Opened 2 years ago
Closed 20 months ago
#29314 closed enhancement (fixed)
update GAP to version 4.11, libsemigroup to 1.0.9
Reported by:  dimpase  Owned by:  

Priority:  major  Milestone:  sage9.3 
Component:  packages: standard  Keywords:  
Cc:  arojas, ghtimokau, soehms, ghtobiasdiez  Merged in:  
Authors:  Dima Pasechnik  Reviewers:  Matthias Koeppe, Tobias Diez 
Report Upstream:  N/A  Work issues:  
Branch:  a28138c (Commits, GitHub, GitLab)  Commit:  a28138c2fc1396171734b12fdbe5904b79bf1ec1 
Dependencies:  Stopgaps: 
Description (last modified by )
GAP 4.11.0 and libsemigroup 1.3.1 have been released. (we pick libsemigroup 1.0.9 as the one compatible with GAP's 4.11 semigroups package)
tarball: see upstream_url fields
Attachments (1)
Change History (111)
comment:1 Changed 2 years ago by
 Cc arojas added
comment:2 Changed 2 years ago by
 Cc ghtimokau added
comment:3 Changed 2 years ago by
comment:4 Changed 2 years ago by
Besides changes in tests output, there's only one small change needed due to the VERSION alias removal. Patch at https://aur.archlinux.org/cgit/aur.git/tree/sagemathgap4.11.patch?h=sagemathgit
I haven't tested the gappackages update
comment:5 Changed 2 years ago by
 Milestone changed from sage9.1 to sage9.2
comment:6 Changed 2 years ago by
 Branch set to u/dimpase/packages/gap411
 Commit set to 1b80d95959282e2b20331721fae67f4d276217d1
 Description modified (diff)
 Summary changed from update GAP to version 4.11 to update GAP to version 4.11, libsemigroup to 1.3.1
comment:7 Changed 2 years ago by
 Commit changed from 1b80d95959282e2b20331721fae67f4d276217d1 to f361b88fa462485cd7f03725845ae7c741d9d011
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
f361b88  libsemigroups update

comment:8 Changed 2 years ago by
 Description modified (diff)
 Summary changed from update GAP to version 4.11, libsemigroup to 1.3.1 to update GAP to version 4.11, libsemigroup to 1.0.9
sage t warnlong 105.7 randomseed=0 src/sage/libs/gap/element.pyx # 6 doctests failed sage t warnlong 105.7 randomseed=0 src/sage/libs/gap/libgap.pyx # 1 doctest failed
something to be fixed 1st
comment:9 Changed 2 years ago by
 Dependencies set to #30496
comment:10 Changed 2 years ago by
 Commit changed from f361b88fa462485cd7f03725845ae7c741d9d011 to 8429a9c6e3f03a94003c32536541f08f0b38528a
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
82191ca  fix conversion from gap polynomial with valence > 0

c582e80  better syntax for libgap calls

bbd7419  version bumps, checksums, patch removal, packages: updated names

87c6a6b  libsemigroups update

8429a9c  patches from Arch (cf #29314)

comment:11 Changed 2 years ago by
 Commit changed from 8429a9c6e3f03a94003c32536541f08f0b38528a to 08193ae145223f5f8b25f0e44bb11096f37c6548
Branch pushed to git repo; I updated commit sha1. New commits:
08193ae  tagged #random tests with output depending upon gap_packages installed

comment:12 Changed 2 years ago by
 Commit changed from 08193ae145223f5f8b25f0e44bb11096f37c6548 to c90360ba618188c4b8874f8f56d1759b2bd898f1
Branch pushed to git repo; I updated commit sha1. New commits:
c90360b  one more doctest fix

comment:13 Changed 2 years ago by
 Commit changed from c90360ba618188c4b8874f8f56d1759b2bd898f1 to 21211413f3399e93051696a149bcff0e5d4c936e
Branch pushed to git repo; I updated commit sha1. New commits:
2121141  more robust test, so that GAP's packages don't matter

comment:14 Changed 2 years ago by
 Status changed from new to needs_review
there seems to be one failing doctest that is macOSspecific, in src/sage/groups/cubic_braid.py
,
but I still think we have to proceed (it's probably a platformspecific GAP bug).
comment:15 Changed 2 years ago by
on macOS 10.15.6 with and without gap_packages installed
sage t warnlong 70.9 randomseed=0 src/sage/groups/cubic_braid.py ********************************************************************** File "src/sage/groups/cubic_braid.py", line 1454, in sage.groups.cubic_braid.CubicBraidGroup.as_matrix_group Failed example: m_back = C5(m) Exception raised: Traceback (most recent call last): File "/Users/dima/software/sagetracmirror/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 715, in _run self.compile_and_execute(example, compiler, test.globs) File "/Users/dima/software/sagetracmirror/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1139, in compile_and_execute exec(compiled, globs) File "<doctest sage.groups.cubic_braid.CubicBraidGroup.as_matrix_group[4]>", line 1, in <module> m_back = C5(m) File "sage/structure/parent.pyx", line 900, in sage.structure.parent.Parent.__call__ (build/cythonized/sage/structure/parent.c:9336) return mor._call_(x) File "sage/structure/coerce_maps.pyx", line 161, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (build/cythonized/sage/structure/coerce_maps.c:4623) raise File "sage/structure/coerce_maps.pyx", line 156, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_ (build/cythonized/sage/structure/coerce_maps.c:4515) return C._element_constructor(x) File "/Users/dima/software/sagetracmirror/local/lib/python3.7/sitepackages/sage/groups/cubic_braid.py", line 1314, in _element_constructor_ return map_to.lift(x) File "/Users/dima/software/sagetracmirror/local/lib/python3.7/sitepackages/sage/groups/libgap_morphism.py", line 514, in lift if h.gap() not in phi.Image(): File "sage/libs/gap/element.pyx", line 656, in sage.libs.gap.element.GapElement.__contains__ (build/cythonized/sage/libs/gap/element.c:7753) return GAP_IN(other, self).sage() File "sage/libs/gap/element.pyx", line 2525, in sage.libs.gap.element.GapElement_Function.__call__ (build/cythonized/sage/libs/gap/element.c:19780) sig_on() sage.libs.gap.util.GAPError: Error, reached the preset memory limit (change it with the o command line option)
can't reproduce this on Linux
comment:16 followup: ↓ 28 Changed 2 years ago by
 Cc soehms added
Sebastian, could you reproduce this computation in GAP? I suspect it's a "pure" GAP bug.
comment:17 followup: ↓ 18 Changed 2 years ago by
It's not macOSspecific, I've been seeing this on Arch since I updated GAP. It only happens when running the full test suite, testing only the groups/cubic_braid.py file or even the entire groups module works.
comment:18 in reply to: ↑ 17 Changed 2 years ago by
Replying to arojas:
It's not macOSspecific, I've been seeing this on Arch since I updated GAP. It only happens when running the full test suite, testing only the groups/cubic_braid.py file or even the entire groups module works.
On macOS it's reproducible at Sage prompt.
comment:19 Changed 2 years ago by
I'll just do

src/sage/interfaces/gap.py
a b def get_gap_memory_pool_size(): 277 277 # Don't eat all address space if the user set ulimit v 278 278 suggested_size = min(suggested_size, vmax // 10) 279 279 # ~220MB is the minimum for long doctests 280 suggested_size = max(suggested_size, 250 * 1024**2)280 suggested_size = max(suggested_size, 350 * 1024**2) 281 281 return suggested_size
this limit has not been chnaged for 7 years, so that's OK :)
comment:20 Changed 2 years ago by
 Commit changed from 21211413f3399e93051696a149bcff0e5d4c936e to f02f6e1d67dfbff7a4d1f96533ea14be765c418a
Branch pushed to git repo; I updated commit sha1. New commits:
f02f6e1  increase memory pool for libgap

comment:21 Changed 2 years ago by
made it 400m
comment:22 Changed 2 years ago by
GitHub Actions tests on https://github.com/sagemath/sage/pull/98
comment:23 Changed 2 years ago by
https://github.com/sagemath/sage/actions just needs some housekeeping  there are lots of workflowed from the WSL pull request that are no longer needed
comment:24 Changed 2 years ago by
ping?
comment:25 Changed 2 years ago by
 Reviewers set to Matthias Koeppe
 Status changed from needs_review to positive_review
The updated libsemigroup
fails to build on the outdated platforms ubuntutrusty
, debianjessie
, linuxmint17
. This is a regression regarding platform support, but I think that's fine for an optional package (also normaliz
has the same problem).
Otherwise looks fine.
comment:26 Changed 2 years ago by
Does the upgrade fix something "critical"?
comment:27 Changed 2 years ago by
it removes a lot of patches (in fact, all the patches we have for gap
and gap_packages
), for one, which is always good. It incorporates numerous upstream bug fixes too, and it's a bit overdue, as 4.11 was released 6 months ago.
comment:28 in reply to: ↑ 16 Changed 2 years ago by
Replying to dimpase:
Sebastian, could you reproduce this computation in GAP? I suspect it's a "pure" GAP bug.
Sorry, that I didn't see that earlier, since I'm on vacation until next weekend! But it seems that you've solved that already.
Do you know the reason why the domains of permutation groups of matrix groups have increased in the new version (see the differences of the doctests of permgroup.py
at line 850 and 899)?
On a first impression I wouldn't take that for an improvement. Anyway, I would break these long doctests lines.
Sebastian.
comment:29 Changed 2 years ago by
 Status changed from positive_review to needs_work
Docbuild hangs forever on buildbots, a strace ends with
$ strace ff ./sage docbuild verbose 99 nopdflinks all html [...] [pid 106971] access("/var/lib/buildbot/slave/sage_git/build/local/share/gap/pkg/resclasses4.7.2/init.g", F_OK) = 0 [pid 106971] access("/var/lib/buildbot/slave/sage_git/build/local/share/gap/pkg/resclasses4.7.2/read.g", F_OK) = 0 [pid 106971] access("/var/lib/buildbot/slave/sage_git/build/local/share/gap/pkg/polenta1.3.9/doc/manual.six", F_OK) = 0 [pid 106971] access("/var/lib/buildbot/slave/sage_git/build/local/share/gap/pkg/resclasses4.7.2/doc/manual.six", F_OK) = 0 [pid 106971] access("/var/lib/buildbot/.gap/gaprc", R_OK) = 1 ENOENT (No such file or directory) [pid 106971] access("/var/lib/buildbot/.gap/gaprc.gz", R_OK) = 1 ENOENT (No such file or directory) [pid 106971] access("/var/lib/buildbot/slave/sage_git/build/local/share/gap/gaprc", R_OK) = 1 ENOENT (No such file or directory) [pid 106971] access("/var/lib/buildbot/slave/sage_git/build/local/share/gap/gaprc.gz", R_OK) = 1 ENOENT (No such file or directory) [pid 106971] access("/var/lib/buildbot/.gap", F_OK) = 1 ENOENT (No such file or directory) [pid 106971] open("/var/lib/buildbot/.gaprc", O_RDONLY) = 1 ENOENT (No such file or directory) [pid 106971] access("/var/lib/buildbot/.gaprc.gz", R_OK) = 1 ENOENT (No such file or directory) [pid 106971] access("/var/lib/buildbot/.gaprc.gz.gz", R_OK) = 1 ENOENT (No such file or directory) [pid 106971] open("/var/lib/buildbot/slave/sage_git/build/local/lib/python3.8/sitepackages/sage/libs/gap/sage.gaprc", O_RDONLY) = 12 [pid 106971] read(12, "# This file is run by Sage when "..., 20000) = 567 [pid 106971] read(12, "", 20000) = 0 [pid 106971] close(12) = 0 [pid 106971] rt_sigaction(SIGCHLD, {SIG_DFL, [CHLD], SA_RESTORERSA_RESTART, 0x7f2bc20154b0}, {0x7f0bc9679880, [CHLD], SA_RESTORERSA_RESTART, 0x7f2bc20154b0}, 8) = 0 [pid 106971] stat("/var/lib/buildbot/slave/sage_git/build/local/lib/python3.8/sitepackages/sage/matrix", {st_mode=S_IFDIR0755, st_size=12288, ...}) = 0 [pid 106971] stat("/var/lib/buildbot/slave/sage_git/build/local/lib/python3.8/sitepackages/sage/matrix/action.cpython38x86_64linuxgnu.so", {st_mode=S_IFREG0755, st_size=1110904, ...}) = 0 [pid 106971] open("/var/lib/buildbot/slave/sage_git/build/local/lib/python3.8/sitepackages/sage/matrix/action.cpython38x86_64linuxgnu.so", O_RDONLYO_CLOEXEC) = 12 [pid 106971] read(12, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\300?\0\0\0\0\0\0"..., 832) = 832 [pid 106971] fstat(12, {st_mode=S_IFREG0755, st_size=1110904, ...}) = 0 [pid 106971] mmap(NULL, 2244824, PROT_READPROT_EXEC, MAP_PRIVATEMAP_DENYWRITE, 12, 0) = 0x7f0babc8a000 [pid 106971] mprotect(0x7f0babca9000, 2093056, PROT_NONE) = 0 [pid 106971] mmap(0x7f0babea8000, 24576, PROT_READPROT_WRITE, MAP_PRIVATEMAP_FIXEDMAP_DENYWRITE, 12, 0x1e000) = 0x7f0babea8000 [pid 106971] mmap(0x7f0babeae000, 216, PROT_READPROT_WRITE, MAP_PRIVATEMAP_FIXEDMAP_ANONYMOUS, 1, 0) = 0x7f0babeae000 [pid 106971] close(12) = 0 [pid 106971] mprotect(0x7f0babea8000, 4096, PROT_READ) = 0 [pid 106971] mmap(NULL, 262144, PROT_READPROT_WRITE, MAP_PRIVATEMAP_ANONYMOUS, 1, 0) = 0x7f0babc4a000 [pid 106971] munmap(0x7f0babc4a000, 262144) = 0 [pid 106971] mmap(NULL, 262144, PROT_READPROT_WRITE, MAP_PRIVATEMAP_ANONYMOUS, 1, 0) = 0x7f0babc4a000 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={16, 968000}, ru_stime={0, 556000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={16, 968000}, ru_stime={0, 556000}, ...}) = 0 [pid 106971] madvise(0x100004a00000, 7344128, MADV_DONTNEED) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={17, 532000}, ru_stime={0, 556000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={17, 532000}, ru_stime={0, 556000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={18, 76000}, ru_stime={0, 556000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={18, 76000}, ru_stime={0, 556000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={18, 624000}, ru_stime={0, 564000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={18, 624000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={19, 172000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={19, 172000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={19, 712000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={19, 712000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={20, 252000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={20, 252000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={20, 788000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={20, 792000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={21, 328000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={21, 328000}, ru_stime={0, 568000}, ...}) = 0 [pid 106971] getrusage(RUSAGE_SELF, {ru_utime={21, 872000}, ru_stime={0, 568000}, ...}) = 0 [... repeat ad infinitum ...]
but not when building locally. I tried to delete the content of sage.gaprc but that didn't help.
comment:30 Changed 2 years ago by
 Branch changed from u/dimpase/packages/gap411 to u/mkoeppe/packages/gap411
comment:31 Changed 2 years ago by
 Commit changed from f02f6e1d67dfbff7a4d1f96533ea14be765c418a to 35649994b528588b33968f860530ad8fef5c38c7
Absolutely no idea what sort of fresh hell this might be.
Time to get rid of buildbots, maybe...
New commits:
3564999  build/pkgs/gap_packages: Use symlinks to refer to gap's tarball

comment:32 Changed 2 years ago by
could it be something like running out of file descriptors?
comment:33 Changed 2 years ago by
Unlikely, it happened also on kucalc which is rather beefy
comment:34 Changed 2 years ago by
OS has a hard limit on the number of them, beefy or not, and if you leak them, then god help you.
could also be some parallelisation crap. Do bildbots try to overparallelise things, with setting MAKE to something etc?
Could also be something similar to https://trac.sagemath.org/ticket/30351  which deals with a hanging docbuild on macOS  maybe this desease is now infecting buildbots too?
comment:35 Changed 2 years ago by
There are multiple physical hosts, its not a resource limit (or at least one thats set up by the docbuilder)
comment:36 Changed 2 years ago by
any idea at what point of docbuild it hangs?
comment:37 Changed 2 years ago by
cd ../.. && sagelogger p './sage docbuild nopdflinks all html j ' logs/dochtml.log [dochtml] [dochtml] Building reference manual, first pass. [dochtml] [dochtml] [reference] building [inventory]: targets for 1 source files that are out of date [dochtml] [reference] updating environment: [new config] 1 added, 0 changed, 0 removed [dochtml] [reference] The inventory files are in local/share/doc/sage/inventory/en/reference/references. [dochtml] Build finished. The built documents can be found in /home/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/references [dochtml] [spkg ] building [inventory]: targets for 271 source files that are out of date [dochtml] [spkg ] updating environment: [new config] 271 added, 0 changed, 0 removed [dochtml] [spkg ] The inventory files are in local/share/doc/sage/inventory/en/reference/spkg. [dochtml] Build finished. The built documents can be found in /home/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/spkg [dochtml] [manifolds] building [inventory]: targets for 78 source files that are out of date [dochtml] [manifolds] updating environment: [new config] 78 added, 0 changed, 0 removed [dochtml] [manifolds] The inventory files are in local/share/doc/sage/inventory/en/reference/manifolds. [dochtml] Build finished. The built documents can be found in /home/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/manifolds [dochtml] [polynomia] building [inventory]: targets for 62 source files that are out of date [dochtml] [polynomia] updating environment: [new config] 62 added, 0 changed, 0 removed [dochtml] [polynomia] The inventory files are in local/share/doc/sage/inventory/en/reference/polynomial_rings. [dochtml] Build finished. The built documents can be found in /home/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/polynomial_rings [dochtml] [repl ] building [inventory]: targets for 35 source files that are out of date [dochtml] [repl ] updating environment: [new config] 35 added, 0 changed, 0 removed [dochtml] [repl ] The inventory files are in local/share/doc/sage/inventory/en/reference/repl. [dochtml] Build finished. The built documents can be found in /home/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/repl [dochtml] [algebras ] building [inventory]: targets for 95 source files that are out of date [dochtml] [algebras ] updating environment: [new config] 95 added, 0 changed, 0 removed [dochtml] [algebras ] The inventory files are in local/share/doc/sage/inventory/en/reference/algebras. [dochtml] Build finished. The built documents can be found in /home/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/algebras [dochtml] [tensor_fr] building [inventory]: targets for 19 source files that are out of date [dochtml] [tensor_fr] updating environment: [new config] 19 added, 0 changed, 0 removed [dochtml] [tensor_fr] The inventory files are in local/share/doc/sage/inventory/en/reference/tensor_free_modules. [dochtml] Build finished. The built documents can be found in /home/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/tensor_free_modules [dochtml] Warning: Missing title for sage.combinat.posets.mobile [dochtml] [combinat ] building [inventory]: targets for 378 source files that are out of date [dochtml] [combinat ] updating environment: [new config] 378 added, 0 changed, 0 removed command timed out: 1200 seconds without output running ['make', 'dochtmlmathjax'], attempting to kill process killed by signal 9 program finished with exit code 1 elapsedTime=1349.554977
@mkoeppe: can you try to reproduce it on a CI build?
comment:38 Changed 2 years ago by
What is the meaning of j
option in ./sage docbuild nopdflinks all html j
?
Is it documented? If it's akin to j
for make
, then, hmm, all bets are off.
comment:39 Changed 2 years ago by
Ah, ok, j
is for MathJax. Is MathJax locally installed?
comment:40 followup: ↓ 41 Changed 2 years ago by
Definitely not on all buildbots...
comment:41 in reply to: ↑ 40 Changed 2 years ago by
Replying to vbraun:
Definitely not on all buildbots...
does it only hang on buildbots without locally installed MathJax ?
comment:42 followup: ↓ 43 Changed 2 years ago by
Here an observation which could help (done under WSL Ubuntu):
If I checkout this ticket on top of 9.2.beta12 and do
make SAGE_SPKG="sagespkg o" gap_packagesclean build
then I get:
sage: B = BraidGroup(8) Traceback (most recent call last): ... GAPError: Error, no method found! Error, no 2nd choice method found for `InverseSameMutability' on 1 arguments
I came accross that while looking at the docbuild failure noted in #30346 (which seems to be caused by this ticket as well).
comment:43 in reply to: ↑ 42 ; followup: ↓ 51 Changed 2 years ago by
Replying to soehms:
Here an observation which could help (done under WSL Ubuntu):
If I checkout this ticket on top of 9.2.beta12 and do
make SAGE_SPKG="sagespkg o" gap_packagesclean buildthen I get:
sage: B = BraidGroup(8) Traceback (most recent call last): ... GAPError: Error, no method found! Error, no 2nd choice method found for `InverseSameMutability' on 1 argumentsI came accross that while looking at the docbuild failure noted in #30346 (which seems to be caused by this ticket as well).
I tried B = BraidGroup(8)
on this branch, without and with gap_packages
installed, and it works for me. (On Gentoo Linux  so this might be an WSL problem).
comment:44 Changed 2 years ago by
to support gcc10 we need https://github.com/gappackages/cohomolo/pull/25 here
comment:45 Changed 2 years ago by
Can this upstream patch be applied to the existing gap version (4.10.2) as well? Then that should probably be done on a separate ticket
comment:46 Changed 23 months ago by
 Branch changed from u/mkoeppe/packages/gap411 to u/dimpase/packages/gap411
 Commit changed from 35649994b528588b33968f860530ad8fef5c38c7 to 3435c24a53490f484ff28267b61498282c8afbbb
 Status changed from needs_work to needs_review
added a patch needed for gap_packages on XCode 12
New commits:
b0d8fc8  version bumps, checksums, patch removal, packages: updated names

c0b35f9  libsemigroups update

6a6c8ce  patches from Arch (cf #29314)

3c45832  tagged #random tests with output depending upon gap_packages installed

07968eb  one more doctest fix

2728be6  more robust test, so that GAP's packages don't matter

b2fa6d8  increase memory pool for libgap

dd39f33  build/pkgs/gap_packages: Use symlinks to refer to gap's tarball

3435c24  clang 12 (macOS XCode 12) needs extra includes

comment:47 Changed 23 months ago by
 Commit changed from 3435c24a53490f484ff28267b61498282c8afbbb to ca2c40a570cb0cd03fc110298c2dc436370cf846
Branch pushed to git repo; I updated commit sha1. New commits:
ca2c40a  version bump

comment:48 Changed 23 months ago by
 Reviewers changed from Matthias Koeppe to Matthias Koeppe, https://github.com/mkoeppe/sage/actions/runs/270864243
comment:49 Changed 23 months ago by
 Commit changed from ca2c40a570cb0cd03fc110298c2dc436370cf846 to 5549ee60a915dbcb01bdbce9bdae9d6555b1fda9
Branch pushed to git repo; I updated commit sha1. New commits:
5549ee6  fix cohomolo pkg code to allow build with gcc10

comment:50 Changed 23 months ago by
added forgotten gcc10 patch
comment:51 in reply to: ↑ 43 ; followup: ↓ 52 Changed 23 months ago by
Replying to dimpase:
Replying to soehms:
Here an observation which could help (done under WSL Ubuntu):
....
I tried
B = BraidGroup(8)
on this branch, without and withgap_packages
installed, and it works for me. (On Gentoo Linux  so this might be an WSL problem).
Dima, I'm having the same problem on LinuxMint 19.1
. So, its probably not a WSL issue but maybe a problem with the person in front of the computer. Can you please post how I have to build Sage after checking out the branch?
comment:52 in reply to: ↑ 51 ; followup: ↓ 53 Changed 23 months ago by
Replying to soehms:
Dima, I'm having the same problem on
LinuxMint 19.1
. So, its probably not a WSL issue but maybe a problem with the person in front of the computer. Can you please post how I have to build Sage after checking out the branch?
 pull the branch
 ./sage f gap
 ./sage f gap_packages # (optional)
 make build
comment:53 in reply to: ↑ 52 Changed 23 months ago by
Replying to dimpase:
Replying to soehms:
Dima, I'm having the same problem on
LinuxMint 19.1
. So, its probably not a WSL issue but maybe a problem with the person in front of the computer. Can you please post how I have to build Sage after checking out the branch?
 pull the branch
 ./sage f gap
 ./sage f gap_packages # (optional)
 make build
Thank you! Unfortunately that didn't solve the problem. Is it possible that there is a dependency missing in the ticket description?
The list of doctest failures under groups
I'm getting under WSL
and LinuxMint
looks like this:
... sage t randomseed=0 src/sage/groups/braid.py # 289 doctests failed sage t randomseed=0 src/sage/groups/raag.py # 145 doctests failed sage t randomseed=0 src/sage/groups/libgap_wrapper.pyx # 13 doctests failed sage t randomseed=0 src/sage/groups/free_group.py # Killed due to segmentation fault sage t randomseed=0 src/sage/groups/finitely_presented.py # 251 doctests failed ...
In the case of finitely_presented.py
I also got longjmp
error messages:
*** longjmp causes uninitialized stack frame ***: /home/sebastian/develop/sage/local/bin/python3 terminated *** longjmp causes uninitialized stack frame ***: /home/sebastian/develop/sage/local/bin/python3 terminated
comment:54 followup: ↓ 57 Changed 23 months ago by
 try removing
~/.sage/gap/
, or even~/.sage/
.
 Could it be you have GAP installed systemwide, and you get an interference?
Or perhaps something in your
gap.ini
orgaprc
files, cf. https://www.gapsystem.org/Manuals/doc/ref/chap3.html#X7FD66F977A3B02DF ?
 Test the Sage's GAP 4.11 installation, e.g. by
$ SAGE_CHECK=yes ./sage f gap
 Try building this branch from scratch.
comment:55 Changed 23 months ago by
 Commit changed from 5549ee60a915dbcb01bdbce9bdae9d6555b1fda9 to 40a2d0f2109daf56293c51e153747cc5ca3b25ff
Branch pushed to git repo; I updated commit sha1. New commits:
40a2d0f  remove old workaround from #22626

comment:56 Changed 23 months ago by
 Status changed from needs_review to positive_review
Volker, could we try this again? I gather that the commit in comment:55 should change the behaviour of buildbots in comment:29, where crunch seems to happen after reading sage.gaprc
(and this commit removes an overlooked GAP 4.10specific workaround in sage.gaprc
)
comment:57 in reply to: ↑ 54 ; followup: ↓ 59 Changed 23 months ago by
Replying to dimpase:
Thanks for the advices! Here my results:
 try removing
~/.sage/gap/
, or even~/.sage/
.
no succsess
 Could it be you have GAP installed systemwide, and you get an interference? Or perhaps something in your
gap.ini
orgaprc
files ...
yes, on both of the platforms there is gap 4.8.8, but I was not aware of that. I once installed Sage via apt
which is an old version (8.1). My guess is that the systemwide gap came along with that (possible?).
But anyway, I have an older computer running under LinuxMint 18
without a systemwide gap installed and the bug shows there, as well, even after your latest commit. Furthermore I didn't find gap.ini
and gaprc
below local/share/gap
.
 Test the Sage's GAP 4.11 installation, e.g. by
$ SAGE_CHECK=yes ./sage f gap
The gap testsuite passed through successfully (in all cases).
 Try building this branch from scratch.
On the WSL
machine I build from a fresh git clone. The bug still shows.
The error output on the older machine produced backtrace information for the longjmp errors. Shall I upload a logfile?
comment:58 Changed 23 months ago by
 Commit changed from 40a2d0f2109daf56293c51e153747cc5ca3b25ff to 2ffc24af85679499aff4846b1f135f8cea22b8c0
 Status changed from positive_review to needs_review
Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:
2ffc24a  this file should exist  leave just comments there

comment:59 in reply to: ↑ 57 ; followup: ↓ 60 Changed 23 months ago by
Replying to soehms:
Replying to dimpase:
Thanks for the advices! Here my results:
 try removing
~/.sage/gap/
, or even~/.sage/
.no succsess
 Could it be you have GAP installed systemwide, and you get an interference? Or perhaps something in your
gap.ini
orgaprc
files ...yes, on both of the platforms there is gap 4.8.8, but I was not aware of that. I once installed Sage via
apt
which is an old version (8.1). My guess is that the systemwide gap came along with that (possible?).
Could it be that you have an old libgap too, somewhere, from Sage 8.1?
libgap and GAP share stuff under Sage, and if something came from GAP 4.8.8 then certainly there is a high chance that things break. Could you remove the old GAP and old Sage and try again?
But anyway, I have an older computer running under
LinuxMint 18
without a systemwide gap installed and the bug shows there, as well, even after your latest commit. Furthermore I didn't findgap.ini
andgaprc
belowlocal/share/gap
.
Please make sure there no traces of other GAP installations, .gaprc
etc on that other machine.
 Test the Sage's GAP 4.11 installation, e.g. by
$ SAGE_CHECK=yes ./sage f gapThe gap testsuite passed through successfully (in all cases).
 Try building this branch from scratch.
On the
WSL
machine I build from a fresh git clone. The bug still shows.The error output on the older machine produced backtrace information for the longjmp errors. Shall I upload a logfile?
Hopefully it's just stale bits that cause this error. Could you post the linkage of libgap Python module, i.e. the output of
ldd local/lib/python3*/sitepackages/sage/libs/gap/libgap.*.so
comment:60 in reply to: ↑ 59 Changed 23 months ago by
Replying to dimpase:
Replying to soehms:
Replying to dimpase:
......
Hopefully it's just stale bits that cause this error. Could you post the linkage of libgap Python module, i.e. the output of
ldd local/lib/python3*/sitepackages/sage/libs/gap/libgap.*.so
Here the one from the LinuxMint 18
local/lib/python3.7/sitepackages/sage/libs/gap/libgap.cpython37mx86_64linuxgnu.so: linuxvdso.so.1 => (0x00007ffd3a776000) libgap.so.0 => /home/sebastian/develop/sage/local/lib/libgap.so.0 (0x00007efc33b3c000) libpython3.7m.so.1.0 => not found libpthread.so.0 => /lib/x86_64linuxgnu/libpthread.so.0 (0x00007efc3391f000) libc.so.6 => /lib/x86_64linuxgnu/libc.so.6 (0x00007efc33555000) libgmp.so.10 => /usr/lib/x86_64linuxgnu/libgmp.so.10 (0x00007efc332d5000) libz.so.1 => /lib/x86_64linuxgnu/libz.so.1 (0x00007efc330bb000) libreadline.so.6 => /home/sebastian/develop/sage/local/lib/libreadline.so.6 (0x00007efc32e71000) libm.so.6 => /lib/x86_64linuxgnu/libm.so.6 (0x00007efc32b68000) libdl.so.2 => /lib/x86_64linuxgnu/libdl.so.2 (0x00007efc32964000) libutil.so.1 => /lib/x86_64linuxgnu/libutil.so.1 (0x00007efc32761000) /lib64/ldlinuxx8664.so.2 (0x00007efc34a8c000) libtinfo.so.6 => /home/sebastian/develop/sage/local/lib/libtinfo.so.6 (0x00007efc32528000) local/lib/python3.8/sitepackages/sage/libs/gap/libgap.cpython38x86_64linuxgnu.so: linuxvdso.so.1 => (0x00007fff44b9d000) libgap.so.0 => /home/sebastian/develop/sage/local/lib/libgap.so.0 (0x00007fdca3ad8000) libpthread.so.0 => /lib/x86_64linuxgnu/libpthread.so.0 (0x00007fdca38bb000) libc.so.6 => /lib/x86_64linuxgnu/libc.so.6 (0x00007fdca34f1000) libgmp.so.10 => /usr/lib/x86_64linuxgnu/libgmp.so.10 (0x00007fdca3271000) libz.so.1 => /lib/x86_64linuxgnu/libz.so.1 (0x00007fdca3057000) libreadline.so.6 => /home/sebastian/develop/sage/local/lib/libreadline.so.6 (0x00007fdca2e0d000) libm.so.6 => /lib/x86_64linuxgnu/libm.so.6 (0x00007fdca2b04000) libdl.so.2 => /lib/x86_64linuxgnu/libdl.so.2 (0x00007fdca2900000) libutil.so.1 => /lib/x86_64linuxgnu/libutil.so.1 (0x00007fdca26fd000) /lib64/ldlinuxx8664.so.2 (0x00007fdca4a29000) libtinfo.so.6 => /home/sebastian/develop/sage/local/lib/libtinfo.so.6 (0x00007fdca24c4000)
Here from WSL
case
linuxvdso.so.1 (0x00007ffff0e43000) libgap.so.0 => /home/sebastian/devel/sage/local/lib/libgap.so.0 (0x00007f53a2a65000) libpthread.so.0 => /lib/x86_64linuxgnu/libpthread.so.0 (0x00007f53a2830000) libc.so.6 => /lib/x86_64linuxgnu/libc.so.6 (0x00007f53a2430000) libgmp.so.10 => /usr/lib/x86_64linuxgnu/libgmp.so.10 (0x00007f53a21a0000) libz.so.1 => /lib/x86_64linuxgnu/libz.so.1 (0x00007f53a1f80000) libreadline.so.7 => /lib/x86_64linuxgnu/libreadline.so.7 (0x00007f53a1d30000) libm.so.6 => /lib/x86_64linuxgnu/libm.so.6 (0x00007f53a1980000) libdl.so.2 => /lib/x86_64linuxgnu/libdl.so.2 (0x00007f53a1770000) libutil.so.1 => /lib/x86_64linuxgnu/libutil.so.1 (0x00007f53a1560000) /lib64/ldlinuxx8664.so.2 (0x00007f53a3600000) libtinfo.so.5 => /lib/x86_64linuxgnu/libtinfo.so.5 (0x00007f53a1330000)
comment:61 followup: ↓ 62 Changed 23 months ago by
Linux Mint case looks a bit funny, as you have both python 3.7 and 3.8 in one installation? Or they are different?
Could you also post the errors you get in src/sage/groups/libgap_wrapper.pyx ? (which is the root cause of the other errors, I gather)
Anyhow, I'm now testing on Linux Mint 19 (in an lxc container), let's see if this is reproducible.
comment:62 in reply to: ↑ 61 Changed 23 months ago by
Replying to dimpase:
Could you also post the errors you get in src/sage/groups/libgap_wrapper.pyx ? (which is the root cause of the other errors, I gather)
See the attached file!
comment:63 followup: ↓ 66 Changed 23 months ago by
I've installed Linux Mint Tara (i.e. 19) in an xlc container, built this branch there, and ran tests  and everything worked. Here is what I have in the apt sources list
deb http://packages.linuxmint.com tara main upstream import backport deb http://archive.ubuntu.com/ubuntu bionic main restricted universe multiverse deb http://archive.ubuntu.com/ubuntu bionicupdates main restricted universe multiverse deb http://security.ubuntu.com/ubuntu bionicsecurity main restricted universe multiverse
the kernel is
Linux m1 5.4.4806434gd868196d13af #1 SMP PREEMPT Wed Jul 29 00:32:34 PDT 2020 x86_64 x86_64 x86_64 GNU/Linux
So it looks as if everything should run just fine  I guess something is wrong with the particular box, sorry.
comment:64 Changed 23 months ago by
 Status changed from needs_review to positive_review
comment:65 Changed 23 months ago by
 Reviewers changed from Matthias Koeppe, https://github.com/mkoeppe/sage/actions/runs/270864243 to Matthias Koeppe
comment:66 in reply to: ↑ 63 ; followup: ↓ 67 Changed 23 months ago by
Replying to dimpase:
So it looks as if everything should run just fine  I guess something is wrong with the particular box, sorry.
Dima, one thing common to my platforms is, that I have gap3
installed (from https://webusers.imjprg.fr/~jean.michel/gap3/ according to the advices given in src/sage/interfaces/gap3.py
, and I'm using it inside Sage). Did you test with gap3
, as well?
BTW: removing gap 4.8.8 did not help!
comment:67 in reply to: ↑ 66 ; followup: ↓ 69 Changed 23 months ago by
Replying to soehms:
Replying to dimpase:
So it looks as if everything should run just fine  I guess something is wrong with the particular box, sorry.
Dima, one thing common to my platforms is, that I have
gap3
installed (from https://webusers.imjprg.fr/~jean.michel/gap3/ according to the advices given insrc/sage/interfaces/gap3.py
, and I'm using it inside Sage). Did you test withgap3
, as well?
I just tried installing gap3 experimental package and running tests, and nothing is broken for me (in Linux Mint container, too).
I don't know the advantage of following the manual instructions in src/sage/interfaces/gap3.py
instead  are there any?
Perhaps they should be marked as obsolete, or just removed. In any event, WARNING
about broken pexpect
there should go.
Needless to say, if you mangle your Sage installation manually in some way, then all the bets are off, we can't say that Sage has a bug then. :)
comment:68 Changed 23 months ago by
for the latter, see #30686.
comment:69 in reply to: ↑ 67 ; followup: ↓ 70 Changed 23 months ago by
Replying to dimpase:
Replying to soehms: ...
I just tried installing gap3 experimental package and running tests, and nothing is broken for me (in Linux Mint container, too).
Thanks for your help! In the meantime I realized that gap3 isn't the reason for my desaster, either (since against my expectation it was not present on the WSL).
I don't know the advantage of following the manual instructions in
src/sage/interfaces/gap3.py
instead  are there any?
I don't know. I did that years ago when I was new to Sage, and probably didn't know it better.
Perhaps they should be marked as obsolete, or just removed. In any event,
WARNING
about brokenpexpect
there should go.Needless to say, if you mangle your Sage installation manually in some way, then all the bets are off, we can't say that Sage has a bug then. :)
I agree! But that was not my point. I have to fix my facilities until this ticket is released (or completely switch to working in docker containers).
comment:70 in reply to: ↑ 69 ; followup: ↓ 71 Changed 23 months ago by
Replying to soehms:
do you have a particular "interesting" hardware for WSL and Mint  is it the same box? Unusual toolchain?
Could you maybe spin a WSL somewhere else and try to reproduce?
I agree! But that was not my point. I have to fix my facilities until this ticket is released (or completely switch to working in docker containers).
any test errors in src/sage/libs/gap/
? in src/sage/groups/matrix_gps/
?
Or is your problem specifically related to free groups and finitely presented groups?
comment:71 in reply to: ↑ 70 Changed 23 months ago by
Replying to dimpase:
Replying to soehms:
Thanks again for your hints!
do you have a particular "interesting" hardware for WSL and Mint  is it the same box? Unusual toolchain?
The three cases above where all Lenovo ThinkPads (L560 WSL, X240 LinuxMint 19.1, L520 LinuxMint 18, all running on Intel i5). In addition I have now a fourth test case: SonyVaio (on Intel i5, as well, and LinuxMint 17.3).
On the X240 I created a Docker image for the ticket using the $SAGE_ROOT/docker/Dockerfile
. The bug does not show in the corresponding container. So, I think the issue has nothing to do with the hardware.
Could you maybe spin a WSL somewhere else and try to reproduce?
I will check that out.
any test errors in src/sage/libs/gap/ ? in src/sage/groups/matrix_gps/ ? Or is your problem specifically related to free groups and finitely presented groups?
Yes:
File "src/sage/libs/gap/element.pyx", line 1335, in sage.libs.gap.element.GapElement.sage File "src/sage/libs/gap/element.pyx", line 1336, in sage.libs.gap.element.GapElement.sage File "src/sage/libs/gap/element.pyx", line 1338, in sage.libs.gap.element.GapElement.sage File "src/sage/libs/gap/element.pyx", line 1347, in sage.libs.gap.element.GapElement.sage File "src/sage/libs/gap/element.pyx", line 1348, in sage.libs.gap.element.GapElement.sage File "src/sage/libs/gap/element.pyx", line 1350, in sage.libs.gap.element.GapElement.sage File "src/sage/libs/gap/libgap.pyx", line 351, in sage.libs.gap.libgap.Gap._construct_matrix sage t warnlong 46.3 randomseed=0 src/sage/libs/gap/element.pyx # 6 doctests failed sage t warnlong 46.3 randomseed=0 src/sage/libs/gap/libgap.pyx # 1 doctest failed
Under src/sage/groups
there are in sum 1182 failing doctests, 78 of them under sage.groups.matrix_gps
. Free groups and finitely presented groups are just the top scores. Probably they all have the same origin.
comment:72 followup: ↓ 76 Changed 23 months ago by
By the way, do you by any chances have any stray/old patches in build/pkgs/gap/patches
or in build/pkgs/gap_packages/patches
?
Certainly, errors in src/sage/libs/gap/element.pyx
and src/sage/libs/gap/libgap.pyx
are the root of the problem, and should be relatively easy to debug, as it's more or less direct interaction with libgap, and welllocalised  everything has to do with dealing with a GAP variable x
.
So what happens if you run the stuff around line 1335 from libs/gap/element.pyx
?
sage: x = libgap.Integers.Indeterminate("x") sage: x sage: x+1 sage: x^2 sage: p = x^2  2*x + 3
comment:73 followup: ↓ 78 Changed 23 months ago by
 Status changed from positive_review to needs_work
Still hangs the buildbot
[dochtml] [algebras ] building [inventory]: targets for 95 source files that are out of date [dochtml] [algebras ] updating environment: [new config] 95 added, 0 changed, 0 removed [dochtml] [algebras ] The inventory files are in local/share/doc/sage/inventory/en/reference/algebras. [dochtml] Build finished. The built documents can be found in /var/lib/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/algebras [dochtml] [tensor_fr] building [inventory]: targets for 19 source files that are out of date [dochtml] [tensor_fr] updating environment: [new config] 19 added, 0 changed, 0 removed [dochtml] [tensor_fr] The inventory files are in local/share/doc/sage/inventory/en/reference/tensor_free_modules. [dochtml] Build finished. The built documents can be found in /var/lib/buildbot/slave/sage_git/build/local/share/doc/sage/inventory/en/reference/tensor_free_modules [dochtml] Warning: Missing title for sage.combinat.posets.mobile [dochtml] [combinat ] building [inventory]: targets for 379 source files that are out of date [dochtml] [combinat ] updating environment: [new config] 379 added, 0 changed, 0 removed command timed out: 1200 seconds without output running ['make', 'dochtmlmathjax'], attempting to kill process killed by signal 9 program finished with exit code 1 elapsedTime=1394.804628
comment:74 Changed 23 months ago by
 Milestone changed from sage9.2 to sage9.3
How about backporting the patch added for Xcode 12 and leaving the gap upgrade to the 9.3 series.
comment:75 Changed 23 months ago by
Created #30720 for this
comment:76 in reply to: ↑ 72 ; followup: ↓ 77 Changed 23 months ago by
Replying to dimpase:
By the way, do you by any chances have any stray/old patches in
build/pkgs/gap/patches
or inbuild/pkgs/gap_packages/patches
?
No!
Certainly, errors in
src/sage/libs/gap/element.pyx
andsrc/sage/libs/gap/libgap.pyx
are the root of the problem, and should be relatively easy to debug, as it's more or less direct interaction with libgap, and welllocalised  everything has to do with dealing with a GAP variablex
.So what happens if you run the stuff around line 1335 from
libs/gap/element.pyx
?sage: x = libgap.Integers.Indeterminate("x") sage: x sage: x+1 sage: x^2 sage: p = x^2  2*x + 3
The crash already occured at the addition x+1
, more precisely in local/lib/python3.8/sitepackages/cysignals/macros.h
. It jumped to line 134 even though cysigs.sig_on_count
was zero.
(gdb) n __pyx_f_4sage_4libs_3gap_7element_10GapElement__add_ (__pyx_v_self=0x7f5e227f1840, __pyx_v_right=0x7f5e2281eb00, __pyx_skip_dispatch=<optimized out>) at build/cythonized/sage/libs/gap/element.c:10206 10206 __pyx_t_5 = sig_on(); if (unlikely(__pyx_t_5 == ((int)0))) __PYX_ERR(0, 1007, __pyx_L4_error) (gdb) s _sig_on_prejmp (message=0x0, file=0x7f5e31f0c728 "build/cythonized/sage/libs/gap/element.c", line=10206) at /home/sebastian/develop/sage/local/lib/python3.8/sitepackages/cysignals/macros.h:117 117 cysigs.s = message; (gdb) s 132 if (cysigs.sig_on_count > 0) (gdb) p cysigs.sig_on_count $2 = 0 (gdb) l 127 fprintf(stderr, "\n*** ERROR *** sig_on() with sig_on_count = %i, block_sigint = %i\n", 128 (int)cysigs.sig_on_count, (int)cysigs.block_sigint); 129 print_backtrace(); 130 } 131 #endif 132 if (cysigs.sig_on_count > 0) 133 { 134 cysigs.sig_on_count++; 135 return 1; 136 } (gdb) s 134 cysigs.sig_on_count++; (gdb) p cysigs.sig_on_count $3 = 0
Therefore, I ran
sage f cysignals make build
and that solved the problem!
But, why did I have to do that even in the case where I build fro scratch? Anyway, thanks a lot for your patience!
comment:77 in reply to: ↑ 76 ; followup: ↓ 96 Changed 23 months ago by
Replying to soehms: [...]
Therefore, I ran
sage f cysignals make buildand that solved the problem!
Great!
But, why did I have to do that even in the case where I build fro scratch? Anyway, thanks a lot for your patience!
Could be #30687 (with the original suject: "local/lib/python3*" must be removed)  unless
you did run make distclean
which removes local/
completely anyway...
comment:78 in reply to: ↑ 73 Changed 23 months ago by
Replying to vbraun:
Still hangs the buildbot
Someone has to debug this somehow, I have no clue what's going on there. Could you do another strace ff ...
as in comment:29 ?
comment:79 Changed 23 months ago by
 Work issues set to rebase on top of #30720
comment:80 Changed 23 months ago by
 Commit changed from 2ffc24af85679499aff4846b1f135f8cea22b8c0 to 649bc8defe5c4f58da7582b1f7bfa10f1c3f793e
Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:
2033e4a  libsemigroups update

540d761  patches from Arch (cf #29314)

98267a5  tagged #random tests with output depending upon gap_packages installed

aec0937  one more doctest fix

8a2251e  more robust test, so that GAP's packages don't matter

d2fb822  increase memory pool for libgap

22c7420  build/pkgs/gap_packages: Use symlinks to refer to gap's tarball

b54ec20  version bump

3b22dd9  remove old workaround from #22626

649bc8d  this file should exist  leave just comments there

comment:81 Changed 23 months ago by
 Dependencies changed from #30496 to #30720
 Status changed from needs_work to needs_review
 Work issues rebase on top of #30720 deleted
rebased over #30720
comment:82 Changed 23 months ago by
The patches for gap_packages
don't work:
Applying patches from ../patches... Applying ../patches/cohomologcc10.patch can't find file to patch at input line 5 Perhaps you used the wrong p or strip option? The text leading up to this was:  diff git a/pkg/cohomolo1.6.7/standalone/progs.d/crp1.c b/pkg/cohomolo1.6.7/standalone/progs.d/crp1.c index 3bbdc45..7df699f 100644  a/pkg/cohomolo1.6.7/standalone/progs.d/crp1.c +++ b/pkg/cohomolo1.6.7/standalone/progs.d/crp1.c  File to patch: Skip this patch? [y] Skipping patch. 4 out of 4 hunks ignored can't find file to patch at input line 54 Perhaps you used the wrong p or strip option? The text leading up to this was:  diff git a/pkg/cohomolo1.6.7/standalone/progs.d/nq+chfns.c b/pkg/cohomolo1.6.7/standalone/progs.d/nq+chfns.c index a7396b2..658496f 100644  a/pkg/cohomolo1.6.7/standalone/progs.d/nq+chfns.c +++ b/pkg/cohomolo1.6.7/standalone/progs.d/nq+chfns.c  File to patch: Skip this patch? [y] Skipping patch. 4 out of 4 hunks ignored can't find file to patch at input line 98 Perhaps you used the wrong p or strip option? The text leading up to this was:  diff git a/pkg/cohomolo1.6.7/standalone/progs.d/nqmfns.c b/pkg/cohomolo1.6.7/standalone/progs.d/nqmfns.c index 0896551..6841bc8 100644  a/pkg/cohomolo1.6.7/standalone/progs.d/nqmfns.c +++ b/pkg/cohomolo1.6.7/standalone/progs.d/nqmfns.c  File to patch: Skip this patch? [y] Skipping patch. 4 out of 4 hunks ignored can't find file to patch at input line 135 Perhaps you used the wrong p or strip option? The text leading up to this was:  diff git a/pkg/cohomolo1.6.7/standalone/progs.d/nqmp.c b/pkg/cohomolo1.6.7/standalone/progs.d/nqmp.c index 01cf914..0144883 100644  a/pkg/cohomolo1.6.7/standalone/progs.d/nqmp.c +++ b/pkg/cohomolo1.6.7/standalone/progs.d/nqmp.c  File to patch: Skip this patch? [y] Skipping patch. 2 out of 2 hunks ignored Error applying '../patches/cohomologcc10.patch' ************************************************************************ Error applying patches ************************************************************************
comment:83 Changed 23 months ago by
I see: the versions are wrong. Here's a fix.
comment:84 Changed 23 months ago by
 Branch changed from u/dimpase/packages/gap411 to u/jhpalmieri/packages/gap411
comment:85 followup: ↓ 91 Changed 23 months ago by
 Commit changed from 649bc8defe5c4f58da7582b1f7bfa10f1c3f793e to 47fcc169297fdf7cc7b58c8f454255bb29f955c5
This (including libsemigroups
and gap_packages
) builds for me on OS X with Xcode 12.
New commits:
47fcc16  trac 29314: fix version numbers in patches for gap_packages

comment:86 Changed 23 months ago by
Building the documentation, I see
Error, reached the preset memory limit (change it with the o command line option)
I don't remember ever seeing this before. (The documentation build continues, but the error message was strange.)
comment:87 followup: ↓ 89 Changed 23 months ago by
Then patching the failing packages in #30729 using the diff to GAP 4.11 would be a way forward
comment:88 Changed 23 months ago by
Doctests pass for me (with libsemigroups
and gap_packages
installed).
comment:89 in reply to: ↑ 87 Changed 23 months ago by
comment:90 followup: ↓ 92 Changed 23 months ago by
There are unresolved problems with this upgrade
comment:91 in reply to: ↑ 85 ; followup: ↓ 95 Changed 23 months ago by
Replying to jhpalmieri:
This (including
libsemigroups
andgap_packages
) builds for me on OS X with Xcode 12.
thanks for fixing this. What XCode 12 are you on? 12.0? 12.2?
comment:92 in reply to: ↑ 90 Changed 23 months ago by
Replying to mkoeppe:
There are unresolved problems with this upgrade
and a problem I cannot debug, as it's essentially a privately run network of buildbots which (in part?) seem to hang on our damn docbuild :(
comment:93 Changed 23 months ago by
 Status changed from needs_review to needs_work
comment:94 Changed 23 months ago by
It does not seem realistic to get this ticket done for 9.2. So let's do #30729
comment:95 in reply to: ↑ 91 Changed 23 months ago by
Replying to dimpase:
Replying to jhpalmieri:
This (including
libsemigroups
andgap_packages
) builds for me on OS X with Xcode 12.thanks for fixing this. What XCode 12 are you on? 12.0? 12.2?
12.0.1
comment:96 in reply to: ↑ 77 Changed 22 months ago by
Replying to dimpase:
Replying to soehms: [...]
Therefore, I ran
sage f cysignals make buildand that solved the problem!
Great!
But, why did I have to do that even in the case where I build fro scratch? Anyway, thanks a lot for your patience!
Could be #30687 (with the original suject: "local/lib/python3*" must be removed)  unless you did run
make distclean
which removeslocal/
completely anyway...
It must be an independent problem. As it appears now on all of my systems (by whatever reason) I have to rebuild cysignals
whenever I switch back and forth between gap 4.10 and 4.11. This is regardless of whether I merged #30687 in or not.
comment:97 Changed 22 months ago by
perhaps buildbot hanging is a multithreading issue  libgap in not multithreaded, calling it from several threads is asking for trouble: https://github.com/gapsystem/gap/issues/2893#issuecomment707700408
comment:98 followup: ↓ 101 Changed 22 months ago by
we should move PackageManager GAP package from gap_packages to gap  it is small and useful.
comment:99 Changed 21 months ago by
 Status changed from needs_work to needs_review
The ball here is in Volker's court. I have no idea why his buildbots hang.
comment:100 Changed 21 months ago by
 Reviewers changed from Matthias Koeppe to Matthias Koeppe, ...
comment:101 in reply to: ↑ 98 ; followup: ↓ 102 Changed 21 months ago by
Replying to dimpase:
we should move PackageManager GAP package from gap_packages to gap  it is small and useful.
+1  separate ticket or here?
comment:102 in reply to: ↑ 101 Changed 21 months ago by
comment:103 Changed 21 months ago by
 Branch changed from u/jhpalmieri/packages/gap411 to u/dimpase/packages/gap411
 Commit changed from 47fcc169297fdf7cc7b58c8f454255bb29f955c5 to 9836f794b7bf90f9c3b6c1b2928f032f4a7bd093
 Dependencies #30720 deleted
comment:104 Changed 21 months ago by
rebased over the latest beta, moved PackageManager GAP package as discussed.
comment:105 followup: ↓ 106 Changed 21 months ago by
 Cc ghtobiasdiez added
 Reviewers changed from Matthias Koeppe, ... to Matthias Koeppe, Tobias Diez, ...
I've used this ticket in #30371, and it runs well on the github action (https://github.com/tobiasdiez/sage/runs/1413136300?check_suite_focus=true). In particular, there was no "hanging" or multithreading problem.
The only gap related doc tests that fail are:
20201117T17:27:35.4675866Z sage t randomseed=0 /__w/sage/sage/src/sage/interfaces/gap_workspace.py 20201117T17:27:35.4676910Z ********************************************************************** 20201117T17:27:35.4677821Z File "/__w/sage/sage/src/sage/interfaces/gap_workspace.py", line 55, in sage.interfaces.gap_workspace.gap_workspace_file 20201117T17:27:35.4681873Z Failed example: 20201117T17:27:35.4683784Z name1 = Popen([sys.executable, 'c', cmd], stdout=PIPE).communicate()[0] 20201117T17:27:35.4684739Z Expected nothing 20201117T17:27:35.4685235Z Got: 20201117T17:27:35.4686344Z /__w/sage/sage/src/sage/calculus/functional.py:57: DeprecationWarning: invalid escape sequence \d 20201117T17:27:35.4687468Z """ 20201117T17:27:39.4060681Z ********************************************************************** 20201117T17:27:39.4062343Z File "/__w/sage/sage/src/sage/interfaces/gap_workspace.py", line 56, in sage.interfaces.gap_workspace.gap_workspace_file 20201117T17:27:39.4063371Z Failed example: 20201117T17:27:39.4065030Z name2 = Popen([sys.executable, 'c', cmd], stdout=PIPE).communicate()[0] 20201117T17:27:39.4065813Z Expected nothing 20201117T17:27:39.4066315Z Got: 20201117T17:27:39.4067147Z /__w/sage/sage/src/sage/calculus/functional.py:57: DeprecationWarning: invalid escape sequence \d 20201117T17:27:39.4067993Z """ 20201117T17:27:39.4129689Z **********************************************************************
But that could also very well be a result of the somewhat unusual setup of #30371. So from my side this looks good.
comment:106 in reply to: ↑ 105 Changed 21 months ago by
Replying to ghtobiasdiez:
I've used this ticket in #30371, and it runs well on the github action (https://github.com/tobiasdiez/sage/runs/1413136300?check_suite_focus=true). In particular, there was no "hanging" or multithreading problem.
The only gap related doc tests that fail are:
Thanks. I can't reproduce these, they don't seem to originate from this ticket.
comment:107 Changed 20 months ago by
 Branch changed from u/dimpase/packages/gap411 to u/mkoeppe/packages/gap411
comment:108 Changed 20 months ago by
 Commit changed from 9836f794b7bf90f9c3b6c1b2928f032f4a7bd093 to a28138c2fc1396171734b12fdbe5904b79bf1ec1
 Reviewers changed from Matthias Koeppe, Tobias Diez, ... to Matthias Koeppe, Tobias Diez, https://github.com/mkoeppe/sage/actions/runs/409420323
New commits:
a28138c  Merge tag '9.3.beta3' into t/29314/packages/gap411

comment:109 Changed 20 months ago by
 Reviewers changed from Matthias Koeppe, Tobias Diez, https://github.com/mkoeppe/sage/actions/runs/409420323 to Matthias Koeppe, Tobias Diez
 Status changed from needs_review to positive_review
Looks all fine on GH Actions. (comment:25 of course still applies)
comment:110 Changed 20 months ago by
 Branch changed from u/mkoeppe/packages/gap411 to a28138c2fc1396171734b12fdbe5904b79bf1ec1
 Resolution set to fixed
 Status changed from positive_review to closed
Does the upgrade fix #28728?