I have tried with salloc directly : "salloc -N 2 mpiexec /path/my_application" And with "sview" I can see that 2 nodes are allocated simultaneously, so it is great but the log file of my output shows me that my appli ran 2 times. However I don't want to run 2 times but just use 2 nodes to run faster my unique appli... :(
Does anyone has an idea ? advance thanks, Siva ----- Mail original ----- > De: "Moe Jette" <je...@schedmd.com> > À: "slurm-dev" <slurm-dev@schedmd.com> > Envoyé: Vendredi 20 Septembre 2013 17:27:53 > Objet: [slurm-dev] Re: mpich2 for job running in all nodes > > > Slurm use with the various MPI distributions is documented here: > > http://slurm.schedmd.com/mpi_guide.html#mpich2 > > > Quoting Sivasangari Nandy <sivasangari.na...@irisa.fr>: > > > 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 > > > -- Siva sangari NANDY - Plate-forme GenOuest IRISA-INRIA, Campus de Beaulieu 263 Avenue du Général Leclerc 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 25 69 Bureau : D152
