created. Then if you move or copy that directory, the file isn't there, so sagelocation thinks everything is okay, so it doesn't rewrite the .la files.
(This is despite the comment in sagelocation that the files in local/lib get written "during the build". This is also not platformspecific: I just built on sage.math, and there is no file sagelocation.txt until Sage gets run for the first time. I was also wondering why I wasn't seeing the message "The Sage install tree may have moved..." at the start of the upgrade, and this explains it.)
See #10162 for a followup; it's a oneliner.
comment:168 in reply to: ↑ 153 Changed 9 years ago by
 Reviewers set to John Palmieri
Replying to jhpalmieri:
Anyway, I guess now I'm happy with all but one of the patches (trac_9896fix_extension_module_depssagelib.patch), and someone else will have to help with that.
I'll try to review this later today.
comment:169 followup: ↓ 170 Changed 9 years ago by
 Cc cremona added
John Cremona, do you happen to see any problems in trac_9896fix_extension_module_depssagelib.patch?
comment:170 in reply to: ↑ 169 ; followup: ↓ 173 Changed 9 years ago by
Replying to mpatel:
John Cremona, do you happen to see any problems in trac_9896fix_extension_module_depssagelib.patch?
Thanks for asking. For the include files listed, I assume that someone has just gone through the relevant pyx files and listed which of my header files are actually used? I am not sure whether the point here is that (a) if some files are omitted from this list then the build will fail, or (b) if some are omitted then upgrading will not know to recompile something. If (a) then the test is just to see if Sage builds! If (b) I hardly think it matters since either all of eclib is built or none of it, surely?
It is quite possible that everything I have just said is complete nonsense. If so sorry.
About including the pari library: Leif explained this to some extent on sagedevel. I don't know (especially not what may or may not happen on cygwin) sp perhaps it is safer to leave it in?
If anyone ever has suggestions for improving the Makefiles for eclib I am always happy to receive them. They were created during SD6 by editing old Makefiles of my own which had been evolving over years, so there may well be stuff in there which should not be.
Short answer: no.
comment:171 Changed 9 years ago by
I think we need to list eclib headers for these modules, so that during an upgrade, if the eclib package is rebuilt, because eclib and/or a dependent package has changed, the modules are also rebuilt. Is this correct?
I see
$ cd sage4.6.rc0/devel/sage/sage/libs/mwrank $ grep "eclib/" *.c* *.h wrap.cc:#include "eclib/htconst.h" wrap.cc:#include "eclib/interface.h" wrap.h:#include "eclib/curve.h" wrap.h:#include "eclib/egr.h" wrap.h:#include "eclib/descent.h" wrap.h:#include "eclib/points.h" wrap.h:#include "eclib/isogs.h" wrap.h:#include "eclib/marith.h" wrap.h:EXTERN void two_descent_saturate(struct two_descent* t, long sat_bd); // = 1 for default set in eclib/src/qcurves/saturate.h (currently 100)
and
$ cd sage4.6.rc0/devel/sage/sage/libs/cremona $ grep "eclib/" *.cpp  grep v cdef homspace.cpp:#include "eclib/moddata.h" homspace.cpp:#include "eclib/symb.h" homspace.cpp:#include "eclib/cusp.h" homspace.cpp:#include "eclib/homspace.h" mat.cpp:#include "eclib/moddata.h" mat.cpp:#include "eclib/symb.h" mat.cpp:#include "eclib/cusp.h" mat.cpp:#include "eclib/homspace.h" newforms.cpp:#include "eclib/interface.h" newforms.cpp:#include "eclib/bigrat.h" newforms.cpp:#include "eclib/rat.h" newforms.cpp:#include "eclib/curve.h" newforms.cpp:#include "eclib/moddata.h" newforms.cpp:#include "eclib/symb.h" newforms.cpp:#include "eclib/cusp.h" newforms.cpp:#include "eclib/xsplit.h" newforms.cpp:#include "eclib/method.h" newforms.cpp:#include "eclib/oldforms.h" newforms.cpp:#include "eclib/homspace.h" newforms.cpp:#include "eclib/cperiods.h" newforms.cpp:#include "eclib/newforms.h"
For homspace
and mat
, do we need to mention in module_list.py
the eclib/
headers that aren't listed above?
comment:172 followup: ↓ 174 Changed 9 years ago by
I agree that these modules need to be rebuilt if eclib is rebuilt; but I don't see why that means that we have to list header files individually. Can't we make these modules depend on the spkg itself?
comment:173 in reply to: ↑ 170 Changed 9 years ago by
Replying to cremona:
Replying to mpatel:
John Cremona, do you happen to see any problems in trac_9896fix_extension_module_depssagelib.patch?
Thanks for asking. For the include files listed, I assume that someone has just gone through the relevant pyx files and listed which of my header files are actually used?
Exactly. I did that some weeks ago when debugging the original problem...
If any of these header files (to be precise, its modification time) changes, an extension module having it in its dependencies will get rebuilt. (The problem was this did not happen when ECLIB got rebuilt, such that these modules still used  or better: pulledin  the old PARI library, which resulted in segfaults or import / dynamic linker errors.)
Perhaps a little overkill (we just could rebuild all of these modules if any ECLIB header file changes), but as is may save some unnecessary rebuilds. ;)
About including the pari library: Leif explained this to some extent on sagedevel. I don't know (especially not what may or may not happen on cygwin) so perhaps it is safer to leave it in?
Well, I kept it for the moment (here; #9914 would remove the PARI library).
If anyone ever has suggestions for improving the Makefiles for eclib I am always happy to receive them. They were created during SD6 by editing old Makefiles of my own which had been evolving over years, so there may well be stuff in there which should not be.
Ok, I have some patched ECLIB spkg somewhere around. Perhaps needs some more work though.
comment:174 in reply to: ↑ 172 Changed 9 years ago by
Replying to cremona:
I agree that these modules need to be rebuilt if eclib is rebuilt; but I don't see why that means that we have to list header files individually. Can't we make these modules depend on the spkg itself?
The most generic way would be to make any extension module (explicitly) depend on the libraries it is linked to. (Though this certainly would also trigger unnecessary rebuilds, but is easy to implement and safe, assuming libraries change when there headers do.)
Robert B. wanted to improve Cython s.t. we get rid of most of module_list.py
(by using pragmas like clib ...
etc. in the Cython files), which I think would also handle the true dependencies properly.
So I considered my change more or less temporary, and didn't address the dependencies of other modules currently not causing trouble. (As mentioned earlier, upgrading e.g. MPIR (#8664) will require further changes, and unless we get an improved Cython until then, I'll implement the above strategy in setup.py
, but of course on another ticket. This one was at least originally meant to only or especially address the PARI upgrade, i.e. upgrading Sage to a version with the new PARI from one with the old.)
comment:175 Changed 9 years ago by
 Reviewers changed from John Palmieri to John Palmieri, Mitesh Patel
 Status changed from needs_review to positive_review
comment:176 Changed 9 years ago by
Thanks for finishing off the review.
comment:177 followup: ↓ 178 Changed 9 years ago by
Great!
comment:178 in reply to: ↑ 177 Changed 9 years ago by
comment:179 Changed 9 years ago by
Given the number of things that look to be needed to update this, it would be good if one could create a small shell script, something like
#!/bin/sh cd devel/sage hg qimport /patch/to/rawpatch1 hg qpush hg qimport /patch/to/rawpatch2 etc
so that we could check it easily. At the moment, looking at all those patches, it is rather offputting!
Dave
comment:180 Changed 9 years ago by
 Resolution set to fixed
 Status changed from positive_review to closed
comment:181 followup: ↓ 182 Changed 9 years ago by
A followup: on my mac, perhaps because of various symbolic links, whenever I run "sage b", I see a message like
warning: Replacing library search directory in linker command: "/Applications/sage_builds/sage4.6/local/lib" > "/Applications/sage/local/lib"
I can run "sage b" three times in a row, and I see this message all three times.
This may be because of symbolic links: "/Applications/sage" is a link pointing to "/Applications/sage_builds/sage4.6/".
Perhaps in setup.py, we should use os.path.realpath? For example,

setup.py
diff r cdc586ffbdfd setup.py
a b 391 391 self.debug_print( 392 392 "Library dir found in dynamic linker command: " + 393 393 "\"%s\"" % libdir) 394 if libdir != sage_libdir:394 if os.path.realpath(libdir) != os.path.realpath(sage_libdir): 395 395 self.compiler.warn( 396 396 "Replacing library search directory in linker " + 397 397 "command:\n \"%s\" > \"%s\"\n" % (libdir,
If this sounds like a good idea, I can open a new ticket with this patch.
comment:182 in reply to: ↑ 181 Changed 9 years ago by
Replying to jhpalmieri:
A followup: on my mac, perhaps because of various symbolic links, whenever I run "sage b", I see a message like
warning: Replacing library search directory in linker command: "/Applications/sage_builds/sage4.6/local/lib" > "/Applications/sage/local/lib"
I can run "sage b" three times in a row, and I see this message all three times.
Of course. distutils
reads the Python Makefile each time it is invoked by the Sage library's setup()
; we do not (yet) patch that Makefile and pyconfig,h
.
This may be because of symbolic links: "/Applications/sage" is a link pointing to "/Applications/sage_builds/sage4.6/".
Yep.
Perhaps in setup.py, we should use os.path.realpath? If this sounds like a good idea, I can open a new ticket with this patch.
Well, it's just a warning; feel free to open a ticket for that, and I'll probably review it. ;)
comment:183 Changed 9 years ago by
See #10208. I agree that it is just a warning, but it's a warning when there is nothing actually wrong, which might be distracting...
Can we somehow trace the PARI calls that lead to this?