On Fri, Apr 15, 2011 at 11:21:55AM -0500, Steve M. Robbins wrote:
This message is reaching all the listed maintainers of mpi-defaults.
I'd suggest one of you go ahead and make the upload! (If you prefer,
I can do it)
I'm preparing an upload of a new mpi-defaults just now that addresses
all
On Sun, Apr 10, 2011 at 12:20:23PM -0400, Adam C Powell IV wrote:
FWIW, my vote would be to go ahead and replace LAM with MPICH2 on the
non-OpenMPI arches now, and remove LAM and MPICH1 from the archive. Or
if we decide MPICH2 is better than OpenMPI, default to that everywhere.
Either way,
Hi Nicolas!
Thank you very much for investigating and your patches!
On Tue, May 10, 2011 at 08:16:52PM -0700, Nicholas Breen wrote:
The second category are packages that still Build-Depend directly on LAM or
MPICH1, part of the list at [1]. There are only six of them left! I've
submitted
Sorry for jumping in late, I'm recovering from a servere cold at the moment.
I'll probably have some delay in responding in the next days, as I'm not fully
recovered.
On Fri, Apr 08, 2011 at 10:54:47AM +1000, Drew Parsons wrote:
I'm happy to leave bug #575259 untouched if you suspect the patch
On Fri, Feb 18, 2011 at 11:08:20AM +0100, Andreas Tille wrote:
probably not the right list, debian-science list comes rather to mind
because Dirk Eddelbuettel (in CC) is also reading there. So please move
to this list in case you want to continue discussing this issue.
Done. Totally forgot to
Am Montag, den 13.12.2010, 12:24 +0100 schrieb Sylvestre Ledru:
[Putting packages under the Debian Science umbrella] would also
simplify some coordinations on some related works (MPI, linear algebra
libraries, etc). It is one of the reason of the pkg-scicomp = Debian
Science merge.
FWIW,
Am Dienstag, den 23.03.2010, 13:16 +0100 schrieb Lucas Nussbaum:
I'm not the mpi-defaults maintainer :-) Manuel? Adam?
Sorry for replying late!
mpi-defaults was supposed to be an interim solution and in an ideal
world gone already. I know it's not the best solution out there, but the
best we
Am Sonntag, den 21.03.2010, 12:49 +0100 schrieb Thibaut Paumard:
I am about to upload a new package which build-depends on mpi-default-
dev (it will need to be checked by a sponsor and then go through NEW).
It it ok to do so in the next couple of days or should I wait for the
new
Am Dienstag, den 23.03.2010, 19:40 +0100 schrieb Lucas Nussbaum:
I think that the best way to solve this problem is to explicitely
conflict with the other implementations in mpi-defaults.
Just to clarify: Do you mean adding a Build-Conflicts: to mpi-defaults
or Conflicts: to mpi-defaults-dev?
Am Mittwoch, den 17.03.2010, 13:24 +0100 schrieb Lucas Nussbaum:
On 17/03/10 at 09:49 +0100, Marc 'HE' Brockschmidt wrote:
Lucas Nussbaum lu...@lucas-nussbaum.net writes:
So, it looks like it is mostly build system bugs, and it should not be
too hard to fix.
Good to know, thanks for
Hi all,
this is a short status update on this topic.
Am Montag, den 09.11.2009, 16:47 -0800 schrieb Nicholas Breen:
* should we start filing wishlist bugs asking packagers not to build against
MPICH (1) and LAM?
I (finally) got around to file bugs against all packages build-depending
on
Am Dienstag, den 16.02.2010, 13:26 +0100 schrieb Sylvestre Ledru:
Le jeudi 11 février 2010 à 13:20 +0100, Christophe Prud'homme a écrit :
why not subscribe everybody from the pkg-scicomp to Debian science
automatically ?
both for -devel and -commits
-commits requires that we change also
Am Freitag, den 15.01.2010, 10:49 +0100 schrieb Salvatore Bonaccorso:
Ok, if Alexey would not adopt mathgl by himself, then I will inject it
in the debian-science team repository
That's a reasonable thing to do anyway. If mathgl was in Debian already,
we should preserve previous work and
Hi Salvatore!
Am Sonntag, den 10.01.2010, 15:55 +0100 schrieb Salvatore Bonaccorso:
mathgl is a Dependency of udav. Thus I'm interested to keep matgl, and
I would adopt it. But if there is some other interested too, I would
also help comaintain it, or if there is a scientific team which want
Am Sonntag, den 03.01.2010, 23:26 +0100 schrieb Michael Banck:
If one still wants to have a non-MPI package as well, is there a
preferred suffix for the mpi package using the default? foo-mpi?
There is no policy on that (yet) but your suggestion seems very
reasonable.
Best regards
Manuel
--
Am Montag, den 30.11.2009, 22:11 -0800 schrieb Nicholas Breen:
On Tue, Dec 01, 2009 at 03:49:20PM +1100, Drew Parsons wrote:
From the point of view of a client package, what is now best practice
for working with MPI? Is there a website/wiki/document explaining how
to set up an MPI-using
Am Montag, den 09.11.2009, 16:47 -0800 schrieb Nicholas Breen:
* should we start filing wishlist bugs asking packagers not to build against
MPICH (1) and LAM?
If noone objects by the end of the week, I will file the bugs then. The
number of affected packages is really low and the severity
Hi Francesco!
Am Dienstag, den 24.11.2009, 09:04 +0100 schrieb Francesco Pietra:
As the initial trigger of these interventions, may I ask if anything
has been done to provide version 4.0 of GROMACS for amd64 lenny?
Not as far as I know. If it's just for this package, I can send you the
Am Montag, den 23.11.2009, 00:10 +0100 schrieb Francesco Poli:
is there anyone willing to package VisIt for Debian?
My RFP (see bug #395573) was converted into an ITP, but later was
converted back into an RFP...
I did not know about that but started packaging it a while ago. The
files are
Gee, I should stop posting past a certain hour of the day… ;)
On Tue, 2009-11-10 at 18:08 -0500, Adam C Powell IV wrote:
The .so alternatives symlinks only require that the libraries be
API-compatible, which they are (or if not, it's a bug, since they're
supposed to follow the MPI standard).
Am Dienstag, den 10.11.2009, 09:19 -0500 schrieb Adam C Powell IV:
* in mpi-defaults, should MPICH2 replace LAM for architectures not
supported
by OpenMPI?
I think that would make a lot of sense since LAM is end-of-life.
Filed as bug #555653, so we won't forget about that. We should
Am Freitag, den 25.09.2009, 12:23 +0200 schrieb Steffen Moeller:
The question is indeed a valid one. For larger compute clusters, stable
indeed seems to mean invariant. And while as scientists we always want the
very latest, we also want stable compute clusters. This is a dilemma.
Indeed.
Am Sonntag, den 07.06.2009, 13:23 -0500 schrieb Steve M. Robbins:
It turned out that I had libmpich1.0-dev installed as well as OpenMPI
and the former was a higher priority than OpenMPI. Is that a
manifestation of the bug you mean?
Yes. Kind of. The bug results from cruft left around by some
Am Montag, den 01.06.2009, 19:00 -0400 schrieb Adam C Powell IV:
Last week OpenMPI transitioned to a new shared library package,
reflecting an ABI change to version 1.3.x (which wasn't reflected in the
shared lib package name of 1.3-2).
I went to rebuild my spooles package, only to find that
Am Mittwoch, den 08.04.2009, 09:28 +0200 schrieb Jan Beyer:
Actually I read a bit more on jarnal's homepage and it might be messy to
package (quoting from
http://www.dklevine.com/general/software/tc1000/jarnal-down.htm):
-
Source Code: The source is contained in the jar files and can be
in Debian, so
please do not hesitate to express your opinion! :)
On Sat, Mar 14, 2009 at 04:56:41PM +0100, Manuel Prinz wrote:
There are also some other issues: Most MPI implementations do not play
well together, meaning there currently are problems if two or more are
installed. (Yes
Am Samstag, den 14.03.2009, 10:54 +0100 schrieb Francesco P. Lovergine:
while working on HDF5 I'm considering to move MPI support to use
mpi-default-dev
and mpi-default-bin. That would imply providing a single reference platform
support
(openmpi or lam, completely dropping mpich AFAIK)
Am Donnerstag, den 12.02.2009, 08:52 +0100 schrieb Andreas Tille:
The plan for the future is to be able to add *only* a Vcs-* field and
just obtain the other information about prospective packages out of
debian/{control,changelog,copyright} inside the Vcs. Isn't it fun to
be able to keep
Am Dienstag, den 03.02.2009, 15:20 +0100 schrieb Andreas Tille:
Code to obtain the bugs in question just exists in the script which
generates the bugs pages. It would not be very hard to implement
sending a monthly mail according to this using the existing code.
I'd volunteer to give some
Am Dienstag, den 27.01.2009, 14:01 +0100 schrieb Daniel Leidert:
Do you mean: debian-science.alioth.d.o == Debian Science? Are you
kidding me? Please get serious.
No, I did not mean that. The former is a packaging effort and just a
part of the later.
It is maybe a place to pickup
Am Montag, den 26.01.2009, 11:40 -0700 schrieb Paul E Condon:
I subscribed to debian-science in order to lurk to learn about the
state of free software for various scientific endeavors. Now it
appears to be a window on the internal politics of Debian.
Unfortunately, yes.
From poking around
Am Montag, den 26.01.2009, 18:50 +0100 schrieb Daniel Leidert:
This is *not* the policy of Debian Science!
You're right. It's a draft and a recommendation, and it states that.
Being part of Debian Science just requires to care about scientific
packages or related goals. It will (and must)
Am Freitag, den 12.12.2008, 14:38 +0100 schrieb Andreas Tille:
BioPerl, libbio-mage-perl, libbio-ruby, ... are examples for developer
oriented packages that do not end with -dev extension. So there is no
good automatic way to differentiate between developer or user oriented
packages if you
Am Freitag, den 12.12.2008, 13:35 +0100 schrieb Andreas Tille:
On Fri, 12 Dec 2008, Manuel Prinz wrote:
So I wonder if it is reasonable to add -dev packages to the already
existing task pages and modify the scripts that generate the
meta-packages in a way that they sort out all -dev
Am Freitag, den 12.12.2008, 11:27 +0100 schrieb Sylvestre Ledru:
For a lambda user, applications and libraries are two very different
things.
ACK.
I would like to know if we could create a -dev tasks for each category
and move libraries into.
This should be possible. AFAIK you can just
Am Donnerstag, den 20.11.2008, 09:45 -0500 schrieb Adam C Powell IV:
It uses the PETSc system, which Build-Depends on an arch-dependent MPI
implementation, then rules uses readlink to determine which one is the
default alternative, and sets substvars appropriately, whether openmpi,
lam, or
Am Mittwoch, den 19.11.2008, 04:32 -0600 schrieb Steve M. Robbins:
If I may, I'd like to suggest mpi-defaults go ahead despite
good intentions that OpenMPI be ready before squeeze.
That way, maintainers of MPI-using packages (e.g. me) don't have to
deal with the mess from today until the
[ Sorry for the long email! I wanted to express my view and as a
non-native speaker, it's not always easy to be precise. Hope you don't
mind. ]
Am Dienstag, den 18.11.2008, 08:05 -0500 schrieb Adam C Powell IV:
On Sat, 2008-11-15 at 21:04 -0600, Dirk Eddelbuettel wrote:
On 14 November 2008 at
On Thu, 2008-10-30 at 15:21 +0100, Manuel Prinz wrote:
ACK to that. The problem will probably not go away anytime soon. A new
standard seems to be on the way, and I really hope things improve with
it.
Am Donnerstag, den 30.10.2008, 19:48 -0400 schrieb Adam C Powell IV:
Wow, that would
Am Montag, den 27.10.2008, 22:13 +0900 schrieb Charles Plessy:
I have been thinking a bit further about the bibtex references, and wonder
about two questions:
- What kind of unique identifier will we give to them?
I used the scheme First Author, Year, Colon, Software for quite some
time
Am Montag, den 27.10.2008, 15:41 + schrieb Chris Walker:
Manuel Prinz [EMAIL PROTECTED] writes:
I used the scheme First Author, Year, Colon, Software for quite some
time now. Example: Baker2001:apbs for APBS [0]. Until now, I did not
have any problems with that.
If you were to put
Am Donnerstag, den 16.10.2008, 17:41 +0200 schrieb Michael Banck:
The problem I have with doc-base is that it is underused and not very
accessible. At least that is my impression of it as somebody who
doesn't care a lot about it from a packager's POV. I probably should
care more, though.
I
Am Samstag, den 11.10.2008, 15:40 +0100 schrieb Chris Walker:
I do like the approach of having a simple plain text file - while not
machine readable does make it clear the appropriate citation - (and in
this case the request that modified by author, institution, location,
year be added if
Am Samstag, den 11.10.2008, 10:35 -0500 schrieb Dirk Eddelbuettel:
On 11 October 2008 at 15:40, Chris Walker wrote:
| I do like the approach of having a simple plain text file - while not
| machine readable does make it clear the appropriate citation - (and in
FWIW that is was R does. [...]
Hi Onkar!
Am Montag, den 11.08.2008, 02:14 +0530 schrieb Onkar Shinde:
'electric' is an electrical CAD system made using java.[1] The package
has been orphaned/removed from Debian, perhaps because it migrated
from C to Java and there was not enough interest about packaging or
using it.
I
Am Montag, den 07.07.2008, 21:45 +0200 schrieb Andreas Tille:
for ITPs that might interest Debian Med I would now go and add this
ITP to the tasks file in question. Any volunteeer to do this for
Debian Science and add this entry as prospective package to electronics?
Done. (Hope I got the
Am Dienstag, den 08.07.2008, 16:29 +0200 schrieb Sylvestre Ledru:
Ondrej Certikwrote:
is that it, or are there some more packages?
More package are coming like Worldwind, Scilab, libmatio (for me) and
other are managed under the git and svn vcs...
Also, some are under the Debian Science
Hi Debian Science,
I just updated the Debian Science Policy. The changes address the feedback
that I got so far and are rather minor. The commit messages were sent to the
commit mailing list. You can read them there or update your repository clone.
Feedback is --as always-- welcome!
I'm sorry
Am Montag, den 09.06.2008, 23:24 +0200 schrieb Andreas Tille:
On Mon, 9 Jun 2008, Frederic Lehobey wrote:
Done. With the following crontab (user fdl-guest):
0 18 * * * umask 02 ;
/srv/alioth.debian.org/chroot/home/groups/cdd/bin/update-tasks-of-cdd
debian-science
Fine. Now it
Am Mittwoch, den 28.05.2008, 12:33 +0200 schrieb Andreas Tille:
On Wed, 28 May 2008, Manuel Prinz wrote:
git clone git://git.debian.org/git/debian-science/policy.git
Any tips for people sitting behind a firewall that only allows
html (via proxy) and who will get:
$ git clone git
Hi Jordan,
thanks for the feedback!
Am Dienstag, den 27.05.2008, 16:10 -0700 schrieb Jordan Mantha:
I think the gatekeeper workflow is appropriate. However, packaging
the policy and using BTS seems like overkill. It would seem to me that
with git, sending patches or merging from somebody's
Am Mittwoch, den 28.05.2008, 12:50 +0200 schrieb Manuel Prinz:
I will enable it and let you know.
Done, easier as expected. You can now also clone using:
git clone http://git.debian.org/git/debian-science/policy.git
Best regards
Manuel
signature.asc
Description: Dies ist ein digital
Am Mittwoch, den 28.05.2008, 12:39 +0200 schrieb Andreas Tille:
Why not ... licensed under either GPL or BSD? This makes sure that
it might fit any license in case there is some conflict.
In my understanding the problem is not so much about conflicting license
but about mixing compatible
Hi Andreas!
Am Mittwoch, den 28.05.2008, 16:52 +0200 schrieb Andreas Tille:
What I'm missing is a step by step introduction to git which answers
the questions:
1. How can I check out all existing repositories of packages
2. How can I create a new package repository (as I said I'm
Hi Bernhard,
thanks for your feedback!
Am Mittwoch, den 28.05.2008, 15:03 +0200 schrieb Bernhard R. Link:
* Manuel Prinz [EMAIL PROTECTED] [080528 00:34]:
1. What license should we use for the document?
Is there so much in the worth protectable? Otherwise making it public
domain
Hello Debian Science,
a first draft of the Debian Science Policy is now available in the Debian
Science repository and can be checked out with:
git clone git://git.debian.org/git/debian-science/policy.git
For easier reading, you should transform the document into XHTML. You can
simply run
On Wed, May 21, 2008 4:46 pm, David Bremner wrote:
Can I assume that the location
/git/debian-science/packages/foo.git
is the right place for package foo?
I'm fine with that. After all the replies I'd say we have consensus on that.
Best regards
Manuel
--
To UNSUBSCRIBE, email to
Am Samstag, den 24.05.2008, 18:37 +0200 schrieb David Bremner:
OK, one baby-step to coherence :-).
:)
I have updated the wiki,
http://wiki.debian.org/DebianScience/ContributingToDebianScience
I also added a few pointers into the mail archive to a couple of the
git tips and tricks
Am Dienstag, den 20.05.2008, 15:44 +0900 schrieb Charles Plessy:
Le Tue, May 20, 2008 at 08:23:42AM +0200, Andreas Tille a écrit :
For instance I remember that we first had
DM-Upload-Allowed: Yes
in many control files. It turned out that this was case sensitive and
so it was
Am Montag, den 19.05.2008, 13:41 +0200 schrieb Andreas Tille:
Ahh OK, so you mean the just existing tasks files at
http://svn.debian.org/wsvn/cdd/projects/science/trunk/debian-science/tasks/?rev=0sc=0
right?
Exactly! (Did not have the URL at hand.)
On Mon, 19 May 2008, Manuel Prinz
Am Sonntag, 18. Mai 2008 15:56:11 schrieb Sylvestre Ledru:
Looking at the current situation, the repositories are quite
unstructured: The SVN repo contains the tasks created by Sylvestre and
some packages checked in at the same level which is quite confusing.
It is temporary. We have to
Am Dienstag, den 13.05.2008, 09:28 +0200 schrieb Andreas Tille:
On Tue, 13 May 2008, Raphael Hertzog wrote:
I created as SVN repo for debian-science, if you need another kind of
repo, please ask.
Raphael, thanks for the quick action! It's appreciated.
So either Git addictives start action
On Fri, May 9, 2008 3:40 pm, Teemu Ikonen wrote:
As for the other project infrastructure: git subprojects (or a
superproject) will allow checkouts of all packages at once.
I have to say that from my packaging experience with Git I do not think
that this is a good idea since my experience with
On Fri, May 9, 2008 4:45 pm, Daniel Leidert wrote:
I just want to make a suggestion: tags should not be inside the packages
directory. It is IMHO better put outside, [...]
I think you're talking about Subversion for our team packaging effort,
right? This should be no problem with Git, as Git
Hi Daniel,
I just came across this email after sending a comment to your email
regarding tags (darn webmail), so this is somehow related.
On Fri, May 9, 2008 4:52 pm, Daniel Leidert wrote:
Am Freitag, den 09.05.2008, 13:40 +0200 schrieb Manuel Prinz:
[..]
I also do care about the VCS
On Fri, May 9, 2008 3:32 pm, Andreas Tille wrote:
Hope this clarifies things.
It did. Thank you!
Best regards
Manuel
--
To UNSUBSCRIBE, email to [EMAIL PROTECTED]
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Am Freitag, den 09.05.2008, 14:49 +0200 schrieb Andreas Tille:
Well, follow the DoOcracy principle: The doer decides. If I understood
right David Bremner volunteered also to work actively on a repository
with exactly the same preferences like you. So I guess he is not really
unhappy if you
Hi Dirk,
thanks for your reply!
Am Dienstag, den 15.05.2007, 14:40 -0500 schrieb Dirk Eddelbuettel:
Following on a similar thread or two we had here, I have been sponsoring
Gennaro Oliva who has been working on munge [ == authentication service used
by slurm ] packages which we _almost_ got
Hi everyone,
I've to administrate a small cluster and I'm intersted in your opinion
or experience with the resource managers/batch systems you use.
ATM, there's Torque installed, and I'm not too happy with it, especially
with the documentation. I've found a thread on debian-science about
Hello Steffen!
Thanks for your reply!
Am Dienstag, den 15.05.2007, 20:05 +0200 schrieb Steffen Moeller:
Hallo Manuel, a nice domain name you have.
Thanks! ;)
[...] I keep nagging the Torque upstream developers about officiall
supporting Debian or to allow us promoting their work via Debian
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