Grant Goodyear | 17 Apr 17:29 2014

liblapack, libblas, numpy, and python virtualenvs

For reproducibility, I like to have a python virtualenv that has all of the python libraries that I use, relying on portage just for python, virtualenv, and virtualenvwrapper. Building numpy using "pip install numpy" fails if I use the science-overlay versions of the reference lapack and blas libraries, because pip can't find liblapack to link to it. 

Right now I'm cheating and using the non-overlay versions, but I'm sure that somebody has a better solution of how to help pip find the right libraries.  Help?

Grant Goodyear       
e-mail: grant <at>
Thomas Kahle | 16 Apr 08:25 2014

Re: polynomial arithmetic

On 16/04/14 08:15, grozin <at> wrote:
> On Sun, 13 Apr 2014, hasufell wrote:
>> I'm looking for a C lib that can do basic polynomial arithmetic as well
>> as algebraic stuff like modular inverse.
> Maybe GiNaC. It definitely can do polynomials.
> Another possibility is pari. It can be used as a library, not only via
> gp. It is highly optimized and efficient.

I'm pretty sure that this can be done in sage.  You could see
which library they use under the hood.  Taking this to
sci-mailing list, there your question gets a lot more attention.



Thomas Kahle

Andrey G. Grozin | 6 Apr 13:42 2014

Re: [Maxima-discuss] Maxima 5.33.0 release (fwd)

---------- Forwarded message ----------
Date: Sun, 6 Apr 2014 18:39:14 +0700 (NOVT)
From: Andrey G. Grozin <grozin <at>>
To: maxima-discuss <at>
Subject: Re: [Maxima-discuss] Maxima 5.33.0 release

I've committed maxima-5.33.0 ebuild to Gentoo. The running times (in seconds) 
of the testsuite with various lisps on 2 Intel computers, with 32-bit and 
64-bit systems, are

              64-bit  32-bit
sbcl-1.1.16     171     196
cmucl-20e               248
gcl-2.6.10      216     249
ccl-1.9         308     323
ecl-13.5.1      618     581
clisp-2.49     1013     861

cmucl is not available on x86_64.
clisp on my 32-bit computer uses pari-2.3.5 to do multiprecision arithmetica; 
on my 64-bit computer, I have pari-2.5.4, clisp does not compile with pari-2.5, 
and is therefore slower.


Justin (jlec | 6 Apr 13:14 2014


Hi everyone,

I/we need urgent help in fixing a package, namely
sci-biology/ncbi-tools++. I started to work on it, but currently I am
short of time to finish it.

Please take a look into the branch in the overlay.
Following problems occur with that package,

* uses custom build system
* weird internal project dependency checking (Problems with parallel
builds. Maybe we can drop this for the moment)
* bundles quite some stuff
* misuses --with configure option and has automagics

So if you like to contribute a great piece of work, please try to fix
this package. Otherwise our treecleaners will last rite quite a number
of sci-bio packages.

Thanks for your help,

grozin | 30 Mar 11:45 2014

additional packages for sci-mathematics/geomview

Hello *,

Claus-Justus Heine <himself <at>> has recently 
contributed an ebuild for the latest version of geomview plus 8 ebuilds 
for additional "emodules" which extend the functionality of geomview. They 
are rather small packages depending on geomview and sometimes on something 
else. I have committed the bumped geomview (after the necessary changes).

What would be the best way to deal with these emodules?
1. Commit 8 new packages
2. Add 8 USE flags to geomview, and buildinstall these emodules depending 
on the flags
3. Something else

Opinions, please


justin | 30 Jan 14:04 2014

Meeting summary

Hi everyone,

here is the meeting summary for yesterdays meeting


Sorry for the cross-posting.

justin | 29 Jan 08:40 2014

Contribution FAQ

Hi everyone,

Sebastien and I put together a simply guide for contributions to the sci
overlay. Following those few lines should make the contributions even
more flawless.

I hope we will see many more contributions to the overlay!

Cheers Justin

Sébastien Fabbro | 28 Jan 07:44 2014

gentoo science meeting date and agenda

Dear all,

We'll be having a gentoo-science meeting:

Wednesday, January 29, 2014 21:00 UTC
IRC: #gentoo-meetings on freenode

Developers, users, contributors welcome

1. Alternative framework
2. Documentation updates and actions
3. Election of a new leader
Open floor


Nicolas Bock | 25 Jan 23:39 2014

has the ssh host key of been changed?


today I noticed that the ssh host key of has changed. I am getting this value as the fingerprint of the new key:

The fingerprint for the ECDSA key sent by the remote host is

Is that the correct key?


François Bissey | 22 Jan 01:52 2014

blas selection in lapack-reference

We have yet another instance of someone emerging lapack-reference 
a valid blas configuration in
(not their original problem).
I think we should do something about this in lapack-reference and 
other ebuilds.
In pkg_setup, we could run
eselect blas update
to make sure that a valid configuration is active
and display an informational message about the blas provider
used with the output of
eselect blas show

Who thinks is a good/bad idea?


Sébastien Fabbro | 21 Jan 18:16 2014

gentoo-science team meeting

I would like to do a science team IRC meeting.

Proposed agenda:
1. alternatives plan
2. documentation actions
3. election of a new leader, since I'm stepping down

Proposed date:
1.  Jan 23 20:00 UTC 
2.  Jan 30 20:00 UTC
3. doodle it

Who's in?