Slurm use with the various MPI distributions is documented here:
http://slurm.schedmd.com/mpi_guide.html#mpich2
Quoting Sivasangari Nandy <[email protected]>:
Hi,
Does anyone know how to use the mpich2 command pls ?
I wanted to execute Bowtie2 (a mapping tool) using my three nodes :
VM-669, VM-670 and VM-671
and with this command :
srun mpiexec -n 3 -machinefile Mname.txt /omaha-beach/workflow/bowtie2.sh
But I got this error :
srun: error: Only allocated 1 nodes asked for 3
-n for the number of processor (I got one processor per node cf
joined file for slurm conf file)
Mname.txt is my file with nodes name VM ...
bowtie2.sh is like this :
#!/bin/bash
bowtie2 -p 3 -x Indexed_Bowtie -q -I 0 -X 1000 -1 r1.fastq -2
r2.fastq -S bowtie2.sam
Thanks for your help,
Siva
