Re: compiling MPI applications on starcluster

From: Justin Riley <no email>
Date: Thu, 24 Apr 2014 11:13:42 -0400

Hi Torstein,

Can you please describe your cluster configuration (ie size, image id(s),
instance type(s))? Also, you're currently using the SGE/OpenMPI
integration. Have you tried just using mpirun only as described in the
first part of:

http://star.mit.edu/cluster/docs/latest/guides/sge.html#submitting-openmpi-jobs-using-a-parallel-environment

Also, what does 'mpirun --version' show?

~Justin

On Thu, Apr 17, 2014 at 07:19:28PM +0200, Torstein Fjermestad wrote:
> Dear all,
>
> I recently tried to compile an application (Quantum Espresso,
> [1]http://www.quantum-espresso.org/) to be used for parallel computations
> on StarCluster. The installation procedure of the application consists of
> the standard "./configure + make" steps.  At the end of the output from
> ./configure, the statement "Parallel environment detected successfully.\
> Configured for compilation of parallel executables." appears.
>
> The compilation with "make" completes without errors. I then run the
> application in the following way:
>
> I first write a submit script (submit.sh) with the following content:
>
> cp /path/to/executable/pw.x .
> mpirun ./pw.x -in input.inp
> I then submit the job to the queueing system with the following command
>  
> qsub -cwd -pe orte 16 ./submit.sh
>
> However, in the output of the calculation, the following line is repeated
> 16 times:
>
> Parallel version (MPI), running on 1 processors
>
> It therefore seems like the program runs 16 1 processor calculations that
> all write to the same output.
>
> I wrote about this problem to the mailing list of Quantum Espresso, and I
> got the suggestion that perhaps the mpirun belonged to a different MPI
> library than pw.x (a particular package of Quantum Espresso) was compiled
> with.
>
> I compiled pw.x on the same cluster as I executed mpirun. Are there
> several versions of openMPI on the AMIs provided by StarCluster? In that
> case, how can I choose the correct one.
>
> Perhaps the problem has a different cause. Does anyone have suggestions on
> how to solve it?
>
> Thanks in advance for your help.
>
> Yours sincerely,
> Torstein Fjermestad
>
> References
>
> Visible links
> 1. http://www.quantum-espresso.org/

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Received on Thu Apr 24 2014 - 11:13:44 EDT