[sage-devel] Re: M2 algorithm for GB is broken (?)
On Monday, 20 May 2013 22:36:58 UTC+8, William wrote:
>
> On Mon, May 20, 2013 at 2:06 AM, Dima Pasechnik
> >
> wrote:
> > M2 spkg in Sage is so old (ver 1.1, as opposed to just released 1.6:
> > https://github.com/Macaulay2/M2/tree/release-1.6)
> > that it's better to completely remove it from the repo...
> > Just in case, I tried building version 1.6 inside the Sage 5.9 shell,
> and it
> > didn't work due to some GMP incompatibility:
> >
> > In file included from
> > /tmp/M2/M2/BUILD/normal/libraries/final/include/stdinc.h:34:0,
> > from ../../../../Macaulay2/d/version.dd:30:
> > /usr/local/src/sage/sage-5.9/local/include/gmpxx.h: In member function
> > 'intmax_t __gmp_expr<__mpz_struct [1], __mpz_struct [1]>::get_sx()
> const':
> > /usr/local/src/sage/sage-5.9/local/include/gmpxx.h:1710:49: error:
> > 'mpz_get_sx' was not declared in this scope
> >
> > So this is not so easy to get it updated...
>
> It's an experimental package for a reason... M2 is quite difficult
> and time consuming to build.
>
> For https://cloud.sagemath.com I've been just installing M2 using the
> Ubuntu binary packages that they provide on their website. It still
> works fine from Sage, as far as I can tell.
>
> wget
> http://www.math.uiuc.edu/Macaulay2/Downloads/Common/Macaulay2-1.6-common.deb
>
> wget
> http://www.math.uiuc.edu/Macaulay2/Downloads/GNU-Linux/Ubuntu/Macaulay2-1.6-amd64-Linux-Ubuntu-12.04.deb
>
>
> sudo apt-get install libntl-5.4.2 libpari-gmp3
>
> sudo dpkg -i Macaulay2-1.6-common.deb
> Macaulay2-1.6-amd64-Linux-Ubuntu-12.04.deb
>
>
> Since the M2 developers are doing a good job packaging binaries of M2
> for various distros, etc., and Sage doesn't link to M2 at a binary
> level in any way, maybe we don't need an M2 spkg.
>
Does this still mean we need a "plug" spkg, so that Sage knows that M2 is
available on the host,
and so e.g. the interface can be tested automatically?
Dima
>
> William
>
> >
> >
> > On Wednesday, 15 May 2013 18:05:01 UTC+8, Martin Albrecht wrote:
> >>
> >> Hi William,
> >>
> >> I tried to fix the bug and provided a patch at
> >>
> >> http://trac.sagemath.org/sage_trac/attachment/ticket/14587/
> >>
> >> However, I cannot test it as the M2 experimental package won't build
> (on
> >> my
> >> machine).
> >>
> >> On Tuesday 14 May 2013, William Stein wrote:
> >> > Hi,
> >> >
> >> > I actually tried to use something marked #optional, hence not tested,
> >> > hence broken, and it was broken:
> >> >
> >> > P. = PolynomialRing(ZZ,3)
> >> > I = sage.rings.ideal.Katsura(P,3) # regenerate to prevent caching
> >> > I.groebner_basis('macaulay2:gb') # optional - macaulay2
> >> >
> >> > Error in lines 3-3
> >> > Traceback (most recent call last):
> >> > File "/mnt/home/lFqBXyPI/.sagemathcloud/sage_server.py", line 412,
> in
> >> > execute exec compile(block, '', 'single') in namespace, locals
> >> > File "", line 1, in
> >> > File "cachefunc.pyx", line 1462, in
> >> > sage.misc.cachefunc.CachedMethodCaller.__call__
> >> > (sage/misc/cachefunc.c:7556)
> >> > File "cachefunc.pyx", line 2044, in
> >> > sage.misc.cachefunc.CachedMethod._instance_call
> >> > (sage/misc/cachefunc.c:10040)
> >> > File
> >> >
> >> >
> "/usr/local/sage/sage-5.9/local/lib/python2.7/site-packages/sage/rings/pol
> >> > ynomial/multi_polynomial_ideal.py", line 3840, in groebner_basis
> >> > gb = self._groebner_basis_macaulay2(prot=prot, *args, **kwds)
> >> > TypeError: _groebner_basis_macaulay2() got an unexpected keyword
> >> > argument
> >> > 'prot'
> >>
> >> Cheers,
> >> Martin
> >>
> >> --
> >> name: Martin Albrecht
> >> _pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
> >> _otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
> >> _www: http://martinralbrecht.wordpress.com/
> >> _jab: martinr...@jabber.ccc.de
>
>
>
> --
> William Stein
> Professor of Mathematics
> University of Washington
> http://wstein.org
>
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[sage-devel] Re: M2 algorithm for GB is broken (?)
Hell !! So, should we remove the M2 package? > > I think it is definitely better to not have it, and let the user > install his own copy of M2, than to have a package that does not work. > I totally agree with that. We had an argument about the Graphviz spkg on #13624 about the very same problem, and I also think we could do without that one. Nathann -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: M2 algorithm for GB is broken (?)
mmarco wrote: sage-on-gentoo folks have Macaulay2-1.6 working with sage-5.9 fine. So i wonder why compilation fails inside sage-5.9. They presumably build it against GMP rather than MPIR. The *_ux() and *_sx() functions are an extension specific to MPIR AFAIK. -leif On 20 mayo, 11:06, Dima Pasechnik wrote: M2 spkg in Sage is so old (ver 1.1, as opposed to just released 1.6:https://github.com/Macaulay2/M2/tree/release-1.6) that it's better to completely remove it from the repo... Just in case, I tried building version 1.6 inside the Sage 5.9 shell, and it didn't work due to some GMP incompatibility: In file included from /tmp/M2/M2/BUILD/normal/libraries/final/include/stdinc.h:34:0, from ../../../../Macaulay2/d/version.dd:30: /usr/local/src/sage/sage-5.9/local/include/gmpxx.h: In member function 'intmax_t __gmp_expr<__mpz_struct [1], __mpz_struct [1]>::get_sx() const': /usr/local/src/sage/sage-5.9/local/include/gmpxx.h:1710:49: error: 'mpz_get_sx' was not declared in this scope So this is not so easy to get it updated... -- () The ASCII Ribbon Campaign /\ Help Cure HTML E-Mail -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: M2 algorithm for GB is broken (?)
So, should we remove the M2 package? I think it is definitely better to not have it, and let the user install his own copy of M2, than to have a package that does not work. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: M2 algorithm for GB is broken (?)
For the record: Its yum install Macaulay2 on Fedora. On Monday, May 20, 2013 3:36:58 PM UTC+1, William wrote: > > wget > http://www.math.uiuc.edu/Macaulay2/Downloads/Common/Macaulay2-1.6-common.deb > wget > http://www.math.uiuc.edu/Macaulay2/Downloads/GNU-Linux/Ubuntu/Macaulay2-1.6-amd64-Linux-Ubuntu-12.04.deb > > sudo apt-get install libntl-5.4.2 libpari-gmp3 > sudo dpkg -i Macaulay2-1.6-common.deb > Macaulay2-1.6-amd64-Linux-Ubuntu-12.04.deb > > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at http://groups.google.com/group/sage-devel?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
[sage-devel] Re: M2 algorithm for GB is broken (?)
On Mon, May 20, 2013 at 2:06 AM, Dima Pasechnik wrote:
> M2 spkg in Sage is so old (ver 1.1, as opposed to just released 1.6:
> https://github.com/Macaulay2/M2/tree/release-1.6)
> that it's better to completely remove it from the repo...
> Just in case, I tried building version 1.6 inside the Sage 5.9 shell, and it
> didn't work due to some GMP incompatibility:
>
> In file included from
> /tmp/M2/M2/BUILD/normal/libraries/final/include/stdinc.h:34:0,
> from ../../../../Macaulay2/d/version.dd:30:
> /usr/local/src/sage/sage-5.9/local/include/gmpxx.h: In member function
> 'intmax_t __gmp_expr<__mpz_struct [1], __mpz_struct [1]>::get_sx() const':
> /usr/local/src/sage/sage-5.9/local/include/gmpxx.h:1710:49: error:
> 'mpz_get_sx' was not declared in this scope
>
> So this is not so easy to get it updated...
It's an experimental package for a reason... M2 is quite difficult
and time consuming to build.
For https://cloud.sagemath.com I've been just installing M2 using the
Ubuntu binary packages that they provide on their website. It still
works fine from Sage, as far as I can tell.
wget
http://www.math.uiuc.edu/Macaulay2/Downloads/Common/Macaulay2-1.6-common.deb
wget
http://www.math.uiuc.edu/Macaulay2/Downloads/GNU-Linux/Ubuntu/Macaulay2-1.6-amd64-Linux-Ubuntu-12.04.deb
sudo apt-get install libntl-5.4.2 libpari-gmp3
sudo dpkg -i Macaulay2-1.6-common.deb
Macaulay2-1.6-amd64-Linux-Ubuntu-12.04.deb
Since the M2 developers are doing a good job packaging binaries of M2
for various distros, etc., and Sage doesn't link to M2 at a binary
level in any way, maybe we don't need an M2 spkg.
William
>
>
> On Wednesday, 15 May 2013 18:05:01 UTC+8, Martin Albrecht wrote:
>>
>> Hi William,
>>
>> I tried to fix the bug and provided a patch at
>>
>> http://trac.sagemath.org/sage_trac/attachment/ticket/14587/
>>
>> However, I cannot test it as the M2 experimental package won't build (on
>> my
>> machine).
>>
>> On Tuesday 14 May 2013, William Stein wrote:
>> > Hi,
>> >
>> > I actually tried to use something marked #optional, hence not tested,
>> > hence broken, and it was broken:
>> >
>> > P. = PolynomialRing(ZZ,3)
>> > I = sage.rings.ideal.Katsura(P,3) # regenerate to prevent caching
>> > I.groebner_basis('macaulay2:gb') # optional - macaulay2
>> >
>> > Error in lines 3-3
>> > Traceback (most recent call last):
>> > File "/mnt/home/lFqBXyPI/.sagemathcloud/sage_server.py", line 412, in
>> > execute exec compile(block, '', 'single') in namespace, locals
>> > File "", line 1, in
>> > File "cachefunc.pyx", line 1462, in
>> > sage.misc.cachefunc.CachedMethodCaller.__call__
>> > (sage/misc/cachefunc.c:7556)
>> > File "cachefunc.pyx", line 2044, in
>> > sage.misc.cachefunc.CachedMethod._instance_call
>> > (sage/misc/cachefunc.c:10040)
>> > File
>> >
>> > "/usr/local/sage/sage-5.9/local/lib/python2.7/site-packages/sage/rings/pol
>> > ynomial/multi_polynomial_ideal.py", line 3840, in groebner_basis
>> > gb = self._groebner_basis_macaulay2(prot=prot, *args, **kwds)
>> > TypeError: _groebner_basis_macaulay2() got an unexpected keyword
>> > argument
>> > 'prot'
>>
>> Cheers,
>> Martin
>>
>> --
>> name: Martin Albrecht
>> _pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
>> _otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
>> _www: http://martinralbrecht.wordpress.com/
>> _jab: martinr...@jabber.ccc.de
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
--
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[sage-devel] Re: M2 algorithm for GB is broken (?)
Macaulay2 in Fedora also works perfectly fine with Sage. Its just that the
M2 spkg has bitrotted to the point where its useless. And Macaulay2 has a
long list of dependencies that we don't carry, so its not just a case of
packaging a newer release.
On Monday, May 20, 2013 2:29:42 PM UTC+1, mmarco wrote:
>
> sage-on-gentoo folks have Macaulay2-1.6 working with sage-5.9 fine. So
> i wonder why compilation fails inside sage-5.9.
>
> On 20 mayo, 11:06, Dima Pasechnik wrote:
> > M2 spkg in Sage is so old (ver 1.1, as opposed to just released 1.6:
> https://github.com/Macaulay2/M2/tree/release-1.6)
> > that it's better to completely remove it from the repo...
> > Just in case, I tried building version 1.6 inside the Sage 5.9 shell,
> and
> > it didn't work due to some GMP incompatibility:
> >
> > In file included from
> > /tmp/M2/M2/BUILD/normal/libraries/final/include/stdinc.h:34:0,
> > from ../../../../Macaulay2/d/version.dd:30:
> > /usr/local/src/sage/sage-5.9/local/include/gmpxx.h: In member function
> > 'intmax_t __gmp_expr<__mpz_struct [1], __mpz_struct [1]>::get_sx()
> const':
> > /usr/local/src/sage/sage-5.9/local/include/gmpxx.h:1710:49: error:
> > 'mpz_get_sx' was not declared in this scope
> >
> > So this is not so easy to get it updated...
> >
> >
> >
> >
> >
> >
> >
> > On Wednesday, 15 May 2013 18:05:01 UTC+8, Martin Albrecht wrote:
> >
> > > Hi William,
> >
> > > I tried to fix the bug and provided a patch at
> >
> > >http://trac.sagemath.org/sage_trac/attachment/ticket/14587/
> >
> > > However, I cannot test it as the M2 experimental package won't build
> (on
> > > my
> > > machine).
> >
> > > On Tuesday 14 May 2013, William Stein wrote:
> > > > Hi,
> >
> > > > I actually tried to use something marked #optional, hence not
> tested,
> > > > hence broken, and it was broken:
> >
> > > > P. = PolynomialRing(ZZ,3)
> > > > I = sage.rings.ideal.Katsura(P,3) # regenerate to prevent caching
> > > > I.groebner_basis('macaulay2:gb') # optional - macaulay2
> >
> > > > Error in lines 3-3
> > > > Traceback (most recent call last):
> > > > File "/mnt/home/lFqBXyPI/.sagemathcloud/sage_server.py", line 412,
> in
> > > > execute exec compile(block, '', 'single') in namespace, locals
> > > > File "", line 1, in
> > > > File "cachefunc.pyx", line 1462, in
> > > > sage.misc.cachefunc.CachedMethodCaller.__call__
> > > > (sage/misc/cachefunc.c:7556)
> > > > File "cachefunc.pyx", line 2044, in
> > > > sage.misc.cachefunc.CachedMethod._instance_call
> > > > (sage/misc/cachefunc.c:10040)
> > > > File
> >
> > >
> "/usr/local/sage/sage-5.9/local/lib/python2.7/site-packages/sage/rings/pol
> > > > ynomial/multi_polynomial_ideal.py", line 3840, in groebner_basis
> > > > gb = self._groebner_basis_macaulay2(prot=prot, *args, **kwds)
> > > > TypeError: _groebner_basis_macaulay2() got an unexpected keyword
> > > argument
> > > > 'prot'
> >
> > > Cheers,
> > > Martin
> >
> > > --
> > > name: Martin Albrecht
> > > _pgp:http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
> > > _otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
> > > _www:http://martinralbrecht.wordpress.com/
> > > _jab: martinr...@jabber.ccc.de
>
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[sage-devel] Re: M2 algorithm for GB is broken (?)
sage-on-gentoo folks have Macaulay2-1.6 working with sage-5.9 fine. So
i wonder why compilation fails inside sage-5.9.
On 20 mayo, 11:06, Dima Pasechnik wrote:
> M2 spkg in Sage is so old (ver 1.1, as opposed to just released
> 1.6:https://github.com/Macaulay2/M2/tree/release-1.6)
> that it's better to completely remove it from the repo...
> Just in case, I tried building version 1.6 inside the Sage 5.9 shell, and
> it didn't work due to some GMP incompatibility:
>
> In file included from
> /tmp/M2/M2/BUILD/normal/libraries/final/include/stdinc.h:34:0,
> from ../../../../Macaulay2/d/version.dd:30:
> /usr/local/src/sage/sage-5.9/local/include/gmpxx.h: In member function
> 'intmax_t __gmp_expr<__mpz_struct [1], __mpz_struct [1]>::get_sx() const':
> /usr/local/src/sage/sage-5.9/local/include/gmpxx.h:1710:49: error:
> 'mpz_get_sx' was not declared in this scope
>
> So this is not so easy to get it updated...
>
>
>
>
>
>
>
> On Wednesday, 15 May 2013 18:05:01 UTC+8, Martin Albrecht wrote:
>
> > Hi William,
>
> > I tried to fix the bug and provided a patch at
>
> > http://trac.sagemath.org/sage_trac/attachment/ticket/14587/
>
> > However, I cannot test it as the M2 experimental package won't build (on
> > my
> > machine).
>
> > On Tuesday 14 May 2013, William Stein wrote:
> > > Hi,
>
> > > I actually tried to use something marked #optional, hence not tested,
> > > hence broken, and it was broken:
>
> > > P. = PolynomialRing(ZZ,3)
> > > I = sage.rings.ideal.Katsura(P,3) # regenerate to prevent caching
> > > I.groebner_basis('macaulay2:gb') # optional - macaulay2
>
> > > Error in lines 3-3
> > > Traceback (most recent call last):
> > > File "/mnt/home/lFqBXyPI/.sagemathcloud/sage_server.py", line 412, in
> > > execute exec compile(block, '', 'single') in namespace, locals
> > > File "", line 1, in
> > > File "cachefunc.pyx", line 1462, in
> > > sage.misc.cachefunc.CachedMethodCaller.__call__
> > > (sage/misc/cachefunc.c:7556)
> > > File "cachefunc.pyx", line 2044, in
> > > sage.misc.cachefunc.CachedMethod._instance_call
> > > (sage/misc/cachefunc.c:10040)
> > > File
>
> > "/usr/local/sage/sage-5.9/local/lib/python2.7/site-packages/sage/rings/pol
> > > ynomial/multi_polynomial_ideal.py", line 3840, in groebner_basis
> > > gb = self._groebner_basis_macaulay2(prot=prot, *args, **kwds)
> > > TypeError: _groebner_basis_macaulay2() got an unexpected keyword
> > argument
> > > 'prot'
>
> > Cheers,
> > Martin
>
> > --
> > name: Martin Albrecht
> > _pgp:http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
> > _otr: 47F43D1A 5D68C36F 468BAEBA 640E8856 D7951CCF
> > _www:http://martinralbrecht.wordpress.com/
> > _jab: martinr...@jabber.ccc.de
--
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[sage-devel] Re: M2 algorithm for GB is broken (?)
M2 spkg in Sage is so old (ver 1.1, as opposed to just released 1.6:
https://github.com/Macaulay2/M2/tree/release-1.6)
that it's better to completely remove it from the repo...
Just in case, I tried building version 1.6 inside the Sage 5.9 shell, and
it didn't work due to some GMP incompatibility:
In file included from
/tmp/M2/M2/BUILD/normal/libraries/final/include/stdinc.h:34:0,
from ../../../../Macaulay2/d/version.dd:30:
/usr/local/src/sage/sage-5.9/local/include/gmpxx.h: In member function
'intmax_t __gmp_expr<__mpz_struct [1], __mpz_struct [1]>::get_sx() const':
/usr/local/src/sage/sage-5.9/local/include/gmpxx.h:1710:49: error:
'mpz_get_sx' was not declared in this scope
So this is not so easy to get it updated...
On Wednesday, 15 May 2013 18:05:01 UTC+8, Martin Albrecht wrote:
>
> Hi William,
>
> I tried to fix the bug and provided a patch at
>
> http://trac.sagemath.org/sage_trac/attachment/ticket/14587/
>
> However, I cannot test it as the M2 experimental package won't build (on
> my
> machine).
>
> On Tuesday 14 May 2013, William Stein wrote:
> > Hi,
> >
> > I actually tried to use something marked #optional, hence not tested,
> > hence broken, and it was broken:
> >
> > P. = PolynomialRing(ZZ,3)
> > I = sage.rings.ideal.Katsura(P,3) # regenerate to prevent caching
> > I.groebner_basis('macaulay2:gb') # optional - macaulay2
> >
> > Error in lines 3-3
> > Traceback (most recent call last):
> > File "/mnt/home/lFqBXyPI/.sagemathcloud/sage_server.py", line 412, in
> > execute exec compile(block, '', 'single') in namespace, locals
> > File "", line 1, in
> > File "cachefunc.pyx", line 1462, in
> > sage.misc.cachefunc.CachedMethodCaller.__call__
> > (sage/misc/cachefunc.c:7556)
> > File "cachefunc.pyx", line 2044, in
> > sage.misc.cachefunc.CachedMethod._instance_call
> > (sage/misc/cachefunc.c:10040)
> > File
> >
> "/usr/local/sage/sage-5.9/local/lib/python2.7/site-packages/sage/rings/pol
> > ynomial/multi_polynomial_ideal.py", line 3840, in groebner_basis
> > gb = self._groebner_basis_macaulay2(prot=prot, *args, **kwds)
> > TypeError: _groebner_basis_macaulay2() got an unexpected keyword
> argument
> > 'prot'
>
> Cheers,
> Martin
>
> --
> name: Martin Albrecht
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> _www: http://martinralbrecht.wordpress.com/
> _jab: martinr...@jabber.ccc.de
>
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[sage-devel] Re: M2 algorithm for GB is broken (?)
Hi William,
I tried to fix the bug and provided a patch at
http://trac.sagemath.org/sage_trac/attachment/ticket/14587/
However, I cannot test it as the M2 experimental package won't build (on my
machine).
On Tuesday 14 May 2013, William Stein wrote:
> Hi,
>
> I actually tried to use something marked #optional, hence not tested,
> hence broken, and it was broken:
>
> P. = PolynomialRing(ZZ,3)
> I = sage.rings.ideal.Katsura(P,3) # regenerate to prevent caching
> I.groebner_basis('macaulay2:gb') # optional - macaulay2
>
> Error in lines 3-3
> Traceback (most recent call last):
> File "/mnt/home/lFqBXyPI/.sagemathcloud/sage_server.py", line 412, in
> execute exec compile(block, '', 'single') in namespace, locals
> File "", line 1, in
> File "cachefunc.pyx", line 1462, in
> sage.misc.cachefunc.CachedMethodCaller.__call__
> (sage/misc/cachefunc.c:7556)
> File "cachefunc.pyx", line 2044, in
> sage.misc.cachefunc.CachedMethod._instance_call
> (sage/misc/cachefunc.c:10040)
> File
> "/usr/local/sage/sage-5.9/local/lib/python2.7/site-packages/sage/rings/pol
> ynomial/multi_polynomial_ideal.py", line 3840, in groebner_basis
> gb = self._groebner_basis_macaulay2(prot=prot, *args, **kwds)
> TypeError: _groebner_basis_macaulay2() got an unexpected keyword argument
> 'prot'
Cheers,
Martin
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