Upgrade: Singular 4.2.1 #32001

mkoeppe · 2021-06-18T06:20:26Z

released 2021-06-09

Previous update: #31642 (4.2.0p3)

CC: @kiwifb @mkoeppe @orlitzky

Component: packages: standard

Keywords: upgrade, singular

Author: Samuel Lelièvre

Branch/Commit: 0629663

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/32001

The text was updated successfully, but these errors were encountered:

mkoeppe · 2021-06-25T04:07:40Z

comment:1

This will need careful checking in particular on Cygwin.
It appears that the last update to 4.2.0p3 broke Cygwin again - https://github.com/mkoeppe/sage/runs/2909494587?check_suite_focus=true

 [pynac-0.7.27.p8]   /usr/lib/gcc/x86_64-pc-cygwin/10/../../../../x86_64-pc-cygwin/bin/ld: .libs/libpynac_la-mpoly-singular.o:/opt/sage-a9c3c18820b8c96cd2336b90dc480417eaefd6d6/var/tmp/sage/build/pynac-0.7.27.p8/src/ginac/mpoly-singular.cpp:110: undefined reference to `operator-(CanonicalForm const&)'
  [pynac-0.7.27.p8]   /usr/lib/gcc/x86_64-pc-cygwin/10/../../../../x86_64-pc-cygwin/bin/ld: .libs/libpynac_la-mpoly-singular.o: in function `num2canonical':
  [pynac-0.7.27.p8]   /opt/sage-a9c3c18820b8c96cd2336b90dc480417eaefd6d6/var/tmp/sage/build/pynac-0.7.27.p8/src/ginac/mpoly-singular.cpp:94: undefined reference to `operator-(CanonicalForm const&)'
  [pynac-0.7.27.p8]   /usr/lib/gcc/x86_64-pc-cygwin/10/../../../../x86_64-pc-cygwin/bin/ld: /opt/sage-a9c3c18820b8c96cd2336b90dc480417eaefd6d6/var/tmp/sage/build/pynac-0.7.27.p8/src/ginac/mpoly-singular.cpp:104: undefined reference to `operator-(CanonicalForm const&)'
  [pynac-0.7.27.p8]   collect2: error: ld returned 1 exit status
  [pynac-0.7.27.p8]   make[5]: *** [Makefile:560: libpynac.la] Error 1
  [pynac-0.7.27.p8]   make[5]: Target 'all' not remade because of errors.
  [pynac-0.7.27.p8]   make[4]: *** [Makefile:495: all-recursive] Error 1
  [pynac-0.7.27.p8]   make[3]: *** [Makefile:402: all] Error 2
  [pynac-0.7.27.p8]   ********************************************************************************

(this is #32156)

slel · 2021-07-11T22:38:35Z

comment:3

Where to download the sources from? There seems to be two options:

https://github.com/Singular/Singular/releases/tag/Release-4-2-1
ftp://jim.mathematik.uni-kl.de/pub/Math/Singular/SOURCES/

kiwifb · 2021-07-11T22:40:26Z

comment:4

Usually the ftp has a complete dist tarball while github just have the source (not autoconf generated), although I haven't checked lately.

dimpase · 2021-07-18T09:57:13Z

comment:5

GitHub seems to have only the GitHub's automatically generated tarballs.

slel · 2021-07-18T19:01:34Z

Author: Samuel Lelièvre

slel · 2021-07-18T19:01:34Z

Branch: u/slelievre/32001

slel · 2021-07-18T19:01:34Z

Commit: e45bdf7

slel · 2021-07-18T19:01:34Z

comment:6

This branch passes testlong on Debian.

(Except one test in src/sage/modular/local_comp/local_comp.py
which has a hotfix in #29977 and is the object of #32134.)

Launching GitHub actions on this would be useful.

I've pushed a branch to my fork on GitHub:

https://github.com/slel/sage/tree/32001

but I don't remember if that's enough to launch tests
on multiple platforms. I can see

https://github.com/slel/sage/actions/runs/1042993351

which indicates linting tests have failed (unsurprisingly
as linting the whole Sage code base is work in progress);
does that block further tests from running?

New commits:

`e45bdf7`	`32001: Upgrade: Singular 4.2.1`

dimpase · 2021-07-18T19:09:19Z

comment:7

you need to choose TOX workflow by Actions
and pick the branch to test manually

mkoeppe · 2021-07-18T19:09:39Z

comment:8

... or push a tag.

slel · 2021-07-20T00:03:36Z

comment:9

Thanks for the reminder. I pushed tag 32001,
which launched some bots.

https://github.com/slel/sage/actions

dimpase · 2021-07-20T10:01:42Z

comment:10

A new trouble with GH Actions, not enough disk space:

[sagelib-9.4.beta4]   build/cythonized/sage/ext/interpreters/wrapper_rdf.c:9127:1: fatal error: error writing to /tmp/ccRPWbhl.s: No space left on device

:-( (that's on Ubuntu 20.04)

mkoeppe · 2021-07-21T00:11:04Z

comment:11

The pynac failure on cygwin-standard is unfortunately still there with this update https://github.com/slel/sage/runs/3114171604?check_suite_focus=true

slel · 2021-07-22T05:25:21Z

comment:13

Adding #32257 as a dependency as it makes this work on Cygwin.

slel · 2021-07-22T05:25:21Z

Dependencies: #32257

mkoeppe · 2021-07-22T15:55:41Z

comment:14

Another round of GH Actions on top of 9.4.beta5 + #32257 would be good

slel · 2021-07-22T17:11:31Z

Changed commit from e45bdf7 to 9a73ab2

slel · 2021-07-22T17:11:31Z

Changed branch from u/slelievre/32001 to public/32001

slel · 2021-07-22T17:11:31Z

comment:15

Rebased on #32257.

Pushed tag ci-32001 to launch a new round of gh-actions.

https://github.com/slel/sage/actions

New commits:

`d4156f7`	`build/pkgs/singular/patches/0001-factory-canonicalform.h-Add-more-FACTORY_PUBLIC.patch: New`
`9a73ab2`	`32001: Upgrade: Singular 4.2.1`

slel · 2021-07-24T08:24:42Z

comment:16

Some github-actions workflows are running out of disk space.

https://github.com/slel/sage/actions?query=branch%3Aci-32001

dimpase · 2021-07-24T21:40:46Z

comment:17

perhaps one can try this: https://github.com/easimon/maximize-build-space

sagetrac-git · 2021-07-25T12:20:10Z

Changed commit from 9a73ab2 to 367618c

sagetrac-git · 2021-07-25T12:20:10Z

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

`367618c`	`32001: Upgrade: Singular 4.2.1`

slel · 2021-07-25T12:22:14Z

comment:19

Rebased on Sage 9.4.beta6. Pushed tag to run github-actions at:

https://github.com/slel/sage/actions?query=branch:ci-s94b6-32001

slel · 2021-07-26T00:16:55Z

comment:20

Replying to @dimpase:

perhaps one can try this: https://github.com/easimon/maximize-build-space

Thanks for the pointer, looks promising.

Meanwhile, successfully ran make -s V=0 ptestlong on macOS and Debian.

sheerluck · 2021-07-27T05:27:12Z

comment:21

Replying to @slel:

Rebased on Sage 9.4.beta6. Pushed tag to run github-actions at:

https://github.com/slel/sage/actions?query=branch:ci-s94b6-32001

But sci-mathematics/singular-4.2.1 is already installed in gentoo image.
I expected to see

configure: will use system package and not install SPKG singular

dimpase · 2021-07-27T09:02:52Z

comment:22

Replying to @sheerluck:

Replying to @slel:

Rebased on Sage 9.4.beta6. Pushed tag to run github-actions at:

https://github.com/slel/sage/actions?query=branch:ci-s94b6-32001

But sci-mathematics/singular-4.2.1 is already installed in gentoo image.
I expected to see
configure: will use system package and not install SPKG singular

this won't happen until #29024 is done.

You can try putting
https://github.com/sagemath/sage-prod/files/10659352/spkg-configure.m4.gz
into build/pkgs/singular/spkg-configure.m4
and run ./bootstrap
(then, assuming Singular is known to pkg-config, it might work...)

fchapoton · 2021-07-31T09:15:48Z

comment:23

may we please also fix the following cython warning:

diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
index b043ce719a..ec706f3129 100644
--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
+++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
@@ -3181,7 +3181,8 @@ cdef class MPolynomial_libsingular(MPolynomial):
         cdef ring *_ring = parent._ring
         if _ring != currRing: rChangeCurrRing(_ring)
         base = parent._base
-        cdef poly *t, *p = p_Copy(self._poly, _ring)
+        cdef poly *t
+        cdef poly *p = p_Copy(self._poly, _ring)
 
         while p:
             t = pNext(p)

slel · 2021-07-31T12:26:03Z

Changed commit from 367618c to 0629663

slel · 2021-07-31T12:26:03Z

Changed branch from public/32001 to u/slelievre/32001-a

slel · 2021-07-31T12:26:03Z

comment:24

Rebased on Sage 9.4.rc0. Fixed Cython warning as requested.

New commits:

`2abd307`	`32001: Upgrade: Singular 4.2.1`
`0629663`	`32001: Fix Cython warning in multi_polynomial_libsingular.pyx`

slel · 2021-07-31T12:26:03Z

Changed keywords from none to upgrade, singular

mkoeppe · 2021-08-01T21:15:38Z

comment:25

Replying to @fchapoton:

may we please also fix the following cython warning:

I think it is poor practice to put unrelated changes on an update ticket. It just adds ambiguity for packagers.

mkoeppe · 2021-08-01T22:12:57Z

comment:26

As noted in #32323, the file singular.idx is not getting installed (neither before nor after this upgrade). This is an issue both in upstream and our fallback docbuild (which only makes singular.hlp)

mkoeppe · 2021-08-01T22:47:26Z

comment:27

Several of the GH Actions tests failed with:

  [singular-4.2.1]   Attempting to download from ftp://jim.mathematik.uni-kl.de/pub/Math/Singular/SOURCES/4-2-1/singular-4.2.1.tar.gz
  [singular-4.2.1]   [xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]
  [singular-4.2.1]   ERROR [transfer|run:135]: [Errno ftp error] 550 Failed to change directory.
  [singular-4.2.1]   ************************************************************************
  [singular-4.2.1]   Traceback (most recent call last):
  [singular-4.2.1]     File "/sage/build/bin/../sage_bootstrap/download/cmdline.py", line 126, in run_safe

This may have been caused by an intermittent server error

mkoeppe · 2021-08-01T22:49:53Z

Reviewer: Matthias Koeppe

mkoeppe · 2021-08-01T22:49:53Z

comment:28

The tests that went through look fine, including Cygwin.

Thanks for preparing this upgrade!

mkoeppe · 2021-08-01T22:49:53Z

Changed dependencies from #32257 to none

slel · 2021-08-02T12:40:19Z

comment:29

Replying to @mkoeppe:

Replying to @fchapoton:

may we please also fix the following cython warning:

I think it is poor practice to put unrelated changes on an update ticket. It just adds ambiguity for packagers.

Let me know if I should split that off to a separate ticket.

vbraun · 2021-08-29T09:36:18Z

Changed branch from u/slelievre/32001-a to 0629663

mkoeppe added this to the sage-9.4 milestone Jun 18, 2021

mkoeppe added c: packages: standard labels Jun 18, 2021

slel added the s: needs review label Jul 18, 2021

mkoeppe modified the milestones: sage-9.4, sage-9.5 Jul 21, 2021

slel changed the title ~~Singular update: 4.2.1~~ Upgrade: Singular 4.2.1 Jul 31, 2021

mkoeppe added s: positive review and removed s: needs review labels Aug 1, 2021

vbraun removed the s: positive review label Aug 29, 2021

vbraun closed this as completed in f1f5c24 Aug 29, 2021

slel mentioned this issue Jan 29, 2023

Manage disk space constraints in continuous integration #32280

Closed

Upgrade: Singular 4.2.1 #32001

Upgrade: Singular 4.2.1 #32001

Comments

mkoeppe commented Jun 18, 2021

mkoeppe commented Jun 25, 2021

slel commented Jul 11, 2021

kiwifb commented Jul 11, 2021

dimpase commented Jul 18, 2021

slel commented Jul 18, 2021

slel commented Jul 18, 2021

slel commented Jul 18, 2021

slel commented Jul 18, 2021

dimpase commented Jul 18, 2021

mkoeppe commented Jul 18, 2021

slel commented Jul 20, 2021

dimpase commented Jul 20, 2021

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dimpase commented Jul 24, 2021

sagetrac-git mannequin commented Jul 25, 2021

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slel commented Jul 25, 2021

slel commented Jul 26, 2021

sheerluck commented Jul 27, 2021

dimpase commented Jul 27, 2021

fchapoton commented Jul 31, 2021

slel commented Jul 31, 2021

slel commented Jul 31, 2021

slel commented Jul 31, 2021

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mkoeppe commented Aug 1, 2021

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vbraun commented Aug 29, 2021