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 #!/bin/tcsh #$ -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 Joe > > Thanks in advance > > Best regards > > Per > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters -- 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 fax : +1 734 786 8452 or +1 866 888 3112 cell : +1 734 612 4615