[GAP Forum] problem with AutomorphismGroup

Dmitrii (Dima) Pasechnik dima at ntu.edu.sg
Tue May 29 11:29:24 BST 2012 

Dear Markus,
Thanks.
I can confirm that this is a bug in  in Sage's
gap_packages-4.4.12.p1. More precisely,
one of the GAP packages bundled there, namely
the one called "braid" (listed on
http://www.gap-system.org/Packages/undep.html), version 1.0,
overwrites GAP's
Fingerprint function (hmm, is it a method?)
with something  of its own.
There is a later version of this package, 1.1.
However, it still has the same bug.

OK, we'll fix this in Sage in some way, most probably by patching "braid".

Best,
Dmitrii


On 29 May 2012 11:43, Markus Szymik <markus.szymik at gmail.com> wrote:
>
> Dear Dmitrii,
>
> The GAP packages are not included into the Sage distribution. As far as I know, this is
> because of differences in the copyrights. Consequently, I always install them myself.
>
> Best,
>
> Markus
>
> Am 29.05.2012 um 11:14 schrieb Dmitrii (Dima) Pasechnik:
>
>> Hi,
>>
>> On 29 May 2012 07:45, Markus Szymik <markus.szymik at gmail.com> wrote:
>>>
>>>> Do you know if only core GAP is available in this binary?
>>>> I.e., what is the output of
>>>> optional_packages()
>>>> command in Sage?
>>>
>>> sage: optional_packages()
>>> (['database_gap-4.4.12.p1', 'gap_packages-4.4.12.p1'],
>> I wonder if you got them already in the binary.
>> Or have you installed them yourself?
>> Thanks,
>> Dmitrii
>>
>> ['4ti2-1.3.2.p1', 'PyQt_x11-4.9.1.p0', 'TOPCOM-0.16.2.p2',
>> 'ace-5.0.p0', 'biopython-1.57', 'cbc-2.7.5', 'cunningham_tables-1.0',
>> 'database_cremona_ellcurve-20120302', 'database_jones_numfield-v4',
>> 'database_kohel-20060803', 'database_odlyzko_zeta',
>> 'database_sloane_oeis-2005-12', 'database_stein_watkins_mini.p0',
>> 'database_symbolic_data-20070206', 'dot2tex-2.8.7-2',
>> 'extra_docs-20070208', 'fricas-1.0.9', 'fricasaldor-1.0.9',
>> 'gdbm-1.8.3', 'ginv-1.9-20080723', 'git-1.7.9.4', 'gmpy-1.0.1',
>> 'gnuplotpy-1.8', 'graphviz-2.16.1.p0', 'guppy-0.1.8',
>> 'java3d-20070901', 'jsmath_image_fonts-1.4.p3', 'kash3-2008-07-31.p0',
>> 'knoboo-20080411', 'libcocoa-0.9930', 'libogg-1.1.4',
>> 'libtheora-1.1.1', 'lie-2.2.2.p3', 'lrcalc-1.1.6beta', 'lrs-4.2b.p1',
>> 'mpc-0.8.3-dev-svn793', 'mpi4py-1.2.2', 'nauty-24', 'nzmath-1.1.0',
>> 'openmpi-1.4.3', 'openssl-1.0.1a', 'p_group_cohomology-2.1.2',
>> 'phc-2.3.53.p0', 'pycryptoplus-20100809-git', 'pyopenssl-0.8',
>> 'pyx-0.10', 'pyzmq-2.1.11.p0', 'qhull-2010.1', 'sage-mode-0.6',
>> 'sip-4.13.2.p0', 'trac-0.11.5.p0', 'valgrind-3.7.0',
>> 'zeromq-2.2.0.p0'])
>>> sage:
>>>
>>>> Also, you could try reinstalling gap spkg.
>>>>
>>>> That is, in Terminal cd to the directory where Sage is installed, and
>>>> issue the command
>>>> ./sage -f http://www.sagemath.org/packages/standard/gap-4.4.12.p6.spkg
>>>>
>>>> and after it completes (it will download the the source of the package
>>>> and build it, so it will take a little while)
>>>> issue
>>>> ./sage -b
>>>
>>> That did the job; it works fine now. Maybe it was because I had .p1 instead of .p6 ?
>>>
>>> Thanks a lot for your help!
>>>
>>> Markus
>>>
>>>> Thanks,
>>>> Dima
>>>>
>>>>> The Sage version I have installed is the one for Apple OS X, intel, dating from 2012-05-15,
>>>>> 14:37, sage-5.0-OSX-64bit-10.6-x86_64-Darwin-app.dmg .
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Markus
>>>>>
>>>>> Am 25.05.2012 um 14:56 schrieb Dmitrii (Dima) Pasechnik:
>>>>>
>>>>>> It could also be the case that the binary Sage 5.0 you installed is broken...
>>>>>> Could you tell me the exact version you installed?
>>>>>> Thanks,
>>>>>> Dmitrii
>>>>>>
>>>>>> On 25 May 2012 14:10, Markus Szymik <markus.szymik at gmail.com> wrote:
>>>>>>>
>>>>>>> I did that, but it still does not work. :(
>>>>>>>
>>>>>>> Am 25.05.2012 um 13:52 schrieb Dmitrii (Dima) Pasechnik:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> On 25 May 2012 13:09, Markus Szymik <markus.szymik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>> I have removed 4.8 now, and the problem still persists.
>>>>>>>>>
>>>>>>>>> There can be no old files around, since I did not upgrade Sage from within the program.
>>>>>>>>
>>>>>>>> It does not matter. Please remove your ~/.sage/ directory (where ~/
>>>>>>>> stands for the home directory of the user that runs sage), and then
>>>>>>>> try again.
>>>>>>>> This directory does not get changed automatically.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Dmitrii
>>>>>>>>
>>>>>>>>> Instead I downloaded the precompiled binaries and installed them next to 4.8 (which is gone
>>>>>>>>> now), together with fresh versions of the GAP packages I need.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Markus
>>>>>>>>>
>>>>>>>>> Am 25.05.2012 um 12:51 schrieb Dmitrii (Dima) Pasechnik:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>> there are  GAP image files stored in ~/.sage/
>>>>>>>>>> It might be that an old GAP image file is loaded when you
>>>>>>>>>> run Sage 5.0.
>>>>>>>>>> Please check this out.
>>>>>>>>>> Thanks,
>>>>>>>>>> Dmitrii
>>>>>>>>>>
>>>>>>>>>> On 25 May 2012 12:43, Markus Szymik <markus.szymik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Dear Dimitri,
>>>>>>>>>>>
>>>>>>>>>>> I have upgraded to Sage 5.0 last week. Maybe I should remove the old install to
>>>>>>>>>>> ensure that Sage 4.8 is not being called upon by "accident".
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Markus
>>>>>>>>>>>
>>>>>>>>>>> Am 25.05.2012 um 11:56 schrieb Dmitrii (Dima) Pasechnik:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Markus,
>>>>>>>>>>>>
>>>>>>>>>>>> it indeed doesn't seem to work in Sage 4.8, for some reason, but does work
>>>>>>>>>>>> with Sage 5.0 for me.
>>>>>>>>>>>> Can you upgrade?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Dmitrii
>>>>>>>>>>>>
>>>>>>>>>>>> On 25 May 2012 11:40, Markus Szymik <markus.szymik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Dear Alexander,
>>>>>>>>>>>>>
>>>>>>>>>>>>> The error occurred while I was accessing GAP through Sage.
>>>>>>>>>>>>> When I use GAP directly from within a terminal, the problem disappears.
>>>>>>>>>>>>> Thanks a lot for pointing out that it should work.
>>>>>>>>>>>>>
>>>>>>>>>>>>> All the best,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Markus
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Dear Markus,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> For me, this works fine, both with default packages and without packages,
>>>>>>>>>>>>>> for example:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> GAP4, Version: 4.4.12 of 17-Dec-2008, i686-apple-darwin10.8.0-gcc
>>>>>>>>>>>>>> Components:  small 2.1, small2 2.0, small3 2.0, small4 1.0, small5 1.0,
>>>>>>>>>>>>>>            small6 1.0, small7 1.0, small8 1.0, small9 1.0, small10 0.2,
>>>>>>>>>>>>>>            small11 0.1, id2 3.0, id3 2.1, id4 1.0, id5 1.0, id6 1.0, id9 1.0,
>>>>>>>>>>>>>>            id10 0.1, trans 1.0, prim 2.1  loaded.
>>>>>>>>>>>>>> Packages:    AClib 1.1, Polycyclic 2.8.1, Alnuth 2.3.1, AutPGrp 1.4, nq 2.2,
>>>>>>>>>>>>>>            GAPDoc 1.3, IO 3.3, CrystCat 1.1.3, Cryst 4.1.6, CRISP 1.3.4,
>>>>>>>>>>>>>>            CTblLib 1.1.3, TomLib 1.1.4, FactInt 1.5.3, FGA 1.1.0.1,
>>>>>>>>>>>>>>            IRREDSOL 1.2, LAGUNA 3.5.0, Sophus 1.23, MIPLib 1.0,
>>>>>>>>>>>>>>            Polenta 1.2.7, ResClasses 3.0.0  loaded.
>>>>>>>>>>>>>> gap> AutomorphismGroup(DihedralGroup(8));
>>>>>>>>>>>>>> <group of size 8 with 3 generators>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Which version of GAP are you using? How did you install it?
>>>>>>>>>>>>>> Could you copy-and-paste the exact GAP session where you have this error?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best wishes,
>>>>>>>>>>>>>> Alexander
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On 25 May 2012, at 10:05, Markus Szymik wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Dear Forum,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I am trying to compute automorphism groups of p-groups,
>>>>>>>>>>>>>>> and GAP responds with an error message I don't understand.
>>>>>>>>>>>>>>> For example,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>     AutomorphismGroup(DihedralGroup(8));
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> results in:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>     ...
>>>>>>>>>>>>>>>     RuntimeError: Gap produced error output
>>>>>>>>>>>>>>>     Function: number of arguments must be 1 (not 2)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The command works fine for all groups of order less than 8.
>>>>>>>>>>>>>>> What is wrong here?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Markus
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Forum mailing list
>>>>>>>>>>>>>>> Forum at mail.gap-system.org
>>>>>>>>>>>>>>> http://mail.gap-system.org/mailman/listinfo/forum
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Dr. Alexander Konovalov               School of Computer Science
>>>>>>>>>>>>>> & Centre for Interdisciplinary Research in Computational Algebra
>>>>>>>>>>>>>> University of St Andrews                 Tel +44/0 (1334) 461633
>>>>>>>>>>>>>> http://www.cs.st-andrews.ac.uk/~alexk    Fax +44/0 (1334) 463278
>>>>>>>>>>>>>> The University of St Andrews is a charity registered in Scotland:No.SC013532
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
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