update M4RI to newest upstream release #11574

malb · 2011-07-04T16:37:58Z

M4RI 20110601 changed the API, so we need to apply a patch as well,

cf. https://bitbucket.org/malb/m4ri/wiki/M4RI-20110601
cf. https://bitbucket.org/malb/m4ri/wiki/M4RI-20110715

Install http://sage.math.washington.edu/home/malb/spkgs/libm4ri-20110715.spkg
Apply attachment: m4ri_20110601.patch
Apply attachment: trac_11574_m4ri_sse2.patch

Depends on #11261
Depends on #11756

CC: @strogdon @nexttime @alexanderdreyer

Component: packages: standard

Keywords: sd32

Author: Martin Albrecht

Reviewer: Simon King, Alexander Dreyer

Merged: sage-4.7.2.alpha3

Issue created by migration from https://trac.sagemath.org/ticket/11574

malb · 2011-07-04T21:02:26Z

Dependencies: #11261

kcrisman · 2011-07-05T13:55:32Z

comment:3

I'm a little confused. The spkgs here and at #9562 are both libm4ri, and seem to be numbered backwards (the "earlier" one in the dependency is from 2011).

kcrisman · 2011-07-05T14:52:19Z

comment:4

Okay, I think I figured it out. Sorry for the noise.

kcrisman · 2011-07-05T17:05:57Z

comment:5

I don't know what I did wrong, but I still get the problem with the Symbol not found: _m4ri_swap_bits while trying to start, even after this patch. I may have done something wrong, but at any rate I can't spend more time on this now, sorry.

malb · 2011-07-06T16:39:56Z

Author: Martin Albrecht

malb · 2011-07-07T09:26:56Z

comment:7

For the record, I tried spkg + patch on t2 and doctests pass.

malb · 2011-08-15T21:33:30Z

comment:9

applies & passes doctests with 4.7.1.rc2.

simon-king-jena · 2011-08-16T12:08:46Z

Reviewer: Simon King

simon-king-jena · 2011-08-16T12:08:46Z

comment:10

Why is the documentation for matrices over GF(2) not part of the reference manual? I think you should use the upgrade to expose the documentation to the audience.

malb · 2011-08-16T12:29:00Z

comment:11

I am not sure this documentation is much use in the reference manual since most of the interesting functions won't show up. Also, these matrices are expected to behave just as other matrices. On the other hand, there are a few - not many - special functions which are only available for GF(2). I'll take a look.

malb · 2011-08-17T13:57:33Z

comment:12

It seems that you agreed in a different ticket (#9562) that this class doesn't need to be in the reference manual? Hence, returning to needs review. Feel free to change it back, though.

simon-king-jena · 2011-08-17T18:36:44Z

comment:13

I think I can live with not including it into the references. However, currently I am getting segment faults when doctesting on mark (one of the skynet machines). I try to make sure that I properly install everything from scratch again, before reporting details.

simon-king-jena · 2011-08-17T19:51:59Z

comment:14

I did a forced new installation of the polybori spkg, then of the M4RI spkg, and I also installed the patches. I get on mark:

sage: P.<a,b,c,d,e> = PolynomialRing(GF(2), 5, order='lex')
sage: I1 = ideal([a*b + c*d + 1, a*c*e + d*e, a*b*e + c*e, b*c + c*d*e + 1])
sage: B.<a,b,c,d,e> = BooleanPolynomialRing(5, order='lex')
sage: I2 = ideal([B(f) for f in I1.gens()])
sage: I2.groebner_basis()
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

/home/simonking/SAGE/sage-4.7.1.rc1mark/devel/sage-main/<ipython console> in <module>()

/home/simonking/SAGE/sage-4.7.1.rc1mark/local/lib/python2.6/site-packages/sage/rings/polynomial/pbori.so in sage.rings.polynomial.pbori.BooleanPolynomialIdeal.groebner_basis (sage/rings/polynomial/pbori.cpp:26221)()

RuntimeError: Segmentation fault

Of course, it could be that the problem comes from the polybori spkg. That would be unfortunate, since it is already merged.

simon-king-jena · 2011-08-17T20:14:25Z

comment:15

Now, I tried to force re-installation of the original polybori spkg. However, that failed as well. I hope that it will not be needed to rebuild all of sage, which takes ages on mark.

malb · 2011-08-17T21:40:19Z

comment:16

I think the issue is that one needs to install stuff in the right order:

install new M4RI
install new PolyBoRi
apply the M4RI patch
touch sage/libs/polybori/decl.pxd
sage -b

simon-king-jena · 2011-08-18T07:14:16Z

comment:17

Meanwhile I managed to revert to the original state, and can confirm that, with vanilla sage-4.7.1.rc2 on 32-bit solaris, the segfault above does not occur.

I will now try to do things in the order you suggested: In fact, originally I had installed polybori, then m4ri, then the m4ri patch, and then sage -b (without touching decl.pxd).

But how can the new polybori spkg be merged if apparently it depends on the new m4ri?

simon-king-jena · 2011-08-18T08:17:23Z

comment:18

The new installation order did the trick, the segfault has gone. I am now repeating the failing doctests.

simon-king-jena · 2011-08-18T08:19:20Z

comment:19

Or actually I am repeating sage -testall.

malb · 2011-08-29T16:20:36Z

comment:67

The new M4RI SPKG is at #11757

simon-king-jena · 2011-08-29T18:21:23Z

comment:68

Replying to @malb:

The new M4RI SPKG is at #11757

Does that mean that #11757 makes this ticket a duplicate?

strogdon · 2011-08-30T04:27:56Z

comment:69

Replying to @malb:

The updated patch should allow the Sage build to go through. Testing on cicero now. I also added some depends fields as suggested by Leif.

Yes, the updated patch does allow Sage to build and there are no failing tests.

malb · 2011-08-30T10:34:59Z

comment:70

Replying to @simon-king-jena:

Replying to @malb:

The new M4RI SPKG is at #11757

Does that mean that #11757 makes this ticket a duplicate?

I guess one could look at it this way. I'd suggest: We deal with this ticket here first and if people then still have energy and are not sick of M4RI yet we can also include #11757.

malb · 2011-08-31T10:57:44Z

comment:72

So, anybody up for reviewing this? Or are people waiting for attachment: trac_11574_m4ri_sse2.patch being ported to #11757?

strogdon · 2011-09-01T01:06:41Z

comment:73

Replying to @malb:

So, anybody up for reviewing this? Or are people waiting for attachment: trac_11574_m4ri_sse2.patch being ported to #11757?

I should probably defer review to Simon since I got in through the backdoor. However,
since Sage builds here and there are no doctest failures I would give it a positive review. I do have one question. Shouldn't this ticket depend upon ticket #11756, even though that one has a positive review?

nexttime · 2011-09-01T02:48:17Z

comment:74

Replying to @strogdon:

Shouldn't this ticket depend upon ticket #11756, even though that one has a positive review?

Yep, IMHO even if #11756 had already been merged into some devel release.

nexttime · 2011-09-01T02:48:17Z

Changed dependencies from #11261 to #11261 #11756

simon-king-jena · 2011-09-01T11:34:19Z

comment:75

Replying to @strogdon:

Replying to @malb:

So, anybody up for reviewing this? Or are people waiting for attachment: trac_11574_m4ri_sse2.patch being ported to #11757?

I should probably defer review to Simon since I got in through the backdoor.

Sorry, I will probably not be able to review it in the next couple of days. So, iI'd appreciate if someone was quicker than I.

malb · 2011-09-06T15:44:10Z

comment:76

anyone?

alexanderdreyer · 2011-09-07T09:14:52Z

comment:77

The spkg builds and and installs fine. Together with the patches sage -testall was run successfully on a SuSE Linux Enterprise 11 x86_64, Gentoo i486, and Mac OS X 10.5 ppc.

So, I can cordially give a positive review!

alexanderdreyer · 2011-09-07T09:14:52Z

Changed reviewer from Simon King to Simon King, Alexander Dreyer

nexttime · 2011-09-12T06:39:08Z

comment:78

attachment: m4ri_20110601.patch has no ticket number in its commit message.

malb · 2011-09-12T14:12:42Z

rebased to 4.7.1.alpha4

malb · 2011-09-12T14:13:07Z

comment:79

Attachment: m4ri_20110601.patch.gz

fixed.

nexttime · 2011-09-12T18:36:03Z

Merged: sage-4.7.2.alpha3

malb added this to the sage-4.7.2 milestone Jul 4, 2011

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This was referenced Sep 8, 2011

Update PolyBoRi to release 0.8.0 #11575

Closed

PolyBoRi 0.7.1 needs to activate -msse2 #11756

Closed

malb mentioned this issue Oct 6, 2011

update M4RI to version 20110901 or later #11757

Closed

update M4RI to newest upstream release #11574

update M4RI to newest upstream release #11574

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