SubmitMpiJobOnJumilla

Submitting a mpi job in jumilla

bsub -q 1week_parallel /home2/bioinfo/bioinfo/MPICH/bin/mpirun -np 10 -machinefile ~/machines.dat \
 `which xmipp_mpi_MLalign2D` -i img.sel -nref 10 -fast -o ML10ref

It requires a file ~/machines.dat containing the name of the nodes:

rueda.cnb.uam.es
ribera.cnb.uam.es
ribeiro.cnb.uam.es
rioja.cnb.uam.es
cartojal.cnb.uam.es

Sjors' alternative:

Put the script below (calledmpirun_MLalign2D) in your~/bin directory, and launch the job using:

mpirun_MLalign2D-np 10 -q 1week_parallel -i img.sel -nref 10 -fast -o ML10ref

This script also assumes that the file ~/machines.dat as mentioned above exists. The script contains:

#!/usr/bin/csh -f
set np=`echo $argv[*] |awk -F"-np" '{print $NF}' |awk '{print $1}'`
set q=`echo $argv[*] |awk -F"-q" '{print $NF}' |awk '{print $1}'`
echo "Submitting job with "${np}" processors to queue "${q}" ..."
bsub -q ${q} /home2/bioinfo/bioinfo/MPICH/bin/mpirun -np ${np} -machinefile ~/machines.dat `which xmipp_mpi_MLalign2D` $argv[*]