[StarCluster] compiling MPI applications on starcluster

[Justin Riley]

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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