Opened 2 years ago

Closed 23 months ago

Last modified 22 months ago

#29456 closed task (fixed)

configure: Accept gcc/gfortran 10.x

Reported by: mkoeppe Owned by:
Priority: critical Milestone: sage-9.2
Component: porting Keywords: sd109
Cc: dimpase, mjo, fbissey, vbraun, enriqueartal, alexjbest, heluani, charpent Merged in:
Authors: Matthias Koeppe Reviewers: Volker Braun
Report Upstream: N/A Work issues:
Branch: c898920 (Commits, GitHub, GitLab) Commit:
Dependencies: #3360, #29766 Stopgaps:

Status badges

Description (last modified by mkoeppe)

As all build errors of standard packages with gcc/gfortran 10 have been fixed, we change the gcc and gfortran configure scripts to again accept these versions.

This ticket does not change the version of the gcc spkg.

Previous tickets:

  • gf2x: #29390 gf2x build fails on fedora-32-minimal
  • SciPy: Upgrade to SciPy 1.2.3 (last release supporting py2 - #29443) does not fix it
  • #29766: Upgrade NumPy?, scipy, networkx, add pybind11 package (dup: #29425)
  • sympow: see #3360
  • palp: #29859
  • gcc: #29674: fedora-32: Building gcc (9.2.0) spkg fails with gcc 10
  • #30067 gfortran spkg-configure: Reject versions >= 10

Related discussions:

Change History (60)

comment:1 Changed 2 years ago by mkoeppe

  • Priority changed from major to critical
  • Summary changed from Meta-ticket: Support gcc 10 (fedora-32) to Meta-ticket: Support gcc 10, needed for fedora-32 build (scheduled to be released end of April 2020)

comment:2 Changed 2 years ago by mkoeppe

  • Cc mjo fbissey added

comment:3 follow-up: Changed 2 years ago by fbissey

Any more details on palp?

comment:4 follow-up: Changed 2 years ago by fbissey

Also, if we are targeting 9.2 we can move to higher scipy.

comment:5 in reply to: ↑ 3 ; follow-up: Changed 2 years ago by mkoeppe

Replying to fbissey:

Any more details on palp?

For example here: https://github.com/mkoeppe/sage/runs/618646432?check_suite_focus=true

comment:6 in reply to: ↑ 4 Changed 2 years ago by mkoeppe

Replying to fbissey:

Also, if we are targeting 9.2 we can move to higher scipy.

As far as I can see there is no release yet with the fix

comment:7 Changed 2 years ago by mkoeppe

  • Cc vbraun added

Question is whether we want to fix this for 9.1 already.

comment:8 Changed 2 years ago by mkoeppe

  • Description modified (diff)

comment:9 Changed 2 years ago by mkoeppe

  • Description modified (diff)

comment:10 Changed 2 years ago by mkoeppe

Presumably Fedora 32 has patched packages.

comment:11 Changed 2 years ago by mkoeppe

  • Description modified (diff)

comment:12 in reply to: ↑ 5 Changed 2 years ago by dimpase

Replying to mkoeppe:

Replying to fbissey:

Any more details on palp?

For example here: https://github.com/mkoeppe/sage/runs/618646432?check_suite_focus=true

2020-04-26T04:55:26.7728042Z   [palp-2.1.p2]   MoriCone.c: In function 'Triang2dSFan':
2020-04-26T04:55:26.7728579Z   [palp-2.1.p2]   MoriCone.c:489:48: warning: 'Z[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
2020-04-26T04:55:26.7729093Z   [palp-2.1.p2]     489 | #define BZangle(a,b) (ConeAngle(B.x[Z[a]],B.x[Z[b]])) // Gale-points
2020-04-26T04:55:26.7729654Z   [palp-2.1.p2]         |                                                ^
2020-04-26T04:55:26.7730199Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE   -c -o SingularInput.o SingularInput.c
2020-04-26T04:55:26.7730774Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o poly.x poly.o Coord.o Rat.o Vertex.o Polynf.o LG.o
2020-04-26T04:55:26.7731343Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o class.x class.o Coord.o Rat.o Vertex.o Polynf.o Subpoly.o Subadd.o Subdb.o
2020-04-26T04:55:26.7731892Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o cws.x cws.o Coord.o Rat.o Vertex.o Polynf.o LG.o
2020-04-26T04:55:26.7732465Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o nef.x nef.o Coord.o Rat.o Vertex.o Polynf.o E_Poly.o Nefpart.o LG.o
2020-04-26T04:55:26.7733264Z   [palp-2.1.p2]   gcc -O3 -W -Wall  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o mori.x mori.o Coord.o Rat.o Vertex.o Polynf.o MoriCone.o SingularInput.o LG.o
2020-04-26T04:55:26.7733900Z   [palp-2.1.p2]   /usr/bin/ld: MoriCone.o:(.bss+0x0): multiple definition of `nr_SR_elements'; mori.o:(.bss+0x10): first defined here
2020-04-26T04:55:26.7734659Z   [palp-2.1.p2]   /usr/bin/ld: SingularInput.o:(.bss+0x0): multiple definition of `nr_SR_elements'; mori.o:(.bss+0x10): first defined here
2020-04-26T04:55:26.7735158Z   [palp-2.1.p2]   /usr/bin/ld: SingularInput.o: in function `HyperSurfSingular':
2020-04-26T04:55:26.7735673Z   [palp-2.1.p2]   SingularInput.c:(.text+0x1e1): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
2020-04-26T04:55:26.7736112Z   [palp-2.1.p2]   collect2: error: ld returned 1 exit status
2020-04-26T04:55:26.7736565Z   [palp-2.1.p2]   make[4]: *** [Makefile:50: mori] Error 1
2020-04-26T04:55:26.7737028Z   [palp-2.1.p2]   make[4]: Target 'all' not remade because of errors.
2020-04-26T04:55:26.7737532Z   [palp-2.1.p2]   make[4]: Leaving directory '/sage/local/var/tmp/sage/build/palp-2.1.p2/src'
2020-04-26T04:55:26.7738036Z   [palp-2.1.p2]   ********************************************************************************
2020-04-26T04:55:26.7738482Z   [palp-2.1.p2]   Error building palp-2.1.p2
  • before the logs exprire...

comment:13 Changed 2 years ago by mkoeppe

  • Description modified (diff)

comment:14 Changed 2 years ago by mkoeppe

  • Cc enriqueartal added

comment:15 Changed 2 years ago by mkoeppe

  • Summary changed from Meta-ticket: Support gcc 10, needed for fedora-32 build (scheduled to be released end of April 2020) to Meta-ticket: Support gcc 10, needed for fedora-32 build (released end of April 2020)

comment:16 Changed 2 years ago by mkoeppe

  • Description modified (diff)

comment:17 Changed 2 years ago by mkoeppe

  • Description modified (diff)

comment:18 Changed 2 years ago by slelievre

  • Description modified (diff)

comment:19 Changed 2 years ago by enriqueartal

Besides the packages cited in the description (cannot say about gf2x) gap_packages does not build, due to cohomolo package.

comment:20 Changed 2 years ago by gh-timokau

Palp 2.11 mentions gcc 10 compatibility:

palp-2.11.tar.gz: Small change in Mori.h for compatibility with gcc_10 and other minor patches (thanks to J. Puydt) [May 18, 2020].

-- http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html

comment:21 follow-up: Changed 2 years ago by gh-timokau

Unfortunately I'm not sure if the upstream source tarball for palp 2.11 is finalized though. Since I've packaged it 3 days ago (https://github.com/NixOS/nixpkgs/pull/87944) the tarball silently changed.

comment:22 in reply to: ↑ 21 Changed 2 years ago by fbissey

Replying to gh-timokau:

Unfortunately I'm not sure if the upstream source tarball for palp 2.11 is finalized though. Since I've packaged it 3 days ago (https://github.com/NixOS/nixpkgs/pull/87944) the tarball silently changed.

I just adopted the patch already shipped in fedora until a new release.

  • sympow is fixed by upgrading to the new fork.
  • scipy can be fixed by adding some fortran flags until they fix the code, -std=legacy I think. I otherwise built sage-on-gentoo successfully with gcc-10 but I am not sure I have scanned absolutely all the packages.

comment:23 Changed 2 years ago by gh-timokau

For what it's worth, upstream confirmed that palp 2.11 is stable and no further changes are expected.

comment:24 Changed 2 years ago by mkoeppe

  • Keywords sd109 added

comment:25 Changed 2 years ago by mkoeppe

  • Description modified (diff)

I have opened #29859 for palp

comment:26 Changed 2 years ago by mkoeppe

  • Description modified (diff)

comment:27 Changed 2 years ago by dimpase

Homebrew is pushing to use gcc10, their current gcc+gfortran is gcc10, and their current openblas, scipy are all gcc10-dependent.

comment:28 Changed 2 years ago by mkoeppe

  • Dependencies set to #3360, #29766

comment:29 Changed 2 years ago by mkoeppe

  • Branch set to u/mkoeppe/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

comment:30 Changed 2 years ago by mkoeppe

  • Commit set to 5f3b27c4e5a85413a9ed5790d4ab49071b4d33fb
  • Summary changed from Meta-ticket: Support gcc 10, needed for fedora-32 build (released end of April 2020) to Meta-ticket: Support gcc 10

Last 10 new commits:

e592bdcMerge branch 't/29425/trac/local_conda_forge_macos_standard__build_error_with_numpy' into t/29766/packages/networkx24
11bf67fMerge branch 't/29813/add_pytest_as_a_type_optional__source_pip_package' into t/29766/packages/networkx24
db0fa41build/pkgs/scipy: Add patch for scipy pr 11320
2efe841Merge tag '9.2.beta3' into t/29766/packages/networkx24
634ce73build/pkgs: Update numpy to 1.19, scipy to 1.5.1
a2e1978build/pkgs/scipy/patches/pr-11320.patch: Remove
0879c3bbuild/pkgs/{numpy,scipy}/checksums.ini: Set upstream_url to pypi.io
8a70eberight place for warnings.filterwarnings() for networkx & scipy
e9dc48dMerge branch 'u/dimpase/packages/networkx24' of git://trac.sagemath.org/sage into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
5f3b27cbuild/pkgs/gcc/spkg-configure.m4: Do not reject gcc (gnu) >= 10

comment:32 Changed 2 years ago by git

  • Commit changed from 5f3b27c4e5a85413a9ed5790d4ab49071b4d33fb to 87db1a54bebee5cc4f9ef5deb46e603121173aa9

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

bfb2fb4tox.ini: Add environment local-homebrew-usrlocal
aded967Merge commit '8195cb821e01e0cb627240d7135d5634c265cab0' of git://trac.sagemath.org/sage into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
07d657dMerge tag '9.2.beta4' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
bd15fb9build/bin/write-dockerfile.sh, tox.ini: Do not run testsuites that need pip (ssl)
87db1a5Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

comment:33 Changed 2 years ago by mkoeppe

  • Dependencies changed from #3360, #29766 to #3360, #29766, #29929

comment:34 Changed 2 years ago by mkoeppe

  • Dependencies changed from #3360, #29766, #29929 to #3360, #29766, #29929, #30118

comment:35 Changed 2 years ago by git

  • Commit changed from 87db1a54bebee5cc4f9ef5deb46e603121173aa9 to 7feee5cd43aa2ed0ce21090d27b92f28a48db679

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

25393b0Handle SAGE_CHECK_PACKAGES in build/make/Makefile.in, not sage-spkg
5aca238Merge branch 't/30118/handle_sage_check_packages_in_build_make_makefile_in__not_sage_spkg' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
7feee5cMerge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

comment:37 Changed 2 years ago by mkoeppe

  • Summary changed from Meta-ticket: Support gcc 10 to Meta-ticket: Support gcc/gfortran 10

comment:38 Changed 2 years ago by git

  • Commit changed from 7feee5cd43aa2ed0ce21090d27b92f28a48db679 to e5bf863eeef843426f7bde6b760e5a6db0e146f2

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

b25b74aMerge tag '9.2.beta5' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
0356be9Merge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29766/packages/networkx24
abb8c7eMerge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
6954debbuild/pkgs/networkx/dependencies: Conditionalize on SAGE_CHECK_networkx
e5bf863Merge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

comment:40 Changed 2 years ago by enriqueartal

Tested successfully, up to the download of numpy and scipy.

comment:42 Changed 2 years ago by git

  • Commit changed from e5bf863eeef843426f7bde6b760e5a6db0e146f2 to 7cf9a5cefdd2c37b588467e2bdee21e5763b63c9

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

d39817fbuild/pkgs/numpy: Downgrade to 1.18.5 to fix build error on debian-jessie
879375bMerge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
a17c655m4/sage_spkg_collect.m4: Do not include script packages in SAGE_SDIST_PACKAGES
827923abootstrap: Accept 2020s in config.guess version check
c30ac54tox.ini: Add local-nobootstrap
de6464d.github/workflows/tox.yml: Add jobs "dist", "local-macos-nohomebrew
775b7f7Trac #30088: add a few explanatory comments to m4/sage_spkg_collect.m4.
160862fm4/sage_spkg_collect.m4: Mention sagelib in the comment
d1a2cbfMerge branch 't/30088/fix__make_sdist___add_test_run_to_github_actions' into t/29929/tox_ini__add_a_macos_environment_without_homebrew__conda
7cf9a5cMerge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

comment:43 Changed 2 years ago by git

  • Commit changed from 7cf9a5cefdd2c37b588467e2bdee21e5763b63c9 to 4e6d8a39e95d944cdf1182a2689521572bc4480e

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

fcddf69Revert "build/pkgs/numpy: Downgrade to 1.18.5 to fix build error on debian-jessie"
3558737build/pkgs/numpy/patches/16871.patch: New
4e6d8a3Merge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_

comment:44 Changed 2 years ago by git

  • Commit changed from 4e6d8a39e95d944cdf1182a2689521572bc4480e to 2035df27e6fe42202f433fba6e9bf8ef708fb198

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

ba0ccb6Experimental: Use numpy PR 16871
c24d109build/pkgs/cython: Updatt to 0.29.21
79bf297Merge branch 't/29861/upgrade_cython_to_0_29_20' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
2035df2Fixup: Experimental: Use numpy PR 16871

comment:45 Changed 2 years ago by alexjbest

  • Cc alexjbest added

comment:46 Changed 2 years ago by heluani

  • Cc heluani added

comment:47 Changed 23 months ago by mkoeppe

  • Dependencies changed from #3360, #29766, #29929, #30118 to #3360, #29766

comment:48 Changed 23 months ago by git

  • Commit changed from 2035df27e6fe42202f433fba6e9bf8ef708fb198 to 95e8a22f27ad65051423b5f2aa87844da67859d0

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

56fe1c2Merge branch 't/3360/sympow-2.23.2' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
1bf6249Update numpy to 1.19.1, add patches
061e975Merge branch 'u/mkoeppe/upgrade_cython_to_0_29_20' of git://trac.sagemath.org/sage into t/29766/packages/networkx24
fc7592cMerge branch 't/29929/tox_ini__add_a_macos_environment_without_homebrew__conda' into t/29766/packages/networkx24
7fe5985right place for warnings.filterwarnings() for networkx & scipy
5fa0bbabuild/pkgs/scipy: Update to 1.5.2
3890e1abuild/make/Makefile.in: Improve handling of SAGE_CHECK_PACKAGES
5d4b013build/make/Makefile.in: Handle the case in which SAGE_CHECK_PACKAGES is set using a command argument
fb9806aMerge branch 't/29766/packages/networkx24' into t/29456/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_
95e8a22build/pkgs/{gcc,gfortran}/spkg-configure.m4: Accept gcc 10.x

comment:49 Changed 23 months ago by mkoeppe

comment:50 Changed 23 months ago by git

  • Commit changed from 95e8a22f27ad65051423b5f2aa87844da67859d0 to c89892025562e732bb6bf12a992ece975388c791

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

c898920build/pkgs/gcc/spkg-configure.m4: Fixup

comment:51 Changed 23 months ago by enriqueartal

I have just built it successfully. It failed the installation of gap_packages because of package cohomolo but it also fails to compile in gap itself.

comment:52 follow-up: Changed 23 months ago by mkoeppe

Thanks for testing!

If there's no ticket for gap_packages yet, could you open one please?

comment:53 in reply to: ↑ 52 Changed 23 months ago by dimpase

Replying to mkoeppe:

Thanks for testing!

If there's no ticket for gap_packages yet, could you open one please?

I just opened https://github.com/gap-packages/cohomolo/issues/24 (verified that it's a problem with gcc-10 on Gentoo)

comment:54 Changed 23 months ago by mkoeppe

  • Description modified (diff)
  • Status changed from new to needs_review
  • Summary changed from Meta-ticket: Support gcc/gfortran 10 to configure: Accept gcc/gfortran 10.x

comment:55 Changed 23 months ago by mkoeppe

  • Cc charpent added

comment:56 follow-up: Changed 23 months ago by vbraun

  • Authors set to Matthias Koeppe
  • Reviewers set to Volker Braun
  • Status changed from needs_review to positive_review

comment:57 Changed 23 months ago by mkoeppe

Thanks.

comment:58 in reply to: ↑ 56 Changed 23 months ago by charpent

Replying to vbraun:

FWIW, worked for me for the upgrade to 9.2.beta9...

comment:59 Changed 23 months ago by vbraun

  • Branch changed from u/mkoeppe/meta_ticket__support_gcc_10__needed_for_fedora_32_build__released_end_of_april_2020_ to c89892025562e732bb6bf12a992ece975388c791
  • Resolution set to fixed
  • Status changed from positive_review to closed

comment:60 Changed 22 months ago by dimpase

  • Commit c89892025562e732bb6bf12a992ece975388c791 deleted

this seems not to be in beta9, right? should it be in beta10?

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