Opened 5 years ago

Last modified 3 years ago

#22626 closed enhancement

Upgrade to GAP 4.10 — at Version 135

Reported by: nthiery Owned by:
Priority: critical Milestone: sage-8.6
Component: interfaces Keywords: days85, libgap
Cc: alexk, dimpase, embray, fbissey, arojas, gh-sebasguts, jpflori, markuspf, nthiery, slelievre, vbraun, wstein, gh-timokau Merged in:
Authors: Nicolas M. Thiéry, Dima Pasechnik, Jeroen Demeyer Reviewers:
Report Upstream: N/A Work issues: work...
Branch: u/dimpase/WIP/libgap410 Commit: 406cae67f059056df29413b8fa36ac9964eb3c5b
Dependencies: Stopgaps: error handling in libgap, documentation display

Status badges

Description (last modified by jdemeyer)

GAP 4.9 comes with a completely rewritten build system that will simplify our packaging. In particular, libGAP no longer needs to be a separate package.

What the branch does:

  • Remove the libgap spkg
  • Update the gap spkg to the new build system and build and install libgap
  • Replace gap.shi.patch by a plain gap startup script for Sage

Rationale: GAP used to provide a startup shell script. The GAP devs are in the process of getting rid of it and provide a very minimal one. They recommend to just write our own rather than patching it.

  • Update a few doctests w.r.t. changes of output of some GAP functions
  • Possibly controversial: The new libgap currently *does not come* with symbol rewriting (foobar -> libGAP_foobar). This avoids messing around with GAP's sources; in particular opening the door for using a stock GAP from the OS distribution. However there always is a risk of name conflict. And indeed, GAP's constants (actually cpp macros) T_INT, T_FLOAT, ... conflict with Python's constants. This is currently worked around by forcing the inclusion of Python's structmember.h before the gap headers.

Something similar was started by Volker at #19915.

  • Removes configure.patch: it was patching configure for better GMP detection under Cygwin (#13954). This should not be needed anymore with the new build system and use of --with-gmp. If it is, upstream asked for it to be reported and they will fix it.
  • Revert #19726 (not needed anymore)

Status: currently broken - crashes deep inside GAP error handling system after few simple commands.

Basic tests on libgap:

sage: libgap.eval("GAPInfo.Version")
sage: libgap.DihedralGroup(10).CharacterTable()
CharacterTable( <pc group of size 10 with 2 generators> )
sage: libgap.Group(libgap.eval("[(1,2,3),(1,2)]")).Size()
6

Running most relevant tests:

sage -tp 8 sage/groups sage/libs/gap

Current status: lots of errors

Testing packages with dynamic loading (e.g. IO):

Install IO:

cd $SAGE/local/gap/latest/pkg
wget http://www.gap-system.org/pub/gap/gap4/tar.gz/packages/io-4.4.6.tar.gz
tar xvf /tmp/io-4.4.6.tar.gz
mv io-4.4.6 io
cd io
./configure
make

Test it locally:

cd ../..
./gap -l .
gap> LoadPackage("IO");
true

This does not yet work:

sage: libgap.LoadPackage("IO")
ValueError: libGAP: Error, module '/opt/sage-git/local/gap/latest/pkg/io/bin/x86_64-pc-linux-gnu-gcc-default64/io.so' not found

This should be fixed once GAP's gap binary is built on top of libgap. See: https://github.com/markuspf/gap/issues/1.

Note:

  • GAP 4.9.2 was released in July 2018.
  • GAP 4.9.1, released in May 2018, was the first stable release of GAP 4.9 (GAP 4.9.0 was a beta for GAP 4.9).
  • Max Horn reviewed the list of GAP symbols we use in Sage; some have already changed in 4.9. See this pad for notes.

Tarball: https://www.gap-system.org/pub/gap/gap-4.10/tar.bz2/gap-4.10.0.tar.bz2

Change History (136)

comment:1 Changed 5 years ago by nthiery

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comment:2 Changed 5 years ago by nthiery

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comment:3 Changed 5 years ago by nthiery

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comment:4 Changed 5 years ago by nthiery

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comment:5 Changed 5 years ago by nthiery

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comment:6 Changed 5 years ago by nthiery

  • Branch set to u/nthiery/upgrade_to_gap_4_9

comment:7 Changed 5 years ago by git

  • Commit set to 3011ac0908d667c0f245ca21859e336511106b5f

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

1c645e0#22626: remove GAP's symbol prefixing in libgap: libGAP_Foo -> Foo
1ecc67b#22626: doctest update w.r.t. minor changes of output in GAP
e8ebbca#22626: GMP detection patch for cygwin should not be needed anymore
fd65b06#22626: Remove libgap spkg
9511733#22626: replace patch for GAP's startup script template in favor of a custom script
550625e#22626: remove GAP's symbol prefixing in libgap: libGAP_Foo -> Foo, and workaround GAP <-> Python symbol conflict
a9c859c#22626: updated gap spkg w.r.t. GAP's devel version and its new build system; also include compilation and installation of libgap
3011ac0Merge branch 'develop' into t/22626/upgrade_to_gap_4_9

comment:8 Changed 5 years ago by nthiery

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comment:9 Changed 5 years ago by nthiery

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comment:10 Changed 5 years ago by nthiery

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comment:11 Changed 5 years ago by nthiery

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comment:12 Changed 5 years ago by nthiery

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comment:13 Changed 5 years ago by nthiery

  • Cc vbraun dimpase wstein added
  • Keywords days85 libgap added
  • Work issues set to Wait for gap 4.9 release

comment:14 Changed 5 years ago by nthiery

  • Description modified (diff)

comment:15 Changed 5 years ago by fbissey

  • Cc fbissey added

comment:16 Changed 5 years ago by git

  • Commit changed from 3011ac0908d667c0f245ca21859e336511106b5f to 234c54b4b7e0495e343c3ab1b925e2c99f37e391

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

234c54b#22626: revert #19726 as it won't be needed for gap 4.9

comment:17 Changed 5 years ago by nthiery

  • Description modified (diff)

Changed 5 years ago by nthiery

comment:18 Changed 5 years ago by nthiery

  • Description modified (diff)

comment:19 Changed 5 years ago by git

  • Commit changed from 234c54b4b7e0495e343c3ab1b925e2c99f37e391 to 431845f6da27d20c78b5e7a42b5f47bea866201c

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

b301e4c#22626: ReST fix
431845f#22626: better work around for the GAP-Python name clash on T_INT, ...

comment:20 Changed 5 years ago by nthiery

  • Description modified (diff)

New commits:

b301e4c#22626: ReST fix
431845f#22626: better work around for the GAP-Python name clash on T_INT, ...

comment:21 Changed 5 years ago by git

  • Commit changed from 431845f6da27d20c78b5e7a42b5f47bea866201c to 7c04025083d61cab671df3302c32f353c4e28313

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

7c0402522626: document the work around for the GAP-Python name clash on T_INT, ...

comment:22 follow-ups: Changed 5 years ago by fbissey

So if I understand the mechanics involved, at the moment you have to configure and install gap. Then clean and configure and install for libgap. So it is still behaving like "two packages" with the same source code. Do we have an idea on when we'll have just have gap linking on libgap which would also solve this particular problem?

comment:23 in reply to: ↑ 22 Changed 5 years ago by nthiery

Salut François,

Replying to fbissey:

So if I understand the mechanics involved, at the moment you have to configure and install gap. Then clean and configure and install for libgap. So it is still behaving like "two packages" with the same source code.

Exactly.

Do we have an idea on when we'll have just have gap linking on libgap which would also solve this particular problem?

The GAP developers are well aware of that and planning to implement it. They have not yet done yet just to be more incremental; their new build system is a big PR already :-) I would assume that this will be done before GAP 4.9 which they are planning for a couple months from now.

See: https://github.com/markuspf/gap/issues/2

Btw: feel free to comment / expand on the list there. I'll advertise this issue for additional feedback on the sage-packaging mailing list.

comment:24 in reply to: ↑ 22 ; follow-ups: Changed 5 years ago by jdemeyer

Replying to fbissey:

So if I understand the mechanics involved, at the moment you have to configure and install gap. Then clean and configure and install for libgap. So it is still behaving like "two packages" with the same source code.

For this reason, I wonder why you didn't keep the separation GAP + libGAP in Sage too. If it effectively behaves as two packages, it seems more natural to keep it as two packages in Sage too. Imagine for example that we need to patch GAP but not libGAP or conversely, that would be harder with the current approach. That being said, this is mostly bikeshedding. So, if the current setup works well, there might be no reason to change it.

comment:25 in reply to: ↑ 24 ; follow-up: Changed 5 years ago by dimpase

Replying to jdemeyer:

Replying to fbissey:

So if I understand the mechanics involved, at the moment you have to configure and install gap. Then clean and configure and install for libgap. So it is still behaving like "two packages" with the same source code.

For this reason, I wonder why you didn't keep the separation GAP + libGAP in Sage too. If it effectively behaves as two packages, it seems more natural to keep it as two packages in Sage too. Imagine for example that we need to patch GAP but not libGAP or conversely, that would be harder with the current approach. That being said, this is mostly bikeshedding. So, if the current setup works well, there might be no reason to change it.

Two completely separate packages would also mean that gap_packages should come in two different flavours, etc. I'd rather keep it simple and do not multiply these instances (but rather hope that libGAP will support all of GAP packages soon).

comment:26 in reply to: ↑ 25 ; follow-up: Changed 5 years ago by jdemeyer

Replying to dimpase:

Two completely separate packages would also mean that gap_packages should come in two different flavours, etc.

So, you are saying that we need to install gap_packages twice too? Once for GAP and once for libGAP?

comment:27 in reply to: ↑ 24 Changed 5 years ago by nthiery

Replying to jdemeyer:

For this reason, I wonder why you didn't keep the separation GAP + libGAP in Sage too.

I wanted to experiment with how far we were from having a proper single package, so as to give early feedback to the gap developers on any sticking points. And indeed, linking gap to libgap is basically the only sticking point. Since this point will be most likely resolved by the time this ticket gets merged in, we might as well shoot directly for the "right thing".

comment:28 in reply to: ↑ 26 ; follow-up: Changed 5 years ago by dimpase

Replying to jdemeyer:

Replying to dimpase:

Two completely separate packages would also mean that gap_packages should come in two different flavours, etc.

So, you are saying that we need to install gap_packages twice too? Once for GAP and once for libGAP?

no, not at all---I mean to say that there exist GAP packages (not part of Sage ATM) that break libGAP now. As some of these packages are very useful, it's important to have this fixed (but not at expense of having 2 separate gap_packages).

comment:29 in reply to: ↑ 28 Changed 5 years ago by nthiery

Replying to dimpase:

As some of these packages are very useful, it's important to have this fixed

YES. In fact that is my main motivation to work on the libgap integration: I badly want to use Semigroups that requires IO! We went through the details with Markus and Max, and the shared aim is indeed to have this resolved with the upgrade to 4.9.

comment:30 Changed 4 years ago by jpflori

  • Cc jpflori added

comment:31 Changed 4 years ago by jdemeyer

Is there any news here?

comment:32 Changed 4 years ago by slelievre

  • Cc slelievre added

GAP 4.9.0, a beta release for GAP 4.9, has been released.

This means we can start working on building Sage with it.

comment:33 follow-up: Changed 4 years ago by dimpase

Do you know if they now provide a replacement for libGAP?

comment:34 Changed 4 years ago by slelievre

  • Cc alexk markuspf added
  • Description modified (diff)

Cc-ing @alexk and @markuspf.

comment:35 in reply to: ↑ 33 Changed 4 years ago by nthiery

Replying to dimpase:

Do you know if they now provide a replacement for libGAP?

In principle yes: the branch I posted here last April was using their stock alpha version. Now the next step is to revive the branch and adapt it if needed.

I can work on this, but probably not at once. Any volunteer to take over welcome.

Markus: do you foresee any major changes in how GAP's lib is to be built that could affect what I was doing last April?

comment:36 follow-up: Changed 4 years ago by dimpase

I just noticed that in 4.9 smallgrps and transgrps are released under a GPL-compatible license. This is great! We really should make them (i.e. database_gap) standard Sage package, and do away with the extra hurdle of having database_gap optional.

comment:37 follow-up: Changed 4 years ago by jdemeyer

If you're willing to wait 2 months, this might be a good task for the Cernay workshop https://github.com/OpenDreamKit/OpenDreamKit/issues/251

comment:38 in reply to: ↑ 37 Changed 4 years ago by nthiery

Replying to jdemeyer:

If you're willing to wait 2 months, this might be a good task for the Cernay workshop https://github.com/OpenDreamKit/OpenDreamKit/issues/251

Yes indeed; it will be helpful to have GAP people under hand. I may just become impatient before that for some research project of mine, in which case I'll have a head start :-)

comment:39 in reply to: ↑ 36 Changed 4 years ago by nthiery

Replying to dimpase:

I just noticed that in 4.9 smallgrps and transgrps are released under a GPL-compatible license. This is great! We really should make them (i.e. database_gap) standard Sage package, and do away with the extra hurdle of having database_gap optional.

Yes! I can't wait for all the simplifications this will bring to us!

comment:40 in reply to: ↑ 22 ; follow-up: Changed 4 years ago by jdemeyer

Replying to fbissey:

So if I understand the mechanics involved, at the moment you have to configure and install gap. Then clean and configure and install for libgap. So it is still behaving like "two packages".

With the past and future modifications to the Sage build system in mind, I now object more strongly than before to treating two separate packages (GAP + libGAP) as one package.

The reason is that we now try to separate the build and install stages of packages. But that is incompatible with the recipe here of first "build and install GAP" and then "build and install libGAP".

comment:41 Changed 4 years ago by jdemeyer

For an example of two Sage packages with the same sources, see gcc and gfortran. IMHO, you should do the same for GAP and libGAP (unless they are merged upstream but my impression is that this has not happened yet).

comment:42 in reply to: ↑ 40 Changed 4 years ago by fbissey

Replying to jdemeyer:

Replying to fbissey:

So if I understand the mechanics involved, at the moment you have to configure and install gap. Then clean and configure and install for libgap. So it is still behaving like "two packages".

With the past and future modifications to the Sage build system in mind, I now object more strongly than before to treating two separate packages (GAP + libGAP) as one package.

The reason is that we now try to separate the build and install stages of packages. But that is incompatible with the recipe here of first "build and install GAP" and then "build and install libGAP".

Hopefully we will be getting something more serious at final release time, like with pari where you build libpari and then the gp executable. That would be the ideal scenario where it is really one package. Have to see how far they have gone with 4.9.

comment:43 Changed 4 years ago by jdemeyer

A lot of changes on this ticket (also the changes likely to lead to merge conflicts) are related to the unprefixing of libGAP symbols. To ease development, maybe we should try to do that separately from the upgrade to GAP 4.9.

I was thinking to do something like #19915 but changing only the Sage source code (not libGAP) and undoing the prefixing with macros like #define SomeGapFunction libGAP_SomeGapFunction. What do you think?

comment:44 follow-up: Changed 4 years ago by dimpase

there is also libgap unprefixing in Python/Cython? that has to be done. Perhaps separating these from C level unprefixing would help making it smoother.

comment:45 in reply to: ↑ 44 ; follow-up: Changed 4 years ago by jdemeyer

Replying to dimpase:

there is also libgap unprefixing in Python/Cython? that has to be done. Perhaps separating these from C level unprefixing would help making it smoother.

Yes, that is what I meant. Creating a separate ticket for unprefixing only at the Cython level by using macros to translate between the unprefixed names in Cython and the prefixed names in libGAP.

comment:46 in reply to: ↑ 45 ; follow-up: Changed 4 years ago by dimpase

Replying to jdemeyer:

Replying to dimpase:

there is also libgap unprefixing in Python/Cython? that has to be done. Perhaps separating these from C level unprefixing would help making it smoother.

Yes, that is what I meant. Creating a separate ticket for unprefixing only at the Cython level by using macros to translate between the unprefixed names in Cython and the prefixed names in libGAP.

I am not sure I understand. Currently in Cython on can do something like

    from sage.libs.gap.libgap import libgap
    g=libgap.ProjectiveGeneralLinearGroup(3,3)

How will this change under what you propose?

comment:47 in reply to: ↑ 46 Changed 4 years ago by jdemeyer

Replying to dimpase:

    from sage.libs.gap.libgap import libgap
    g=libgap.ProjectiveGeneralLinearGroup(3,3)

How will this change under what you propose?

The Python interface won't change at all. I am talking about how sage.libs.gap calls libGAP.

comment:48 Changed 4 years ago by jdemeyer

As far as I can tell, GAP 4.9 has not been released. Does anybody know how close we are to an actual release?

Last edited 4 years ago by jdemeyer (previous) (diff)

comment:49 Changed 4 years ago by slelievre

I think GAP 4.9.0 is considered a public beta for GAP 4.9.

The list of releases at

still displays GAP 4.8.10 as the latest release.

In the list of past releases there, the GAP 4.8, 4.7, 4.6, 4.5 series start at GAP 4.8.2, 4.7.2, 4.6.2, 4.5.4, so probably GAP 4.x.y with those x and lower y were considered beta.

Still, seeing how 4.9.0 works with Sage would be nice.

comment:50 Changed 3 years ago by jdemeyer

  • Dependencies set to #25273

comment:51 follow-up: Changed 3 years ago by jdemeyer

Where is the GAP source tarball which is supposed to be used here?

comment:52 Changed 3 years ago by jdemeyer

  • Branch changed from u/nthiery/upgrade_to_gap_4_9 to u/jdemeyer/upgrade_to_gap_4_9

comment:53 Changed 3 years ago by git

  • Commit changed from 7c04025083d61cab671df3302c32f353c4e28313 to b7278a120c5db710d1e11297b3dd1411d69d302b

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

72b5066Unprefixed libGAP interface
b7278a1Upgrade to GAP 4.9

comment:54 in reply to: ↑ 51 Changed 3 years ago by dimpase

Replying to jdemeyer:

Where is the GAP source tarball which is supposed to be used here?

here: https://www.gap-system.org/pub/gap/gap-4.9/beta/

comment:55 Changed 3 years ago by jdemeyer

  • Description modified (diff)

comment:56 in reply to: ↑ description Changed 3 years ago by jdemeyer

Replying to nthiery:

The branch attached to this ticket updates Sage to run on top of a branch of GAP by Markus Pfeiffer that adds libgap compilation and will be merged soon in the devel version of GAP.

It seems that this branch which "will be merged soon" is still not merged. It would be good to have an idea of whether or not that will happen.

comment:57 Changed 3 years ago by git

  • Commit changed from b7278a120c5db710d1e11297b3dd1411d69d302b to 40e644a16bafa77e4b93e72c215f53a4afb19cc1

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

d28b575Unprefixed libGAP interface
daf8754Unprefixed libGAP interface
40e644aUpgrade to GAP 4.9

comment:58 Changed 3 years ago by nthiery

According to https://github.com/gap-system/gap/pull/1205#issuecomment-385670578, Markus's libgap branch won't be merged in GAP 4.9: it's not yet ready enough. Bummer.

We are discussing with Sebastian and Thomas what we can do to move forward here. They are very interested as well by libgap for the integration between GAP and Julia.

Tentative steps:

  • As a warm up, upgrade our current gap and libgap spkg to 4.8.10
  • Upgrade our current gap and libgap spkg to 4.9; with the many changes to the build system, this may get more tricky
  • To make the switch to GAP's libgap less urgent, investigate whether we could change our current libgap spkg to not prefix GAP symbols, in order to be able to use GAP's dynamic packages; see #25273
  • On the GAP side: move toward more incremental changes. In particular, extract the changesets from Markus branch that are non controversial and ready, and get them merged in GAP (4.9? 4.10?)
Last edited 3 years ago by nthiery (previous) (diff)

comment:59 Changed 3 years ago by nthiery

  • Cc ghsebasguts added

comment:60 Changed 3 years ago by gh-antonio-rojas

  • Cc gh-antonio-rojas added

comment:61 Changed 3 years ago by slelievre

  • Description modified (diff)
  • Milestone changed from sage-8.0 to sage-8.3

GAP 4.9.1 was released in May 2018.

This is the first stable release of GAP 4.9 (GAP 4.9.0 was a beta for GAP 4.9).

comment:62 Changed 3 years ago by slelievre

  • Cc embray gh-sebasguts nthiery added; ghsebasguts removed

comment:63 Changed 3 years ago by gh-antonio-rojas

I'm confused - I just built GAP 4.9.1 from the upstream tarball and 'make install' *does* install /usr/lib/libgap.so and libgap's headers. Is this a different libgap than the one mentioned here to be included in 4.10?

comment:64 Changed 3 years ago by slelievre

One comment at pull request 1205 in GAP's github repo said GAP won't ship libGAP before GAP 4.10:

Maybe this was changed though.

comment:65 Changed 3 years ago by nthiery

  • Description modified (diff)

comment:66 follow-up: Changed 3 years ago by jdemeyer

Has anybody asked GAP developers for a policy on the prefixing?

In Cernay, I proposed that GAP should prefix some/all of their names like T_INT -> GAP_T_INT. For compiling GAP (+ GAP packages) itself, we can use a file with defines like

#define  T_INT  GAP_T_INT

to ensure backwards compatibility. This way, in GAP itself, one could use either T_INT or GAP_T_INT. Outside of GAP, only GAP_T_INT would work.

I think this is relatively easy to implement (I'm willing to do it) but I don't know what upstream GAP thinks of it.

comment:67 Changed 3 years ago by arojas

  • Cc arojas added; gh-antonio-rojas removed

comment:68 Changed 3 years ago by slelievre

  • Description modified (diff)

GAP 4.9.2 was released in July 2018.

comment:69 Changed 3 years ago by gh-timokau

  • Cc gh-timokau added

comment:70 Changed 3 years ago by nthiery

Hi,

For the record: I experimented a bit a month ago and a bit more this morning with Dima with the latest gap master that has make libgap and make install-libgap rules. See the following branch, which builds libgap from GAP's pristine sources:

https://git.sagemath.org/sage.git/log/?h=u/nthiery/gap-libgap

Note that, at this stage, Sage won't start with it; maybe even not compile.

Last edited 3 years ago by nthiery (previous) (diff)

comment:71 in reply to: ↑ 66 Changed 3 years ago by nthiery

Has anybody asked GAP developers for a policy on the prefixing?

In Cernay, I proposed that GAP should prefix some/all of their names like T_INT -> GAP_T_INT. For compiling GAP (+ GAP packages) itself, we can use a file with defines like

#define  T_INT  GAP_T_INT

to ensure backwards compatibility. This way, in GAP itself, one could use either T_INT or GAP_T_INT. Outside of GAP, only GAP_T_INT would work.

I think this is relatively easy to implement (I'm willing to do it) but I don't know what upstream GAP thinks of it.

That's the idea indeed. Eventually they will provide a standalone header file that will define the official GAP API, and where all symbols will be prefixed. To bootstrap the process, we (well mostly Max!) reviewed and annotated the symbols that are used in Sage:

https://hackmd.io/emNi76svSWCh1fBeLKqPdA#

comment:72 Changed 3 years ago by gh-timokau

Thank you for working on this! Sage using an up-to-date gap and doing away with the additional libgap package will simplify packaging.

comment:73 Changed 3 years ago by vdelecroix

  • Milestone changed from sage-8.3 to sage-8.4

update milestone 8.3 -> 8.4

comment:74 Changed 3 years ago by slelievre

GAP 4.9.3 was released.

comment:75 Changed 3 years ago by dimpase

  • Description modified (diff)
  • Summary changed from Upgrade to GAP 4.9 to Upgrade to GAP 4.10
  • Work issues changed from Wait for gap 4.9 release to Wait for gap 4.10 release

comment:76 Changed 3 years ago by dimpase

  • Description modified (diff)

comment:77 Changed 3 years ago by dimpase

  • Description modified (diff)

note that the prefix of the tarball should start with src/ - else one gets weird error messages from the python's tar.

GAPs make install target now works in a preliminary form - on Linux for sure.

comment:78 Changed 3 years ago by dimpase

  • Branch changed from u/jdemeyer/upgrade_to_gap_4_9 to u/dimpase/WIP/libgap410
  • Commit changed from 40e644a16bafa77e4b93e72c215f53a4afb19cc1 to f06912253d01557727041fe3b4d03e459fb90a11

This is WIP - builds, but libgap.pyx interaction loop has to be rewritten using new API.

Also, sage --gap is broken

gap: hmm, I cannot find 'lib/init.g' maybe use option '-l <gaproot>'?

New commits:

c766ad6Merge branch 'u/jdemeyer/upgrade_to_gap_4_9' of trac.sagemath.org:sage into libgap
5152637building GAP and libGAP from GAP
6bed83achanges for using libGAP from GAP - part 1
f069122removing util*

comment:79 Changed 3 years ago by dimpase

oops, one still needs initialize() from util.pyx, in some form...

comment:80 Changed 3 years ago by git

  • Commit changed from f06912253d01557727041fe3b4d03e459fb90a11 to 9c22e727f7a87271c26885e9cdc9b52583f598c5

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

8c28e13Revert "removing util*"
9c22e72few comments

comment:81 Changed 3 years ago by nthiery

Great to see the progress! Sounds like a productive week in Siegen. Thanks so much.

comment:82 Changed 3 years ago by dimpase

  • Description modified (diff)

comment:83 Changed 3 years ago by git

  • Commit changed from 9c22e727f7a87271c26885e9cdc9b52583f598c5 to 14919d3d32074d36ece1da26815e5f5d7a24812b

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

14919d3update util and the GAP package

comment:84 Changed 3 years ago by git

  • Commit changed from 14919d3d32074d36ece1da26815e5f5d7a24812b to 8b5ccbe6323feb8ded8cf71cf1d00faa71da59c5

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

b3dc304Merge branch 'develop' into libgap
8a8a146use MarkBag instead of MARK_BAG
c5a5d4fno more *_BAG, and a call signature fix
d13fc80more compilation fixes
8b5ccberemoved debugging utils (they need a rewrite)

comment:85 Changed 3 years ago by git

  • Commit changed from 8b5ccbe6323feb8ded8cf71cf1d00faa71da59c5 to a0616deb562afcf9d5b1a8a4e02406b4a0479038

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

a0616deadding --nointeract to libgap startup options

comment:86 Changed 3 years ago by dimpase

at this point I am at

sage: libgap(1)
Error, Variable: '_rich_repr_' must have a value
Error, Variable: '_ipython_canary_method_should_not_exist_' must have a\
 value
[... several more errors like above]
gap: panic, could not open *errout*!

comment:87 Changed 3 years ago by git

  • Commit changed from a0616deb562afcf9d5b1a8a4e02406b4a0479038 to 9cc327f6004c1a16819774fd34cf5fc48ff4a001

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

9cc327fadding --nointeract to libgap startup options

comment:88 follow-up: Changed 3 years ago by dimpase

In the current branch I am able to run

sage: g=libgap.SymmetricGroup(4)
sage: print(g.Order())
24
sage: i=g.Order().sage()
sage: i
24

So it's outputting GAP object that is broken ATM.

I'll try fixing the "old" GAP interface, perhaps it will help.

comment:89 in reply to: ↑ 88 ; follow-up: Changed 3 years ago by nthiery

Replying to dimpase:

In the current branch I am able to run

sage: g=libgap.SymmetricGroup(4)
sage: print(g.Order())
24
sage: i=g.Order().sage()
sage: i
24

Nice! Making good progress!

So it's outputting GAP object that is broken ATM. I'll try fixing the "old" GAP interface, perhaps it will help.

I am not sure what's broken above?

comment:90 in reply to: ↑ 89 Changed 3 years ago by dimpase

Replying to nthiery:

So it's outputting GAP object that is broken ATM. I'll try fixing the "old" GAP interface, perhaps it will help.

I am not sure what's broken above?

see comment:86 - displaying (lib)GAP objects is broken. Also,

sage: gap(1)
** Gap crashed or quit executing 'SetUserPreference("HistoryMaxLines", 30);' **
Restarting Gap and trying again
** Gap crashed or quit executing '\$sage1:=1;;' **
...

the latter is probably due to some scripts gotten messed up by the upgrade.

And error handling in libgap interface needs work, too.

comment:91 Changed 3 years ago by dimpase

libgap's display problem seems to be ipython-specific. Indeed

$ ./sage --python
Python 2.7.15 (default, Sep 15 2018, 05:05:36) 
[GCC 8.2.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from sage.all import *
>>> libgap(1)
1

comment:92 Changed 3 years ago by dimpase

Some discussions related to libgap API:

and an accepted PR to fix a bug that was breaking libgap/Sage interface:

https://github.com/gap-system/gap/pull/2840

Last edited 3 years ago by dimpase (previous) (diff)

comment:93 Changed 3 years ago by git

  • Commit changed from 9cc327f6004c1a16819774fd34cf5fc48ff4a001 to ece8cfc39e5f4258a5ec2c8dc2a307f988218891

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

ece8cfcfix gap() interface and gap_console, removed some old stuff

comment:94 Changed 3 years ago by git

  • Commit changed from ece8cfc39e5f4258a5ec2c8dc2a307f988218891 to 043fb95c1ee6360ef5df9ac879d643a662bf6dbc

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

043fb95fixing all but one doctests in interfaces/gap.py

comment:95 Changed 3 years ago by dimpase

One error - tab completion does not work on GAP objects:

sage -t --long --warn-long 49.3 src/sage/interfaces/gap.py
**********************************************************************
File "src/sage/interfaces/gap.py", line 1628, in sage.interfaces.gap.GapElement._tab_completion
Failed example:
    'Centralizer' in s5._tab_completion()
Exception raised:
    Traceback (most recent call last):
      File "/mnt/opt/Sage/sage-dev/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 659, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/mnt/opt/Sage/sage-dev/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1070, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.gap.GapElement._tab_completion[1]>", line 1, in <module>
        'Centralizer' in s5._tab_completion()
      File "sage/misc/cachefunc.pyx", line 2316, in sage.misc.cachefunc.CachedMethodCallerNoArgs.__call__ (build/cythonized/sage/misc/cachefunc.c:13467)
        self.cache = f(self._instance)
      File "/mnt/opt/Sage/sage-dev/local/lib/python2.7/site-packages/sage/interfaces/gap.py", line 1633, in _tab_completion
        v = P.eval(r'\$SAGE.OperationsAdmittingFirstArgument(%s)'%self.name())
      File "/mnt/opt/Sage/sage-dev/local/lib/python2.7/site-packages/sage/interfaces/gap.py", line 583, in eval
        result = Expect.eval(self, input_line, **kwds)
      File "/mnt/opt/Sage/sage-dev/local/lib/python2.7/site-packages/sage/interfaces/expect.py", line 1354, in eval
        for L in code.split('\n') if L != ''])
      File "/mnt/opt/Sage/sage-dev/local/lib/python2.7/site-packages/sage/interfaces/gap.py", line 789, in _eval_line
        raise RuntimeError(message)
    RuntimeError: Gap produced error output
    Error, no method found! For debugging hints type ?Recovery from NoMethodFound
    Error, no 1st choice method found for `Iterator' on 1 arguments

       executing \$SAGE.OperationsAdmittingFirstArgument(x);
**********************************************************************
1 item had failures:
   1 of   3 in sage.interfaces.gap.GapElement._tab_completion

comment:96 Changed 3 years ago by dimpase

  • Stopgaps set to tab completion on GAP objects, error handling in libgap

comment:97 Changed 3 years ago by git

  • Commit changed from 043fb95c1ee6360ef5df9ac879d643a662bf6dbc to 0128112b501a6c66d21b570dde09526ecf63c9b1

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

0128112few important Cython types fixed

comment:98 Changed 3 years ago by git

  • Commit changed from 0128112b501a6c66d21b570dde09526ecf63c9b1 to 732cbdd54e24ac35c3fd52c75fb7608ad41603ce

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

c4d128epass the correct error callback function
732cbddremoving libgap_enter/exit

comment:99 Changed 3 years ago by dimpase

in gap.* interface, tab completion is broken due to outdated code in src/ext/gap/sage.g: with GAP 4.10 one gets

gap> Read("sage.g");
gap> s5:=SymmetricGroup(5);
Sym( [ 1 .. 5 ] )
gap> \$SAGE.OperationsAdmittingFirstArgument(s5);
Error, no method found! For debugging hints type ?Recovery from NoMethodFound
Error, no 1st choice method found for `Iterator' on 1 arguments at /mnt/opt/Sage/sage-dev/local/gap/latest/lib/methsel2.g:250 called from
OPERATIONS[i + 1] at sage.g:69 called from
<function "LastReadValue">( <arguments> )
 called from read-eval loop at *stdin*:4
type 'quit;' to quit to outer loop

in GAP 4.8.6 this works:

gap> Read("sage.g");
gap> s5:=SymmetricGroup(5);
Sym( [ 1 .. 5 ] )
gap> \$SAGE.OperationsAdmittingFirstArgument(s5);
[ <Operation "ViewObj">, <Operation "ViewString">, <Operation "NameFunction">, <Operation "SetNameFunction">, 
...

I've asked here, as this is due to format change of internal GAP data...

Last edited 3 years ago by dimpase (previous) (diff)

comment:100 Changed 3 years ago by dimpase

Very similar outdated code is in OperationInspector.operations in sage/libs/gap/operations.py.

comment:101 Changed 3 years ago by git

  • Commit changed from 732cbdd54e24ac35c3fd52c75fb7608ad41603ce to 41218248115922fdae5c4ebb01a03a7df7bafc91

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

4121824fix for tab completion for GAP interface

comment:102 Changed 3 years ago by git

  • Commit changed from 41218248115922fdae5c4ebb01a03a7df7bafc91 to 1d60fdd386b98b11474df00074039f3b3ef26bca

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

1d60fddfix tab completion in libgap interface

comment:103 Changed 3 years ago by dimpase

  • Dependencies #25273 deleted
  • Stopgaps changed from tab completion on GAP objects, error handling in libgap to error handling in libgap

broken error handling:

sage: a=libgap(1)
sage: getattr(a,'_rich_repr_',None)
Error, Variable: '_rich_repr_' must have a value
sage: 

(with a default argument, getattr should just return it, with raising anything)

comment:104 Changed 3 years ago by dimpase

  • Stopgaps changed from error handling in libgap to error handling in libgap, documentation display

Please see https://github.com/gap-system/gap/issues/2874 for the current sticking point, which is error handling and processing of error messages. Basically, the question is whether it's possible to retain the behaviour of libGAP without patches to the GAP's kernel.

I'd like someone who knows more about libGAP error handling to have a look at badly butchered by me parts in the branch dealing with it, and suggest what should be done.

Another (easier) thing to fix is GAP and libgap documentation display.

comment:105 Changed 3 years ago by dimpase

  • Status changed from new to needs_info

comment:106 Changed 3 years ago by git

  • Commit changed from 1d60fdd386b98b11474df00074039f3b3ef26bca to e352f7e4ad34dfc1422afc04506332ef7674755a

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

e352f7emodest progress - can do libgap(1)

comment:107 Changed 3 years ago by dimpase

  • Status changed from needs_info to needs_work
  • Work issues changed from Wait for gap 4.10 release to work...

the interaction with ipython (which tries to get things like _rich_repr_ from GAP to display GAP objects) is far from done. The current problem:

sage: a=libgap(41)
sage: a
41
sage: b=libgap(42)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
...
ValueError: libGAP: PrintTo: cannot open stream for output
Error, Length: <list> must be a list (not a boolean or fail)
...

this looks like a bug in my new (bad) implementation of GAP objects printing in Sage.

comment:108 Changed 3 years ago by dimpase

perhaps we should rather try rebasing libGAP to GAP 4.10, which looks a less daunting task now than a total replacement with "native" GAP's libgap, get it working, and then replace all the libgap_* functions by the native ones.

comment:109 follow-up: Changed 3 years ago by git

  • Commit changed from e352f7e4ad34dfc1422afc04506332ef7674755a to 406cae67f059056df29413b8fa36ac9964eb3c5b

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

406cae6still the interaction with ipython is broken

comment:110 Changed 3 years ago by dimpase

On the present branch, I get

sage: a=libgap(1)
sage: a
*** trouble in PRINT_OR_APPEND_TO_STREAM***
...
*** trouble in PRINT_OR_APPEND_TO_STREAM***
1

after this GAP is pretty much nuked. This happens during ipython's attempts to pretty-print a, so that it tries to find _rich_repr_ etc. Specifically, at least on the system I am running this, the trouble starts not immediately, but where _rich_png_ (or the previous thing in the loop) is checked for by get_real_method in IPython/utils/dir2.py.

If I run the same from ./sage --python (after loading Sage there as usual) at least this much (and more) works.

I don't have a good idea how to debug this, so I'd like to pass the token now.

Last edited 3 years ago by dimpase (previous) (diff)

comment:111 Changed 3 years ago by dimpase

  • Status changed from needs_work to needs_review

oops, wrong ticket

Last edited 3 years ago by dimpase (previous) (diff)

comment:112 Changed 3 years ago by dimpase

  • Status changed from needs_review to needs_work

comment:113 Changed 3 years ago by embray

As long as we're upgrading GAP we should make sure DESTDIR builds work now; see #25044 which this conflicts with. But if this can get done soon we can skip #25044 and incorporate it into this. I'll give you a patch for it if you want.

I'm working on testing this on Cygwin now.

comment:114 Changed 3 years ago by embray

Okay, I am again confused as to what upstream tarball to use, because the one in the ticket description no longer matches the checksum.

comment:115 Changed 3 years ago by dimpase

I just checked that md5=017738e0ba9e166a19084d68123d3e1f as in GAP package checksum matches the md5 of https://github.com/dimpase/gap/releases/download/dev/gap-4.dev.tar.gz

Perhaps your download just got corrupted?

comment:116 follow-up: Changed 3 years ago by thansen

GAP 4.9.3 was uploaded to Debian unstable yesterday, the sagemath Debian package is broken until we can use GAP 4.9. Is the patch here already enough to use libgap from GAP 4.9 directly? It does not apply cleanly to sage 8.4. Or would you say updating the separate libgap to 4.9 is a better idea?

comment:117 in reply to: ↑ 116 Changed 3 years ago by dimpase

Replying to thansen:

GAP 4.9.3 was uploaded to Debian unstable yesterday, the sagemath Debian package is broken until we can use GAP 4.9. Is the patch here already enough to use libgap from GAP 4.9 directly? It does not apply cleanly to sage 8.4.

the patch here is very far from a working one.

Or would you say updating the separate libgap to 4.9 is a better idea?

If you could manage this, it would be great and very useful, but it's a very nontrivial amount of work, due to substantial changes in GAP internals that happened in GAP 4.9.

comment:118 follow-up: Changed 3 years ago by thansen

I see. If there was progress on this from you guys it would be very much appreciated. The freeze period for the next Debian release starts in January. If we can't fix the problem in time, sage will not be in the next Debian release, which will be the stable release for two years.

comment:119 in reply to: ↑ 118 Changed 3 years ago by jdemeyer

Replying to thansen:

The freeze period for the next Debian release starts in January.

For those of us who are not Debian experts, where is this documented? And what kind of changes are still allowed during the "freeze" period? For example, suppose for the sake of argument that this SageMath ticket is only merged in February, could it still be added as a patch to the Debian SageMath package?

comment:120 Changed 3 years ago by thansen

It is documented here: https://release.debian.org/buster/freeze_policy.html

The broken sagemath will eventually be automatically removed from Debian testing, which will become the next Debian release. After February 12 it cannot migrate back to testing even if it is fixed. The earlier transition freeze on January 12 means that no more library updates with SONAME change can be done (which might be relevant for a sage update too).

comment:121 follow-up: Changed 3 years ago by thansen

About the example you mentioned: This ticket does not need to be merged, we just need a usable patch. It seems that the gap maintainer is open to providing libgap.la, see https://bugs.debian.org/912862 . It is not yet clear if gap 4.10 is released in time to be included before the freeze.

comment:122 Changed 3 years ago by embray

  • Milestone changed from sage-8.4 to sage-8.5

This ticket mentions GAP 4.10, but should we not be focusing instead on GAP 4.9? Or would getting Sage working against GAP 4.10 imply support for 4.9 as well? I would want to check against both, and starting with the existing release (4.9) seems simpler...

Is there something at the system integration level I could be able to help with? ISTM this needs to be a high priority.

comment:123 in reply to: ↑ 121 Changed 3 years ago by embray

Replying to thansen:

About the example you mentioned: This ticket does not need to be merged, we just need a usable patch. It seems that the gap maintainer is open to providing libgap.la, see https://bugs.debian.org/912862 . It is not yet clear if gap 4.10 is released in time to be included before the freeze.

If that's the case, for the sake of integration, it might make more sense to pin GAP in Debia to 4.9 and focus on getting a Sage out that works against GAP 4.9 instead of focusing on 4.10. Given the amount of time left to do this, waiting on an uncertain GAP 4.10 package(s) landing in Debian seems a bit risky...

comment:124 Changed 3 years ago by dimpase

  • Description modified (diff)
  • Priority changed from major to critical

comment:125 Changed 3 years ago by dimpase

I think getting Sage's libGAP work with GAP 4.9 and/or 4.10 is much harder than in used to be in 4.8.x, due to major changes to GAP internals (although I have not tried it yet).

comment:126 follow-up: Changed 3 years ago by nthiery

Posting on behalf of Alexander Konovalov who does not yet have a trac account:

http://www.gap-system.org/pub/gap/gap-4.10/

has now GAP 4.10.0. The website will be updated in due course, but that means that GAP 4.10 is out.

That's excellent news. Now it's up to Sage to catch up.

comment:127 Changed 3 years ago by embray

Great! From what I saw yesterday it seemed like there were some doubts about how soon 4.10 would be released. But this being the case I rescind my previous comment.

comment:128 in reply to: ↑ 109 ; follow-up: Changed 3 years ago by embray

Replying to git:

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

406cae6still the interaction with ipython is broken

If I'm to understand correctly, you just added this patch for debugging purposes, right? It's not intended to go into the final product is it? I'm going to look into this problem.

comment:129 in reply to: ↑ 128 Changed 3 years ago by dimpase

Replying to embray:

Replying to git:

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

406cae6still the interaction with ipython is broken

If I'm to understand correctly, you just added this patch for debugging purposes, right? It's not intended to go into the final product is it? I'm going to look into this problem.

That's right, it's for debugging purposes (although it merely shows that something is going wrong, not more :-)). You might like to coordinate this with Jeroen, as he's going to work on this branch too...

comment:130 Changed 3 years ago by embray

I'm updating it right now to the 4.10 release. Jeroen is probably a better person to work on the LibGAP integration just because he has more experience with it. But if there any specific segfaults or anything I could look at I will. I'll take a look, for example, at the tab-completion issue...

comment:131 Changed 3 years ago by embray

I'm also rebasing this branch on current develop, which needs a bit of work...

comment:132 in reply to: ↑ 126 Changed 3 years ago by dimpase

Replying to nthiery:

Posting on behalf of Alexander Konovalov who does not yet have a trac account:

http://www.gap-system.org/pub/gap/gap-4.10/

Alex should be aware that he can post on trac using his github account!

comment:133 Changed 3 years ago by embray

Another thing that it seems still hasn't been done is to update the spkg-install for GAP to use DESTDIR-based installation. I'll just work on that simultaneously with this. If we have to upgrade GAP anyways that should be part of the process (and may expose some flaws in GAP's new installation process...)

Last edited 3 years ago by embray (previous) (diff)

comment:134 Changed 3 years ago by embray

Needed to modify build/make/deps to directly make GAP a build dependency of sagelib as well, which is now needed (and remove the obsolete reference to the libgap spkg).

comment:135 Changed 3 years ago by jdemeyer

  • Authors changed from Nicolas M. Thiéry, ... to Nicolas M. Thiéry, Dima Pasechnik, Jeroen Demeyer
  • Description modified (diff)
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