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Subject: Re: [OMPI users] Problem with running openMPI program
From: Gus Correa (gus_at_[hidden])
Date: 2009-04-28 17:16:37


Hi Ankush

Glad to hear that your MPI and cluster project were successful.

I don't know if you would call these "mathematical computation"
or "real life applications" of MPI and clusters, but here are a
few samples I am familiar with (Earth Science):

Weather forecast:
http://www.wrf-model.org/index.php
http://www.mmm.ucar.edu/mm5/

Climate, Atmosphere and Ocean circulation modeling:
http://www.ccsm.ucar.edu/models/ccsm3.0/
http://www.jamstec.go.jp/esc/index.en.html
http://www.metoffice.gov.uk/climatechange/
http://www.gfdl.noaa.gov/fms
http://www.nemo-ocean.eu/

Earthquakes, computational seismology, and solid Earth dynamics:
http://www.gps.caltech.edu/~jtromp/research/index.html
http://www-esd.lbl.gov/GG/CCS/

A couple of other areas:

Computational Fluid Dynamics, Finite Element Method, etc:
http://www.foamcfd.org/
http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM

Computational Chemistry, molecular dynamics, etc:
http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page
http://classic.chem.msu.su/gran/gamess/
http://ambermd.org/
http://www.gromacs.org/
http://www.charmm.org/

Gus Correa

Ankush Kaul wrote:
> Thanks everyone(esp Gus and Jeff) for the support and guidance. We are
> almost at the verge of completing our project which could have not been
> possible without all u guys.
>
> I would like to know one more thing, what are real life applications
> that i can use the cluster for (except mathematical computation)? Can i
> use if for my web server, if yes then how?
>
>
>
> On Fri, Apr 24, 2009 at 12:01 AM, Jeff Squyres <jsquyres_at_[hidden]
> <mailto:jsquyres_at_[hidden]>> wrote:
>
> Excellent answer. One addendum -- we had a really nice FAQ entry
> about this kind of stuff on the LAM/MPI web site, which I was
> horrified to see that we had not copied to the Open MPI site. So I
> copied it over this morning. :-)
>
> Have a look at these 3 FAQ (brand new) entries:
>
>
> http://www.open-mpi.org/faq/?category=building#overwrite-pre-installed-ompi
> http://www.open-mpi.org/faq/?category=building#where-to-install
>
> http://www.open-mpi.org/faq/?category=running#do-i-need-a-common-filesystem
>
> Hope that helps.
>
>
>
>
> On Apr 23, 2009, at 10:34 AM, Gus Correa wrote:
>
> Hi Ankush
>
> Jeff already sent clarifications about image processing,
> and the portable API nature of OpenMPI (and other MPI
> implementations).
>
> As for "mpicc: command not found" this is again a problem with your
> PATH.
> Remember the "locate" command? :)
> Find where mpicc is installed, and put that directory on your PATH.
>
> In any case, I would suggest that you choose a central NFS mounted
> file system on your cluster master node, and install OpenMPI there,
> configuring and building it from source (not from yum).
> If this directory is mounted on all nodes, the same OpenMPI will be
> available on all nodes.
> This will give you a single standard version of OpenMPI across
> the board.
>
> Clustering can become a very confusing and tricky business if you
> have heterogeneous nodes, with different OS/Linux versions,
> different MPI versions etc, software installed in different
> locations
> on each node, etc, regardless of whether you use mpiselector or
> you set the PATH variable on each node, or you use environment
> modules
> package, or any other technique to setup your environment.
> Installing less software, rather than more software,
> and doing so in a standardized homogeneous way across all
> cluster nodes,
> will give you a cleaner environment, which is easier to understand,
> control, upgrade, and update.
>
> A relatively simple way to install a homogeneous cluster is
> to use the Rocks Clusters "rolls" suite,
> which is free and based on CentOS.
> It will probably give you some extra work in the beginning,
> but may be worthwhile in the long run.
> See this:
> http://www.rocksclusters.org/wordpress/
>
>
> My two cents.
>
> Gus Correa
> ---------------------------------------------------------------------
> Gustavo Correa
> Lamont-Doherty Earth Observatory - Columbia University
> Palisades, NY, 10964-8000 - USA
> ---------------------------------------------------------------------
>
> Ankush Kaul wrote:
> > @Gus, Eugene
> > I read all you mails and even followed the same procedure, it
> was blas
> > that was giving the problem.
> >
> > Thanks
> >
> > I am again stuck on a problem, i connected a new node to my
> cluster and
> > installed CentOS 5.2 on it. after that i use yum to install
> > openmpi,openmpi-libs and openmpi-devel sucessfully.
> >
> > But still when i run mpicc command it gives me error :
> > /bash: mpicc: command not found/
> >
> > i found out there is a command *mpi-selector* but dont know
> hoe to use it.
> > Is this a new version of openmpi? how do i configure it?
> >
> >
> >
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> >
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>
>
> --
> Jeff Squyres
> Cisco Systems
>
>
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