Re: [opensuse-project] Science and Education repos/ Scientific packages
On Thursday 16 September 2010 19:49:26 Thomas Hertweck wrote:
On 16/09/10 11:17, Alin Marin Elena wrote:
[...] First I would like to know what is the Education repo and what is the science repo.. which of them would be the best place to push scientific packages.
Could you give examples of what you would typically classify as "scientific packages"? Tools like "octave", "gnuplot" etc are part of the standard distribution as far as I know. These are tools that I would classify as "general purpose science tools". I will give you example of only few packages from my immediate area of research. They may look obscure to you and a lot of other people but keep in mind that linux distros are used almost exclusively in science research labs. One of the point that weighs a lot in what distro is installed by the admins is the availability of these obscure packages...
cp2k,gromacs,octopus, abinit, alps and the list can continue and if on top of this you add that they come in 4 flavours usually (serial, mpi, openmp and mpi/openmp). You can easily harvest the list of packages opensource installed on different supercomputing sites. Alin -- Without Questions there are no Answers! _____________________________________________________________________ Alin Marin ELENA http://alin.elenaworld.net http://www.google.com/profiles/alinm.elena alinm.elena@gmail.com ______________________________________________________________________
On Thu, Sep 16, 2010 at 3:04 PM, Alin Marin Elena <alinm.elena@gmail.com> wrote:
On Thursday 16 September 2010 19:49:26 Thomas Hertweck wrote:
On 16/09/10 11:17, Alin Marin Elena wrote:
[...] First I would like to know what is the Education repo and what is the science repo.. which of them would be the best place to push scientific packages.
Could you give examples of what you would typically classify as "scientific packages"? Tools like "octave", "gnuplot" etc are part of the standard distribution as far as I know. These are tools that I would classify as "general purpose science tools". I will give you example of only few packages from my immediate area of research. They may look obscure to you and a lot of other people but keep in mind that linux distros are used almost exclusively in science research labs. One of the point that weighs a lot in what distro is installed by the admins is the availability of these obscure packages...
cp2k,gromacs,octopus, abinit, alps and the list can continue and if on top of this you add that they come in 4 flavours usually (serial, mpi, openmp and mpi/openmp). You can easily harvest the list of packages opensource installed on different supercomputing sites.
Alin
Alin, You can look for yourself at: http://software.opensuse.org/search Here is the list for gromacs http://software.opensuse.org/search?q=gromacs&baseproject=openSUSE%3A11.3&lang=en&exclude_filter=home%3A&exclude_debug=true You can see for 11.3 it is part of the main distribution and it is in the education repo. Unfortunately the rest of the packages in your list don't seem to be in the OBS. (I did not search home dirs). openSUSE is a very open distro. If you or anyone else wants to get a OBS account they can build the various packages you find of interest. Then push them up to an appropriate repo. I'm not sure if the education repo is the right one, or if a science repo should be created. Creating a repo is a simple matter of filing a bugzilla requesting one iirc. The more difficult task is building all the packages and pushing them into the repo(s). But again all of the above can be down by anyone. Greg -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
On 16 September 2010 20:44, Greg Freemyer <greg.freemyer@gmail.com> wrote:
On Thu, Sep 16, 2010 at 3:04 PM, Alin Marin Elena <alinm.elena@gmail.com> wrote:
On Thursday 16 September 2010 19:49:26 Thomas Hertweck wrote:
On 16/09/10 11:17, Alin Marin Elena wrote:
[...] First I would like to know what is the Education repo and what is the science repo.. which of them would be the best place to push scientific packages.
Could you give examples of what you would typically classify as "scientific packages"? Tools like "octave", "gnuplot" etc are part of the standard distribution as far as I know. These are tools that I would classify as "general purpose science tools". I will give you example of only few packages from my immediate area of research. They may look obscure to you and a lot of other people but keep in mind that linux distros are used almost exclusively in science research labs. One of the point that weighs a lot in what distro is installed by the admins is the availability of these obscure packages...
cp2k,gromacs,octopus, abinit, alps and the list can continue and if on top of this you add that they come in 4 flavours usually (serial, mpi, openmp and mpi/openmp). You can easily harvest the list of packages opensource installed on different supercomputing sites.
Alin
Alin,
You can look for yourself at: http://software.opensuse.org/search
Here is the list for gromacs http://software.opensuse.org/search?q=gromacs&baseproject=openSUSE%3A11.3&lang=en&exclude_filter=home%3A&exclude_debug=true
You can see for 11.3 it is part of the main distribution and it is in the education repo.
Unfortunately the rest of the packages in your list don't seem to be in the OBS. (I did not search home dirs).
openSUSE is a very open distro. If you or anyone else wants to get a OBS account they can build the various packages you find of interest. Then push them up to an appropriate repo.
I'm not sure if the education repo is the right one, or if a science repo should be created.
Creating a repo is a simple matter of filing a bugzilla requesting one iirc. The more difficult task is building all the packages and pushing them into the repo(s). But again all of the above can be down by anyone.
Greg
Greg, a science repo exists already so no need to create it what I want is to bring it alive... and useful for scientists. freeze cycles that govern distro and education make them irrelevant for the scientific community. some packages have to be updated pretty often due to addition of new features or fixes of bugs. the scientific computational community is not a big one in numbers... but is a community in which linux is predominant and unfortunately is not opensuse... if opensuse wants to make itself relevant at desk level for scientists providing a rich and up to date science repo is crucial. on gromacs the version offered is 3.3.1 the current version is 4.5.1. also only sequential version is offered. have you ever tried to push anything to the science repo? Alin -- _____________________________________________________________________ Without Questions there are no Answers! _____________________________________________________________________ Mr Alin Marin ELENA http://alin.elenaworld.net http://www.google.com/profiles/alinm.elena alinm.elena@gmail.com ______________________________________________________________________ -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
Hi,
have you ever tried to push anything to the science repo?
I'm in a similar position. Up to now, I'm building scientific packages in my home project on OBS, since that makes it already much less of a burden to install stuff on four dozen machines of varying openSUSE releases. Of course, it would be great if others could profit from these packages as well, so I'm all for a "real" repository. The home page of the science repo gives a mail address to contact for prospective participants, but I never got an answer to my message. I'm mainly interested in biophysics packages (e.g. coot, qtiplot, xdrawchem). As for Gromacs, we're using it quite a lot (mainly on an HPC cluster). However, our software developer makes frequent changes, so an external (to our department) package does us no good. Since he also prefers to install the package manually on an NFS server ("/usr/local"), gromacs is not on my OBS list. A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
2010/9/17 Esztermann, Ansgar <Ansgar.Esztermann@mpi-bpc.mpg.de>:
Hi,
have you ever tried to push anything to the science repo?
I'm in a similar position. Up to now, I'm building scientific packages in my home project on OBS, since that makes it already much less of a burden to install stuff on four dozen machines of varying openSUSE releases. Of course, it would be great if others could profit from these packages as well, so I'm all for a "real" repository. The home page of the science repo gives a mail address to contact for prospective participants, but I never got an answer to my message.
I'm mainly interested in biophysics packages (e.g. coot, qtiplot, xdrawchem). As for Gromacs, we're using it quite a lot (mainly on an HPC cluster). However, our software developer makes frequent changes, so an external (to our department) package does us no good. Since he also prefers to install the package manually on an NFS server ("/usr/local"), gromacs is not on my OBS list.
What's exactly the problem? $ osc meta prj science | fgrep maintainer <person role="maintainer" userid="pbleser"/> <person role="maintainer" userid="pnemec"/> <person role="maintainer" userid="sbrabec"/> <person role="maintainer" userid="bwalle"/> <person role="maintainer" userid="werner2101"/> <person role="maintainer" userid="dsteuer"/> <person role="maintainer" userid="dstoecker"/> <person role="maintainer" userid="prusnak"/> <person role="maintainer" userid="dannori"/> <person role="maintainer" userid="ashigabou"/> <person role="maintainer" userid="pgajdos"/> <person role="maintainer" userid="ferichter"/> <person role="maintainer" userid="matwey"/> <person role="maintainer" userid="anubisg1"/> <person role="maintainer" userid="WernerFink"/> <person role="maintainer" userid="akos_ladanyi"/> <person role="maintainer" userid="grayswandir12"/> <group groupid="factory-maintainers" role="maintainer"/> With so many maintainers I'm sure that if any of you create submit requests they will be reviewed/accepted. There are at least four names in that list that I recognise since they are very active. -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
On Friday 17 September 2010 18:50:29 Cristian Morales Vega wrote: Hi,
What's exactly the problem?
$ osc meta prj science | fgrep maintainer <person role="maintainer" userid="pbleser"/> <person role="maintainer" userid="pnemec"/> <person role="maintainer" userid="sbrabec"/> <person role="maintainer" userid="bwalle"/> <person role="maintainer" userid="werner2101"/> <person role="maintainer" userid="dsteuer"/> <person role="maintainer" userid="dstoecker"/> <person role="maintainer" userid="prusnak"/> <person role="maintainer" userid="dannori"/> <person role="maintainer" userid="ashigabou"/> <person role="maintainer" userid="pgajdos"/> <person role="maintainer" userid="ferichter"/> <person role="maintainer" userid="matwey"/> <person role="maintainer" userid="anubisg1"/> <person role="maintainer" userid="WernerFink"/> <person role="maintainer" userid="akos_ladanyi"/> <person role="maintainer" userid="grayswandir12"/> <group groupid="factory-maintainers" role="maintainer"/>
With so many maintainers I'm sure that if any of you create submit requests they will be reviewed/accepted. There are at least four names in that list that I recognise since they are very active.
In case you haven't heard of submit requests yet, please take a look at http://en.opensuse.org/openSUSE:Build_Service_Collaboration It will tell you our idea of working together on stuff in the buildservice for the benefit of the users. We would be happy if you could help to make our Science Repo attractive again. I am also sure that you quickly can get the status of a maintainer of the project which will shorten the cycles more. Thanks, klaas -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
On Sep 18, 2010, at 21:05 , Klaas Freitag wrote:
In case you haven't heard of submit requests yet, please take a look at http://en.opensuse.org/openSUSE:Build_Service_Collaboration
Thanks for the pointer. How would one go about adding a new package? In that case, there is nothing to fork, after all. Thanks, A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
2010/9/22 Esztermann, Ansgar <Ansgar.Esztermann@mpi-bpc.mpg.de>:
On Sep 18, 2010, at 21:05 , Klaas Freitag wrote:
In case you haven't heard of submit requests yet, please take a look at http://en.opensuse.org/openSUSE:Build_Service_Collaboration
Thanks for the pointer. How would one go about adding a new package? In that case, there is nothing to fork, after all.
Just ignore that part. If the sred package doesn't exists it will be created. -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
On Sep 22, 2010, at 16:36 , Cristian Morales Vega wrote:
Thanks for the pointer. How would one go about adding a new package? In that case, there is nothing to fork, after all.
Just ignore that part. If the sred package doesn't exists it will be created.
Oh. Quite simple, if you think about it. Thanks! A. -- Ansgar Esztermann DV-Systemadministration Max-Planck-Institut für biophysikalische Chemie, Abteilung 105 -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
Hi Christian, On Freitag, 17. September 2010, Cristian Morales Vega wrote:
2010/9/17 Esztermann, Ansgar <Ansgar.Esztermann@mpi-bpc.mpg.de>:
I'm mainly interested in biophysics packages (e.g. coot, qtiplot, xdrawchem). As for Gromacs, we're using it quite a lot (mainly on an HPC cluster). However, our software developer makes frequent changes, so an external (to our department) package does us no good. Since he also prefers to install the package manually on an NFS server ("/usr/local"), gromacs is not on my OBS list.
What's exactly the problem?
$ osc meta prj science | fgrep maintainer <person role="maintainer" userid="pbleser"/> <person role="maintainer" userid="pnemec"/> <person role="maintainer" userid="sbrabec"/> <person role="maintainer" userid="bwalle"/> <person role="maintainer" userid="werner2101"/> <person role="maintainer" userid="dsteuer"/> <person role="maintainer" userid="dstoecker"/> <person role="maintainer" userid="prusnak"/> <person role="maintainer" userid="dannori"/> <person role="maintainer" userid="ashigabou"/> <person role="maintainer" userid="pgajdos"/> <person role="maintainer" userid="ferichter"/> <person role="maintainer" userid="matwey"/> <person role="maintainer" userid="anubisg1"/> <person role="maintainer" userid="WernerFink"/> <person role="maintainer" userid="akos_ladanyi"/> <person role="maintainer" userid="grayswandir12"/> <group groupid="factory-maintainers" role="maintainer"/>
With so many maintainers I'm sure that if any of you create submit requests they will be reviewed/accepted. There are at least four names in that list that I recognise since they are very active.
There are to many maintainers? If you have so many responsible persons, nobody feels to be responsable at all. :-( I've updated the project statement [1] and I'm trying to find some more maintainers that are willing to invest some work into the repostitory. Regards Werner [1] https://build.opensuse.org/project/show?project=science -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
Hi Alin, On Freitag, 17. September 2010, Alin Marin Elena wrote:
On 16 September 2010 20:44, Greg Freemyer <greg.freemyer@gmail.com> >
Creating a repo is a simple matter of filing a bugzilla requesting one iirc. The more difficult task is building all the packages and pushing them into the repo(s). But again all of the above can be down by anyone.
a science repo exists already so no need to create it
what I want is to bring it alive... and useful for scientists. freeze cycles that govern distro and education make them irrelevant for the scientific community. some packages have to be updated pretty often due to addition of new features or fixes of bugs.
Yes the science repository needs more love or should be merged into the Education repository.
the scientific computational community is not a big one in numbers... but is a community in which linux is predominant and unfortunately is not opensuse...
if opensuse wants to make itself relevant at desk level for scientists providing a rich and up to date science repo is crucial.
on gromacs the version offered is 3.3.1 the current version is 4.5.1. also only sequential version is offered.
have you ever tried to push anything to the science repo?
I'm sorry. I wasn't very active over the last year. I've only maintained the rpms for electronical engineering and some python packages. I think we need a few more active maintainers if we like to have an up to date science repository. If you'd like to take care of the chemistry/physics packages, you're of course very welcome. I can add you to the maintainer list, too. Regards Werner -- To unsubscribe, e-mail: opensuse-project+unsubscribe@opensuse.org For additional commands, e-mail: opensuse-project+help@opensuse.org
participants (6)
-
Alin Marin Elena -
Cristian Morales Vega -
Esztermann, Ansgar -
Greg Freemyer -
Klaas Freitag -
Werner Hoch