[Bioclusters] MPI environment

Joe Landman landman at scalableinformatics.com
Thu Aug 24 15:40:19 EDT 2006

Hi Per:

Per Jr. Greisen wrote:
> Hey,
> I am new to clusters and hope that it is okay for me to pose a questions 
> here. I have tried to submit a program which should be executed parallel 

Which program?

> but as I submit it - it only runs on one processor. First I used the 
> chm-parallel environment which is default at this cluster. Than I tried 
> to change the parallel environment to mpi and use mpirun but it gave me 
> the error-message that it couldnt find the mpi environment.

If this is SGE, try

	qconf -spl

to see which parallel environments you have.

> I have used the mpirun on the "helloworld.c"-program and when executed 
> alone it returns from the specified notes.

Hmmm.... what is the helloworld.c program?  Is it an MPI program or is 
it a simple C program?

> When I go to opt/sge - both the chm and mpi environment are there - how 
> can I enforce it to use the mpi environment? - Given the full-path and 
> to which file in the directory? (there is a startmpi.sh ?)

	qsub -pe mpi N /path/to/a/batch/script/to/run/your/program

where N is the number of CPUs you want to run.  So, for example, to run 
runme.mpi which will launch your program for you, on 8 CPUs, try

	qsub -pe mpi 8 ./runme.mpi

where runme.mpi looks something like this

	#$ -S /bin/tcsh
	#$ -cwd
	#$ -j y
	setenv MPI /path/to/mpi/binary/directory
	setenv BINARY /path/to/your/mpi/program/binary
	$MPI/mpirun -np $NSLOTS -machinefile $TMPDIR/machines $BINARY


> Thanks in advance
> Best regards
> Per
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Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
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