Opened 5 years ago
Closed 5 years ago
#23596 closed enhancement (fixed)
Update GLPK to 4.63
Reported by:  fbissey  Owned by:  

Priority:  blocker  Milestone:  sage8.1 
Component:  packages: standard  Keywords:  
Cc:  dcoudert  Merged in:  
Authors:  François Bissey  Reviewers:  Jeroen Demeyer 
Report Upstream:  N/A  Work issues:  
Branch:  a6e1d23 (Commits, GitHub, GitLab)  Commit:  a6e1d232142c8e7c6a2746ec64c04793b9e763ec 
Dependencies:  Stopgaps: 
Description (last modified by )
Routine upgrade glpk 4.61 and over break a debugging doctest as a source file has changed location and name.
tarball: http://sagetrac.lipn.univparis13.fr/sage/glpk4.63.tar.bz2
Change History (38)
comment:1 Changed 5 years ago by
 Branch set to u/fbissey/glpk4.63
 Commit set to 23102fece7febe7a6afd068d497f3f462a95c251
 Description modified (diff)
 Status changed from new to needs_review
comment:2 Changed 5 years ago by
comment:3 Changed 5 years ago by
 Reviewers set to Jeroen Demeyer
 Status changed from needs_review to positive_review
comment:4 Changed 5 years ago by
 Status changed from positive_review to needs_info
There is something strange happening when reinstalling GLPK 4.60 (the current version in Sage) after installing 4.63. The libraries look like this:
lrwxrwxrwx 1 jdemeyer jdemeyer 17 Aug 11 14:19 local/lib/libglpk.so > libglpk.so.40.1.0 lrwxrwxrwx 1 jdemeyer jdemeyer 17 Aug 11 14:19 local/lib/libglpk.so.40 > libglpk.so.40.2.2 rwxrxrx 1 jdemeyer jdemeyer 3592384 Aug 11 14:19 local/lib/libglpk.so.40.1.0 rwxrxrx 1 jdemeyer jdemeyer 3626448 Aug 8 20:45 local/lib/libglpk.so.40.2.2
Note how both versions are installed and how local/lib/libglpk.so.40
points to the new version instead of the old.
This leads to doctest failures because the new version is still used by Sage.
Since this might mask other problems, I am unsetting positive_review until this is clarified.
comment:5 Changed 5 years ago by
 Branch changed from u/fbissey/glpk4.63 to 23102fece7febe7a6afd068d497f3f462a95c251
 Resolution set to fixed
 Status changed from needs_info to closed
comment:6 Changed 5 years ago by
 Commit 23102fece7febe7a6afd068d497f3f462a95c251 deleted
 Resolution fixed deleted
 Status changed from closed to new
comment:7 followup: ↓ 8 Changed 5 years ago by
Yes, this is curious. Is there anything interesting in your log of glpk4.60 when you downgrade? It may be a quirk from libtool, but we can deal with that with a removal of old libraries first.
comment:8 in reply to: ↑ 7 ; followups: ↓ 10 ↓ 12 Changed 5 years ago by
Replying to fbissey:
we can deal with that with a removal of old libraries first.
Not quite, we cannot retroactively patch the current version of GLPK.
comment:9 Changed 5 years ago by
We don't really make any promises about downgrades, so I wouldn't be overly concerned...
comment:10 in reply to: ↑ 8 Changed 5 years ago by
comment:11 Changed 5 years ago by
OK, I can reproduce the issue and it is weird.
[glpk4.60.p0] libtool: install: (cd /home/fbissey/sandbox/gitfork/sage/local/lib && { ln s f libglpk.so.40.1.0 libglpk.so.40  { rm f libglpk.so.40 && ln s libglpk.so.40.1.0 libglpk.so.40; }; }) [glpk4.60.p0] libtool: install: (cd /home/fbissey/sandbox/gitfork/sage/local/lib && { ln s f libglpk.so.40.1.0 libglpk.so  { rm f libglpk.so && ln s libglpk.so.40.1.0 libglpk.so; }; })
So the first operation silently fails but the second one succeeds. In fact I would say the first one is not executed.
comment:12 in reply to: ↑ 8 Changed 5 years ago by
Replying to jdemeyer:
Replying to fbissey:
we can deal with that with a removal of old libraries first.
Not quite, we cannot retroactively patch the current version of GLPK.
Going back to this one. We cannot make glpk4.60
behave retroactively. But we can prevent the problem to happen again in the future.
I have suspicions other libtool packages may behave the same way. Apart from future proofing at the spkg level, Erik's work in #22509 is probably the only thing that will enable a working downgrade path for that case. Again all this is for future improvements.
comment:13 Changed 5 years ago by
 Branch changed from 23102fece7febe7a6afd068d497f3f462a95c251 to u/fbissey/glpk4.63
 Commit set to 30c496fb7ab510df7b0a88e0ccae3050799ebdc6
 Status changed from new to needs_review
@Jeroen: As I said I don't think we can fix the downgrade to 4.60[1]. I added a commit to remove old libraries, so that problem won't happen after glpk 4.63.
[1] All right, we could push a 4.60.p1 and then upgrade. But I don't think that's worth the extra work.
New commits:
23102fe  version bump. Slight improvement on skgsrc. Fix broken doctest.

a72d1af  Merge branch 'develop' into glpk4.63

30c496f  Remove old libraries before installing. This potential enable downrade in the future.

comment:14 followup: ↓ 16 Changed 5 years ago by
 Status changed from needs_review to positive_review
I think we can live without going back to 4.60.
comment:15 followup: ↓ 17 Changed 5 years ago by
By the way were our patches ever forwarded upstream? I think I tried but don't remember what happened.
comment:16 in reply to: ↑ 14 Changed 5 years ago by
Replying to jpflori:
I think we can live without going back to 4.60.
Of course. My concern wasn't particularly about 4.60, but there might be a general problem which would occur for every version.
comment:17 in reply to: ↑ 15 Changed 5 years ago by
Replying to jpflori:
By the way were our patches ever forwarded upstream?
error_recovery.patch
was forwarded upstream but rejected.
comment:18 Changed 5 years ago by
 Branch changed from u/fbissey/glpk4.63 to 30c496fb7ab510df7b0a88e0ccae3050799ebdc6
 Resolution set to fixed
 Status changed from positive_review to closed
comment:19 Changed 5 years ago by
 Commit 30c496fb7ab510df7b0a88e0ccae3050799ebdc6 deleted
 Resolution fixed deleted
 Status changed from closed to new
I'm getting crashes on 32bit...
comment:20 followup: ↓ 21 Changed 5 years ago by
Also, with SAGE_DEBUG=yes
********************************************************************** File "src/sage/numerical/backends/glpk_backend.pyx", line 544, in sage.numerical.backends.glpk_backend.GLPKBackend.add_linear_constraint Failed example: q.add_constraint(p.new_variable()[0] <= 1) Expected: Traceback (most recent call last): ... GLPKError: glp_set_mat_row: i = 1; len = 1; invalid row length Error detected in file glpapi01.c at line ... Got: <BLANKLINE> Traceback (most recent call last): File "/mnt/disk/home/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 515, in _run self.compile_and_execute(example, compiler, test.globs) File "/mnt/disk/home/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 885, in compile_and_execute exec(compiled, globs) File "<doctest sage.numerical.backends.glpk_backend.GLPKBackend.add_linear_constraint[10]>", line 1, in <module> q.add_constraint(p.new_variable()[Integer(0)] <= Integer(1)) File "sage/numerical/mip.pyx", line 1816, in sage.numerical.mip.MixedIntegerLinearProgram.add_constraint (/mnt/disk/home/buildslavesage/slave/sage_git/build/src/build/cythonized/sage/numerical/mip.c:13640) self.add_constraint(lhsrhs, max=0, name=name) File "sage/numerical/mip.pyx", line 1804, in sage.numerical.mip.MixedIntegerLinearProgram.add_constraint (/mnt/disk/home/buildslavesage/slave/sage_git/build/src/build/cythonized/sage/numerical/mip.c:13065) self._backend.add_linear_constraint(constraint.items(), min, max, name) File "sage/numerical/backends/glpk_backend.pyx", line 569, in sage.numerical.backends.glpk_backend.GLPKBackend.add_linear_constraint (/mnt/disk/home/buildslavesage/slave/sage_git/build/src/build/cythonized/sage/numerical/backends/glpk_backend.c:6697) sig_on() GLPKError: glp_set_mat_row: i = 1; len = 1; invalid row length Error detected in file api/prob1.c at line 763 ********************************************************************** 1 item had failures: 1 of 12 in sage.numerical.backends.glpk_backend.GLPKBackend.add_linear_constraint [535 tests, 1 failure, 4.87 s]
comment:21 in reply to: ↑ 20 Changed 5 years ago by
Replying to vbraun:
Also, with SAGE_DEBUG=yes
********************************************************************** File "src/sage/numerical/backends/glpk_backend.pyx", line 544, in sage.numerical.backends.glpk_backend.GLPKBackend.add_linear_constraint Failed example: q.add_constraint(p.new_variable()[0] <= 1) Expected: Traceback (most recent call last): ... GLPKError: glp_set_mat_row: i = 1; len = 1; invalid row length Error detected in file glpapi01.c at line ... Got: <BLANKLINE> Traceback (most recent call last): File "/mnt/disk/home/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 515, in _run self.compile_and_execute(example, compiler, test.globs) File "/mnt/disk/home/buildslavesage/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/doctest/forker.py", line 885, in compile_and_execute exec(compiled, globs) File "<doctest sage.numerical.backends.glpk_backend.GLPKBackend.add_linear_constraint[10]>", line 1, in <module> q.add_constraint(p.new_variable()[Integer(0)] <= Integer(1)) File "sage/numerical/mip.pyx", line 1816, in sage.numerical.mip.MixedIntegerLinearProgram.add_constraint (/mnt/disk/home/buildslavesage/slave/sage_git/build/src/build/cythonized/sage/numerical/mip.c:13640) self.add_constraint(lhsrhs, max=0, name=name) File "sage/numerical/mip.pyx", line 1804, in sage.numerical.mip.MixedIntegerLinearProgram.add_constraint (/mnt/disk/home/buildslavesage/slave/sage_git/build/src/build/cythonized/sage/numerical/mip.c:13065) self._backend.add_linear_constraint(constraint.items(), min, max, name) File "sage/numerical/backends/glpk_backend.pyx", line 569, in sage.numerical.backends.glpk_backend.GLPKBackend.add_linear_constraint (/mnt/disk/home/buildslavesage/slave/sage_git/build/src/build/cythonized/sage/numerical/backends/glpk_backend.c:6697) sig_on() GLPKError: glp_set_mat_row: i = 1; len = 1; invalid row length Error detected in file api/prob1.c at line 763 ********************************************************************** 1 item had failures: 1 of 12 in sage.numerical.backends.glpk_backend.GLPKBackend.add_linear_constraint [535 tests, 1 failure, 4.87 s]
That's the error you would get if the patch to sage/numerical/backends/glpk_backend.pyx
is not applied. So for that one at least, it looks like something didn't apply cleanly.
Could we have some access to errors on 32bits?
comment:22 Changed 5 years ago by
comment:23 followup: ↓ 24 Changed 5 years ago by
Yes, thats probably whats going on in :comment:20
But the 32issue is real, I just don't have the logs any more as the buildbot ran out of disks space
comment:24 in reply to: ↑ 23 Changed 5 years ago by
 Status changed from new to needs_review
Replying to vbraun:
But the 32issue is real, I just don't have the logs any more as the buildbot ran out of disks space
I cannot reproduce this on arando
(32bit Linux). Could you please try again, if you are running out of disk space, maybe that could explain why stuff breaks too.
comment:25 Changed 5 years ago by
 Status changed from needs_review to positive_review
comment:26 Changed 5 years ago by
 Status changed from positive_review to needs_work
sage: g = graphs.CycleGraph(5) ## line 4750 ## sage: g.fractional_chromatic_index() ## line 4751 ## 2.5 sage: g.fractional_chromatic_index(solver="PPL") ## line 4756 ## 5/2 sage: g = graphs.PetersenGraph() ## line 4763 ## sage: g.fractional_chromatic_index(solver='GLPK') ## line 4764 ##  /home/buildbot/slave/sage_git/build/local/lib/python2.7/sitepackages/cysignals/signals.so(+0x44e8)[0xf6acc4e8] /home/buildbot/slave/sage_git/build/local/lib/python2.7/sitepackages/cysignals/signals.so(+0x455f)[0xf6acc55f] /home/buildbot/slave/sage_git/build/local/lib/python2.7/sitepackages/cysignals/signals.so(+0x69a7)[0xf6ace9a7] [0xf772ecb0] /home/buildbot/slave/sage_git/build/local/lib/libglpk.so.40(+0x20e89)[0xc593ce89] /home/buildbot/slave/sage_git/build/local/lib/libglpk.so.40(+0x2914c)[0xc594514c] /home/buildbot/slave/sage_git/build/local/lib/libglpk.so.40(+0x29473)[0xc5945473] /home/buildbot/slave/sage_git/build/local/lib/libglpk.so.40(+0x295dc)[0xc59455dc] /home/buildbot/slave/sage_git/build/local/lib/libglpk.so.40(glp_intopt+0x5f5)[0xc59258a5] /home/buildbot/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/numerical/backends/glpk_backend.so(+0x127d5)[0xc60c97d5] /home/buildbot/slave/sage_git/build/local/lib/python2.7/sitepackages/sage/numerical/mip.so(+0xcbf7)[0xcb7e4bf7] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyCFunction_Call+0x109)[0xf75c7299] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x9089)[0xf76357d9] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7c4)[0xf76360e4] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8f05)[0xf7635655] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7c4)[0xf76360e4] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x63)[0xf7636253] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x78e3)[0xf7634033] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7c4)[0xf76360e4] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x8f05)[0xf7635655] /home/buildbot/slave/sage_git/build/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7c4)[0xf76360e4]
comment:27 Changed 5 years ago by
Ok, so this it is timing out. PetersenGraph
that rings a bell, there was something about that recently I think.
comment:28 Changed 5 years ago by
 Cc dcoudert added
It is "caused" by #23658 that just got merged in 8.1.beta4. It seem the test was added to check a similar issue was fixed. Copying David Coudert.
comment:29 followup: ↓ 30 Changed 5 years ago by
Can someone tell me the procedure to test this ticket? I don't know how to do it. Thanks.
comment:30 in reply to: ↑ 29 Changed 5 years ago by
Replying to dcoudert:
Can someone tell me the procedure to test this ticket? I don't know how to do it. Thanks.
Hi David, the problem only seem to be happen on 32bits platforms. You should be able to test it on top of 8.1.beta4 which includes #23658 in which you introduced the test that is now failing. Follow the usual procedure from http://doc.sagemath.org/html/en/developer/manual_git.html#chaptermanualgit . The problem is only with src/sage/graphs/graph.py
on line 1372.
comment:31 Changed 5 years ago by
I follwed the manual_git.html page and got the following (git is not my friend).
confetti:sage dcoudert$ git fetch trac 30c496f fatal: Couldn't find remote ref 30c496f confetti:sage dcoudert$ git fetch trac 30c496fb7ab510df7b0a88e0ccae3050799ebdc6 confetti:sage dcoudert$ git checkout b my_branch FETCH_HEAD fatal: Cannot update paths and switch to branch 'my_branch' at the same time. Did you intend to checkout 'FETCH_HEAD' which can not be resolved as commit?
Anyway, I don't have access to a 32bit machine. So I don't know how to test and help solving the issue.
comment:32 Changed 5 years ago by
 Branch changed from 30c496fb7ab510df7b0a88e0ccae3050799ebdc6 to u/jdemeyer/30c496fb7ab510df7b0a88e0ccae3050799ebdc6
comment:33 followup: ↓ 36 Changed 5 years ago by
 Commit set to a6e1d232142c8e7c6a2746ec64c04793b9e763ec
 Status changed from needs_work to needs_review
comment:34 Changed 5 years ago by
 Priority changed from major to blocker
Changing priority to blocker because the patchbots are all posting doctest failures due to the downgrade bug 4.
comment:35 Changed 5 years ago by
I succeed to install and test the patch (thank you Jeroen for the change in the branch name. It ease my life). For me it's working well, no infinite loop.
comment:36 in reply to: ↑ 33 Changed 5 years ago by
comment:37 Changed 5 years ago by
 Status changed from needs_review to positive_review
Sure, let's get this show back on the road.
comment:38 Changed 5 years ago by
 Branch changed from u/jdemeyer/30c496fb7ab510df7b0a88e0ccae3050799ebdc6 to a6e1d232142c8e7c6a2746ec64c04793b9e763ec
 Resolution set to fixed
 Status changed from positive_review to closed
New commits:
version bump. Slight improvement on skgsrc. Fix broken doctest.