[gentoo-science] Gentoo science status

[gentoo-science] Gentoo science status

[Sébastien Fabbro]

Hello all,

I wanted to get heads up for our science project.

* Manpower:
  First our under staffed recruitment team found some time to
  turn Justin Lecher (jlec) an official Gentoo developer who
  hasn't stopped into helping for the science and chemistry packages.
  Welcome Justin!
  We have a couple of people also in the mentoring process who will be
  great new addition to the team. And as always we need more hands. So
  anyone interested, contact the sci team.

  We also need to know whether we still want a leader. Some time ago
  the question was raised, but got no definite answer.

* Bugs:
  I have not done the counts, but I see we are actually improving quite
  a bit and killing a lot of old and nasty bugs. I think we are still

* Documentation: 
  We need to revamp our project documentation. I started some doc in
  our overlay [1] long time ago, but feel free to update, propose
  patches or rewrite it entirely if you don't like it. Denis had some
  electronics docs in his site, so we could also merge it. A wiki would
  be very nice, but first it would be worth checking how many people are
  actually using Gentoo for science.
  One another simple thing is also add a <longdescription> tag in the
  metadata.xml of our packages which I think useful to discover quickly
  a new package and give credits for upstream.

* Projects:
  - Do not forget to test the g-octave project from Raphael [2], he
    needs feedback.
  - Sage on Gentoo [3] is slowly but surely becoming a reality thanks to
    Christoper and Francois.
  - A reminder for all of you to test the multiple MPI implementation
    system [4] put together by Justin Bronder
  - I plan to update the blas-lapack and the Fortran frameworks with
    long overdue package updates before the Summer. Contact me if you
    want to help.

[1] http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=tree;f=docs
[2] http://g-octave.rafaelmartins.eng.br/
[3] http://github.com/cschwan/sage-on-gentoo
[4] http://dev.gentoo.org/~jsbronder/empi.xml


Best,

--
Sebastien

Re: [gentoo-science] Gentoo science status

[Markus Dittrich]

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Hi Sébastien,

Thanks for the nice summary of the current state
of affairs.

> 
>   We also need to know whether we still want a leader. Some time ago
>   the question was raised, but got no definite answer.

I think if we decide that we want a leader we should clearly
define what we expect her/him to do. We're a very diverse
bunch and the packages in science.g.o span a wide range of
fields so I am not 100% convinced that a lead will necessarily
be very effective. On the other hand, there are a few things
that definitely need improvement, documentation and eclasses
being some candidates here, and it might be nice to have somebody
who feels responsible and coordinates/delegates a bit. I'd
probably need a nudge once in a while ;)

> * Documentation: 
>   We need to revamp our project documentation. I started some doc in
>   our overlay [1] long time ago, but feel free to update, propose
>   patches or rewrite it entirely if you don't like it. Denis had some
>   electronics docs in his site, so we could also merge it. A wiki would
>   be very nice, but first it would be worth checking how many people are
>   actually using Gentoo for science.

Better docs are definitely something we need. It would probably be
good to either have a dev or maybe one of our users assess and then
coordinate this a bit.

cheers,
Markus

-- 
-- 
Markus Dittrich (markusle)
Gentoo Linux Developer
Scientific applications

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Re: [gentoo-science] Gentoo science status

[François Bissey]

Hi all,

On Fri, 05 Feb 2010 15:33:46 Markus Dittrich wrote:
> Hi Sébastien,
> 
> Thanks for the nice summary of the current state
> of affairs.
> 
> >   We also need to know whether we still want a leader. Some time ago
> >   the question was raised, but got no definite answer.
> 
> I think if we decide that we want a leader we should clearly
> define what we expect her/him to do. We're a very diverse
> bunch and the packages in science.g.o span a wide range of
> fields so I am not 100% convinced that a lead will necessarily
> be very effective. On the other hand, there are a few things
> that definitely need improvement, documentation and eclasses
> being some candidates here, and it might be nice to have somebody
> who feels responsible and coordinates/delegates a bit. I'd
> probably need a nudge once in a while ;)
> 

Actually Gentoo hierarchy is quite pragmatic and flexible, we can have
several leads - but I guess the implication would be to effectively split
into sub-project which is fine if we wanted too.

> > * Documentation:
> >   We need to revamp our project documentation. I started some doc in
> >   our overlay [1] long time ago, but feel free to update, propose
> >   patches or rewrite it entirely if you don't like it. Denis had some
> >   electronics docs in his site, so we could also merge it. A wiki would
> >   be very nice, but first it would be worth checking how many people are
> >   actually using Gentoo for science.
> 

I am not sure how people are using Gentoo here now. There is me and a
PhD student for sure but the other big user in the NMR lab has left for 
Oxford. I am not sure if they have kept their machine on Gentoo. They 
certainly should know that I can be pinged for problems - actually I get 
pinged for problems with any distro.

Francois 

Re: [gentoo-science] Gentoo science status

[Donnie Berkholz]

On 02:33 Fri 05 Feb     , Markus Dittrich wrote:
> >   We also need to know whether we still want a leader. Some time ago
> >   the question was raised, but got no definite answer.
> 
> I think if we decide that we want a leader we should clearly
> define what we expect her/him to do. We're a very diverse
> bunch and the packages in science.g.o span a wide range of
> fields so I am not 100% convinced that a lead will necessarily
> be very effective. On the other hand, there are a few things
> that definitely need improvement, documentation and eclasses
> being some candidates here, and it might be nice to have somebody
> who feels responsible and coordinates/delegates a bit. I'd
> probably need a nudge once in a while ;)

One thing I think would be great is someone who would go out into 
"science-land" and publicize how great Gentoo is for science. Perhaps 
individual ambassadors for each branch of science, who would be willing 
to proselytize at conferences, on discipline mailing lists, etc.

Other than that, it seems like things roll along fairly well. The main 
science-wide work seems related to either MPI or Fortran, both of which 
could use some integration with more typical things. Have you noticed 
how Fortran-related things are almost totally different from C++, in 
terms of eclass usage, function naming, etc? No good reason for that.

-- 
Thanks,
Donnie

Donnie Berkholz
Science team developer
Gentoo Linux
Blog: http://dberkholz.wordpress.com

Re: [gentoo-science] Gentoo science status

[Thomas Kahle]

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On 02/21/2010 06:52 AM, Donnie Berkholz wrote:
> On 02:33 Fri 05 Feb     , Markus Dittrich wrote:
>>>   We also need to know whether we still want a leader. Some time ago
>>>   the question was raised, but got no definite answer.
>>
>> I think if we decide that we want a leader we should clearly
>> define what we expect her/him to do. We're a very diverse
>> bunch and the packages in science.g.o span a wide range of
>> fields so I am not 100% convinced that a lead will necessarily
>> be very effective. On the other hand, there are a few things
>> that definitely need improvement, documentation and eclasses
>> being some candidates here, and it might be nice to have somebody
>> who feels responsible and coordinates/delegates a bit. I'd
>> probably need a nudge once in a while ;)
> 
> One thing I think would be great is someone who would go out into 
> "science-land" and publicize how great Gentoo is for science. Perhaps 
> individual ambassadors for each branch of science, who would be willing 
> to proselytize at conferences, on discipline mailing lists, etc.

I have been working on some sci-mathematics ebuilds in the science
overlay and usually upstream was happily surprised to find that there is
a distribution shipping their software. I generally try to spread how
great Gentoo is for math :)

See for instance these two pages mentioning Gentoo:

http://www.math.uiuc.edu/Macaulay2/Downloads/GNU-Linux/Gentoo/

http://wwwopt.mathematik.tu-darmstadt.de/polymake/doku.php/download/start

Regards,
Thomas


-- 
Thomas Kahle

The fundamental theorem of algebra is open source. Like any other
mathematical theorem it can be applied free of charge and everybody
has access to its proof and can convince himself how it works. Why
should software be any different?


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[gentoo-science] Re: Gentoo science status

[Sébastien Fabbro]

>   We also need to know whether we still want a leader. Some time ago
>   the question was raised, but got no definite answer.

It would be nice to have a head count to see how many of us are active
to get an idea how much there is to lead. The mail aliases in
dev.g.o are very different than what the project page states, which is
different than the last round of head counts. I created an empty
dev table on the science overlay draft docs [1]. So each active dev and
contributor, please either update the table with your user name and
role or send me an email so that I can update it if you don't have
access to it.

> * Bugs:
>   I have not done the counts, but I see we are actually improving
> quite a bit and killing a lot of old and nasty bugs. I think we are
> still

...lagging on stabilization of our packages (sorry for the incomplete
sentence). Stabilization bugs are boring and I wish one of us had time
and infrastructure to set up an automated testing framework. Meanwhile,
let's stabilize as much as we can the much overdue packages.

[1] git://git.overlays.gentoo.org/proj/sci.git: docs/proj/index.xml

--
Sébastien

Re: [gentoo-science] Gentoo science status

[Jeff Gardner]

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On 02/03/2010 11:38 AM, Sébastien Fabbro wrote:
> * Manpower:
>   First our under staffed recruitment team found some time to
>   turn Justin Lecher (jlec) an official Gentoo developer who
>   hasn't stopped into helping for the science and chemistry packages.
>   Welcome Justin!


Welcome indeed!


>   We also need to know whether we still want a leader. Some time ago
>   the question was raised, but got no definite answer.


I'm not opposed to having a leader, but I'd be pleasantly suprised if
someone has the time.


>   be very nice, but first it would be worth checking how many people are
>   actually using Gentoo for science.


I know of about 20 scientists in Houston using gentoo right now.


>   One another simple thing is also add a <longdescription> tag in the
>   metadata.xml of our packages which I think useful to discover quickly
>   a new package and give credits for upstream.


Very good idea!


> 
> 
> Best,
> 
> --
> Sebastien
> 
> 

I'm still somewhat active. We've got a newborn (hooray!) and a full time
job, so I'm around...but time is always short.

Poke me if you need my help on anything.

Later,
Jeff Gardner
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Re: [gentoo-science] Gentoo science status

[Donnie Berkholz]

On 01:08 Fri 05 Feb     , Jeff Gardner wrote:
> >   be very nice, but first it would be worth checking how many people 
> >   are actually using Gentoo for science.
> 
> I know of about 20 scientists in Houston using gentoo right now.

Three labs in my old department were using exclusively Gentoo on their 
primarily Linux systems.

Not sure how you could actually reach any scientists using Gentoo in a 
more general way, besides whoever happens to be on this list. Perhaps a 
news item pointing to a survey?

-- 
Thanks,
Donnie

Donnie Berkholz
Science team developer
Gentoo Linux
Blog: http://dberkholz.wordpress.com

Re: [gentoo-science] Gentoo science status

[Björn Thorwirth]

Hi All!

I want to support gentoo-science and especially sage-on-gentoo. I'm also
interested to become official gentoo dev. Whats the way to go .. where
can is tart?

best regrads,

Bjoern Thorwirth
 
Am Mittwoch, den 03.02.2010, 09:38 -0800 schrieb Sébastien Fabbro:
> Hello all,
> 
> I wanted to get heads up for our science project.
> 
> * Manpower:
>   First our under staffed recruitment team found some time to
>   turn Justin Lecher (jlec) an official Gentoo developer who
>   hasn't stopped into helping for the science and chemistry packages.
>   Welcome Justin!
>   We have a couple of people also in the mentoring process who will be
>   great new addition to the team. And as always we need more hands. So
>   anyone interested, contact the sci team.
> 
>   We also need to know whether we still want a leader. Some time ago
>   the question was raised, but got no definite answer.
> 
> * Bugs:
>   I have not done the counts, but I see we are actually improving quite
>   a bit and killing a lot of old and nasty bugs. I think we are still
> 
> * Documentation: 
>   We need to revamp our project documentation. I started some doc in
>   our overlay [1] long time ago, but feel free to update, propose
>   patches or rewrite it entirely if you don't like it. Denis had some
>   electronics docs in his site, so we could also merge it. A wiki would
>   be very nice, but first it would be worth checking how many people are
>   actually using Gentoo for science.
>   One another simple thing is also add a <longdescription> tag in the
>   metadata.xml of our packages which I think useful to discover quickly
>   a new package and give credits for upstream.
> 
> * Projects:
>   - Do not forget to test the g-octave project from Raphael [2], he
>     needs feedback.
>   - Sage on Gentoo [3] is slowly but surely becoming a reality thanks to
>     Christoper and Francois.
>   - A reminder for all of you to test the multiple MPI implementation
>     system [4] put together by Justin Bronder
>   - I plan to update the blas-lapack and the Fortran frameworks with
>     long overdue package updates before the Summer. Contact me if you
>     want to help.
> 
> [1] http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=tree;f=docs
> [2] http://g-octave.rafaelmartins.eng.br/
> [3] http://github.com/cschwan/sage-on-gentoo
> [4] http://dev.gentoo.org/~jsbronder/empi.xml
> 
> 
> Best,
> 
> --
> Sebastien
> 
> 
-- 
Bjoern Thorwirth, Zentrum für Medizinische Biotechnologie,
Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
phone +49 201 183-4026, bjoern.thorwirth@uni-due.de

Re: [gentoo-science] Gentoo science status

[Neil Shephard]

2010/2/17 Björn Thorwirth <bjoern.thorwirth@uni-due.de>:
> Hi All!
>
> I want to support gentoo-science and especially sage-on-gentoo. I'm also
> interested to become official gentoo dev. Whats the way to go .. where
> can is tart?

The Gentoo Developer Handbook is a good starting point, see
http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml

Neil

-- 
"... no scientific worker has a fixed level of significance at which
from year to year, and in all circumstances, he rejects hypotheses; he
rather gives his mind to each particular case in the light of his
evidence and his ideas." - Sir Ronald A. Fisher (1956)

Email - nshephard@gmail.com
Website - http://slack.ser.man.ac.uk/
Photos - http://www.flickr.com/photos/slackline/

Re: [gentoo-science] Gentoo science status

[Björn Thorwirth]

Hi all!

I just want to thank for your suggestions..I've refreshed my knowledge
of the dev handbook and I'm in contact with Christopher Schwan now. I'll
support him by testing sage on amd64 and try to get some experience by
solving the testing issues.

best regards,

Björn Thorwirth


Am Mittwoch, den 17.02.2010, 16:23 +0000 schrieb Neil Shephard:
> 2010/2/17 Björn Thorwirth <bjoern.thorwirth@uni-due.de>:
> > Hi All!
> >
> > I want to support gentoo-science and especially sage-on-gentoo. I'm also
> > interested to become official gentoo dev. Whats the way to go .. where
> > can is tart?
> 
> The Gentoo Developer Handbook is a good starting point, see
> http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml
> 
> Neil
> 
-- 
Bjoern Thorwirth, Zentrum für Medizinische Biotechnologie,
Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
phone +49 201 183-4026, bjoern.thorwirth@uni-due.de

Re: [gentoo-science] Gentoo science status

[Denis Dupeyron]

Hi Björn,

2010/2/23 Björn Thorwirth <bjoern.thorwirth@uni-due.de>:
> I just want to thank for your suggestions..I've refreshed my knowledge
> of the dev handbook and I'm in contact with Christopher Schwan now. I'll
> support him by testing sage on amd64 and try to get some experience by
> solving the testing issues.

You can check my canned recruiter's answer at
http://dev.gentoo.org/~calchan/howtohelp.txt for more links and
pointers to start contributing. It's a general answer so all may not
be pertinent to you.

Denis.

Re: [gentoo-science] Gentoo science status

[Sébastien Fabbro]

Björn Thorwirth wrote:

> Hi All!
> 
> I want to support gentoo-science and especially sage-on-gentoo. I'm
> also interested to become official gentoo dev. Whats the way to go ..
> where can is tart?

Hi,

Thanks for your offer! I would suggest to find us in
irc in #gentoo-science, see also the dev manual [1] and if you are
interested in sage-on-gentoo, contact the main developers.

[1] http://devmanual.gentoo.org/

--
Sébastien

Re: [gentoo-science] Gentoo science status

[François Bissey]

On Thu, 18 Feb 2010 04:26:25 Björn Thorwirth wrote:
> Hi All!
> 
> I want to support gentoo-science and especially sage-on-gentoo. I'm also
> interested to become official gentoo dev. Whats the way to go .. where
> can is tart?
> 
Hi Björn,

The sage-on-gentoo team - that is me and Christopher certainly welcome
helpers. At this point testing things out is useful. But do come on irc as
suggested by Sebastien Fabbro Christopher (gnuke) and I (kiwifb) will be 
happy to discuss what you could do.

Francois