Discussion on science-related applications and integration in Gentoo.

VulK | 9 Aug 2011 05:08

Picon

sage queues

Dear all,
this is my first post to gentoo-science and I am writing because I have some
problems running experimental code from the sage project.
My issue is the following:
I have sci-mathematics/sage-4.7-r2 installed from the  sage-on-gentoo overlay
and I would like to install the combinat queue; I am following these
instructions: http://wiki.sagemath.org/combinat/MercurialStepByStep
The command I am supposed to run is 
# sage -combinat install
unfortunately -combinat is not recognized by sage as a valid option. I
browsed a little bit around the filesystem and I noticed that $SAGE_ROOT is
empty (except for some documentation) while on other installations of sage
(not using the ebuilds) there is plenty of stuff including a devel/combinat
folder.
Is there an option I can use when installing sage to allow for experimental
sources? or is there any other way I can use queues without installing sage
not using portage?
Thanks
VulK

PS: some weird behaviour:

% sage -h
----------------------------------------------------------------------
| Sage Version 4.7, Release Date: 2011-05-23                         |
----------------------------------------------------------------------

Optional arguments:
  file.<sage|py|spyx> -- run given .sage, .py or .spyx files
  -advanced           -- list all command line options

(Continue reading)

fbissey | 9 Aug 2011 06:29

Picon

Re: sage queues

Quoting VulK <etn45p4m <at> gmail.com>:

> Dear all,
> this is my first post to gentoo-science and I am writing because I have some
> problems running experimental code from the sage project.
> My issue is the following:
> I have sci-mathematics/sage-4.7-r2 installed from the  sage-on-gentoo overlay
> and I would like to install the combinat queue; I am following these
> instructions: http://wiki.sagemath.org/combinat/MercurialStepByStep
> The command I am supposed to run is
> # sage -combinat install
> unfortunately -combinat is not recognized by sage as a valid option. I
> browsed a little bit around the filesystem and I noticed that $SAGE_ROOT is
> empty (except for some documentation) while on other installations of sage
> (not using the ebuilds) there is plenty of stuff including a devel/combinat
> folder.
> Is there an option I can use when installing sage to allow for experimental
> sources? or is there any other way I can use queues without installing sage
> not using portage?
> Thanks
> VulK
>
> PS: some weird behaviour:
>
> % sage -h
> ----------------------------------------------------------------------
> | Sage Version 4.7, Release Date: 2011-05-23                         |
> ----------------------------------------------------------------------
>
> Optional arguments:

(Continue reading)

VulK | 9 Aug 2011 07:07

Picon

Re: sage queues

Hi,
Thank you for the explanation: I kind of guessed that some part of sage were
omitted to adapt the two packaging system but your explanation gave me the
details I was missing. 
As you said the combinat queue is/should be a real mess of continuous
updates (at least this is what I was told) so I am not entirely sure how well
an e-build would perform, in case you decide to spend some time on it I will
gladly be a guinea pig for testing it out.
I do not understand sage package system in details so my request may just be
stupid but is it possible to produce separate ebuilds for the different part 
of sage that are now stripped? If not for all of those can this be done for the
various packages in $SAGE_ROOT/devel ? If an e-build is not feasible, can
USE flags be used to select which extensions to include at compile time?
Thank you
S.

* fbissey <at> slingshot.co.nz <fbissey <at> slingshot.co.nz> [2011-08-09 16:29:52]:

> Quoting VulK <etn45p4m <at> gmail.com>:
> 
> > Dear all,
> > this is my first post to gentoo-science and I am writing because I have some
> > problems running experimental code from the sage project.
> > My issue is the following:
> > I have sci-mathematics/sage-4.7-r2 installed from the  sage-on-gentoo overlay
> > and I would like to install the combinat queue; I am following these
> > instructions: http://wiki.sagemath.org/combinat/MercurialStepByStep
> > The command I am supposed to run is
> > # sage -combinat install
> > unfortunately -combinat is not recognized by sage as a valid option. I

(Continue reading)

fbissey | 9 Aug 2011 07:21

Picon

Re: sage queues

Quoting VulK <etn45p4m <at> gmail.com>:

> Hi,
> Thank you for the explanation: I kind of guessed that some part of sage were
> omitted to adapt the two packaging system but your explanation gave me the
> details I was missing.
> As you said the combinat queue is/should be a real mess of continuous
> updates (at least this is what I was told) so I am not entirely sure how well
> an e-build would perform, in case you decide to spend some time on it I will
> gladly be a guinea pig for testing it out.
> I do not understand sage package system in details so my request may just be
> stupid but is it possible to produce separate ebuilds for the different part
> of sage that are now stripped? If not for all of those can this be 
> done for the
> various packages in $SAGE_ROOT/devel ? If an e-build is not feasible, can
> USE flags be used to select which extensions to include at compile time?
>
The details are a bit long to explain but everything provided by sage is
currently split. Technically what is missing is some scripts from the spkg
sage_scripts (provided by our sage-baselayout ebuild). Most of the files in
$SAGE_LOCAL/bin of a vanilla install that starts with sage are provided 
by this
spkg. And we omit a lot of them, some are already installed only on use flag
request. We could add more if it was useful and feasible from a package
management perspective.

I must say that talking with sage-developers interested in sage installed with
portage there is a possibility that some stuff may come back in some form once
we figured it out. Something like sage -combinat creates a new sage branch.
There is a possibility that we could allow such a branch to be created

(Continue reading)

Christopher Schwan | 9 Aug 2011 13:46

Picon

Picon

Re: sage queues

On Tuesday 09 August 2011 01:07:44 you wrote:
> Hi,
> Thank you for the explanation: I kind of guessed that some part of sage were
> omitted to adapt the two packaging system but your explanation gave me the
> details I was missing.
> As you said the combinat queue is/should be a real mess of continuous
> updates (at least this is what I was told) so I am not entirely sure how
> well an e-build would perform, in case you decide to spend some time on it
> I will gladly be a guinea pig for testing it out.
> I do not understand sage package system in details so my request may just be
> stupid but is it possible to produce separate ebuilds for the different
> part of sage that are now stripped? If not for all of those can this be
> done for the various packages in $SAGE_ROOT/devel ? If an e-build is not
> feasible, can USE flags be used to select which extensions to include at
> compile time? Thank you
> S.

If I understand you correctly, you are asking if it is possible to further 
split up the sage ebuild, so that we have individual ebuilds for 
sage.combinat, sage.interfaces and so on. That would make it possible to 
replace individual parts by development versions (which is your original aim) 
- very interesting idea.

Lets assume its done, then I see the following pros and cons:

Pro:
- The option to leave out certain packages and thereby the possiblity to lower 
the number of dependencies (that was my long-term goal)
- Recompiliation of Sage (because of the addition of some patches) would take 
less time

(Continue reading)

VulK | 12 Aug 2011 05:24

Picon

Re: sage queues

* fbissey <at> slingshot.co.nz <fbissey <at> slingshot.co.nz> [2011-08-09 17:21:10]:

> Quoting VulK <etn45p4m <at> gmail.com>:
> 
> > Hi,
> > Thank you for the explanation: I kind of guessed that some part of sage were
> > omitted to adapt the two packaging system but your explanation gave me the
> > details I was missing.
> > As you said the combinat queue is/should be a real mess of continuous
> > updates (at least this is what I was told) so I am not entirely sure how well
> > an e-build would perform, in case you decide to spend some time on it I will
> > gladly be a guinea pig for testing it out.
> > I do not understand sage package system in details so my request may just be
> > stupid but is it possible to produce separate ebuilds for the different part
> > of sage that are now stripped? If not for all of those can this be 
> > done for the
> > various packages in $SAGE_ROOT/devel ? If an e-build is not feasible, can
> > USE flags be used to select which extensions to include at compile time?
> >
> The details are a bit long to explain but everything provided by sage is
> currently split. Technically what is missing is some scripts from the spkg
> sage_scripts (provided by our sage-baselayout ebuild). Most of the files in
> $SAGE_LOCAL/bin of a vanilla install that starts with sage are provided 
> by this
> spkg. And we omit a lot of them, some are already installed only on use flag
> request. We could add more if it was useful and feasible from a package
> management perspective.
> 
> I must say that talking with sage-developers interested in sage installed with
> portage there is a possibility that some stuff may come back in some form once

(Continue reading)

fbissey | 12 Aug 2011 05:38

Picon

Re: sage queues

Quoting VulK <etn45p4m <at> gmail.com>:
>
> Do you mean that in a distant future sage package system *might* become
> portage?
>

Hi VuLK,

there is a distinct possibility. A number of developers are
thinking about it and we have a proof of concept that kind of run
on linux. It still has rough edges and we don't spend as much
time on it as necessary to give it some polish at the moment.

https://bitbucket.org/burcin/sage-prefix/wiki/Home

Francois

Thomas Kahle | 14 Aug 2011 00:40

Picon

la files for sci-libs/mpir

Hi science devs,

An amd64 arch tester asked me to 'remove the .la files' from mpir.  I
must admit that I still don't see through this.  Not all .la files are
evil, or are they?  Should the ones coming with mpir not be installed?

Thanks for any hints,
Thomas

--

-- 
Thomas Kahle
http://dev.gentoo.org/~tomka/

Christopher Schwan | 14 Aug 2011 10:53

Picon

Picon

Re: la files for sci-libs/mpir

On Saturday 13 August 2011 23:40:58 you wrote:
> Hi science devs,
> 
> An amd64 arch tester asked me to 'remove the .la files' from mpir.  I
> must admit that I still don't see through this.  Not all .la files are
> evil, or are they?  Should the ones coming with mpir not be installed?
> 
> Thanks for any hints,
> Thomas

Hi Thomas,

most of the time they are just unnecessary - if you do not install both shared 
and static libraries I suggest to drop them. I am not an expert, but Flameeyes 
has some enlightening post on his blog, e.g.

    http://blog.flameeyes.eu/2008/04/14/what-about-those-la-files

I suggest you simply use the autotool-utils.eclass (mpir uses autotools, 
right?) which take care of them. The eclass' manpage provides a nice example 
how to achieve this behavior (note the use of "static-libs" USE-flag).

Cheers,
Christopher

Christoph Junghans | 14 Aug 2011 17:34

Picon

Re: la files for sci-libs/mpir

Hi Thomas,

2011/8/14 Thomas Kahle <tomka <at> gentoo.org>:
> An amd64 arch tester asked me to 'remove the .la files' from mpir.  I
> must admit that I still don't see through this.  Not all .la files are
> evil, or are they?  Should the ones coming with mpir not be installed?
That depends on what depends on mpir!

Basically the .la files contain all dependencies of a library, but
only a GNU build system using libtool makes use of these files, other
build systems like cmake don't.

However there are two cases, where it is 100% safe to delete the .la files:
1.) mpir comes with a pkg-config (.pc) file.
2.) mpir only installs a shared libs, which have an internal
dependencies memory.

But i guess the use of the autotool-utils eclass together with
static-libs useflag is the best solution.

Cheers,

Christoph

>
> Thanks for any hints,
> Thomas
>
> --
> Thomas Kahle

(Continue reading)

Group

gmane.linux.gentoo.science.

Project Web Page

Discussion on science-related applications and integration in Gentoo.

Search Archive

Page

1 | 2 | 3 | 4 | 5 | 6

Articles in period: 56

August 2011

Language

Change language

Options

Current view: Threads only / Showing only 20 lines / Not hiding cited text.
Change to All messages, whole messages, or hide cited text.

Post a message
NNTP Newsgroup
Classic Gmane web interface
XML

XML

RSS Feed
List Information

About Gmane

Recent entries

sci-physics/lammps: question on proper integration of mpi (12 May 2013)
does sage work? (5 May 2013)
common lisps overlay -> tree; maxima, fricas (20 Apr 2013)
sci-libs/atlas from science overlay - is it multithreaded? (9 Apr 2013)
failure to merge sage due to unavailability of cblas (4 Mar 2013)
sage 5.7 (28 Feb 2013)
sage 5.7 (28 Feb 2013)
[sage-on-gentoo] sage-clib-5.7 fails to build (28 Feb 2013)
sage 5.7 (27 Feb 2013)
[sage-on-gentoo] sage-clib-5.7 fails to build (27 Feb 2013)
Coin-3.1.0.tar.gz tarball misssing (13 Feb 2013)
Pull request: new ebuilds for HPX and LibGeoDecomp (3 Feb 2013)
[sage-on-gentoo] sage-5.6 build failure related to cblas (30 Jan 2013)
sage-5.6 build failure (29 Jan 2013)
gentoo-science and gentoo-prefix (25 Jan 2013)
gentoo-science and gentoo-prefix (25 Jan 2013)
[sage-on-gentoo] sage-5.4.1-r3 build failure (26 Dec 2012)
Github commit access broken (10 Dec 2012)
Making ebuilds for sage packages (3 Dec 2012)
ebuild for fullprof (XRD powder fitting programm)? (14 Nov 2012)
is numpy using the old lapack interface? (29 Oct 2012)

Archives

9	May 2013
8	April 2013
13	March 2013
15	February 2013
7	January 2013
18	December 2012
4	November 2012
27	October 2012
8	September 2012
21	August 2012
6	July 2012
21	June 2012
15	May 2012
5	April 2012
5	March 2012
50	February 2012
6	January 2012
15	December 2011
7	November 2011
12	October 2011
37	September 2011
56	August 2011
2	July 2011
19	June 2011
4	May 2011
9	April 2011
6	March 2011
2	February 2011
56	December 2010
35	November 2010
53	October 2010
11	September 2010
37	August 2010
52	July 2010
35	June 2010
51	May 2010
53	April 2010
43	March 2010
21	February 2010
11	January 2010
9	December 2009
7	October 2009
3	September 2009
2	August 2009
17	July 2009
1	June 2009
33	May 2009
1	April 2009
9	March 2009
35	February 2009
24	January 2009
5	December 2008
4	October 2008
7	August 2008
6	July 2008
13	June 2008
7	May 2008
13	April 2008
11	March 2008
16	February 2008
14	January 2008
11	December 2007
44	October 2007
1	September 2007
27	August 2007
26	July 2007
26	June 2007
19	May 2007
4	April 2007
23	March 2007
22	February 2007
23	January 2007
7	December 2006
8	November 2006
8	October 2006
27	September 2006
30	August 2006
18	July 2006
45	June 2006
32	May 2006
9	March 2006
34	February 2006
19	January 2006
18	December 2005
38	November 2005
19	October 2005
6	September 2005
35	August 2005
34	June 2005
19	May 2005
22	April 2005
21	March 2005
40	February 2005
25	January 2005
45	December 2004
62	November 2004
3	October 2004

Design

Zawodny | Right Menu | Left Menu

Your Own Design

Paste the URL of your CSS below. Download CSS template