Try separating your grompp run from your mpirun: You should not really be having the scheduler execute the grompp. Run your grompp step to generate a .tpr either on the head node or on your local machine (then copy it over to the cluster).
(The -p that the scheduler is complaining about only appears in the grompp step, so don't have the scheduler run it). On 2012-03-15 10:04:49AM +0300, James Starlight wrote: > Dear Gromacs Users! > > > I have some problems with running my simulation on multi-modes station wich > use open_MPI > > I've launch my jobs by means of that script. The below example of running > work on 1 node ( 12 cpu). > > #!/bin/sh > #PBS -N gromacs > #PBS -l nodes=1:red:ppn=12 > #PBS -V > #PBS -o gromacs.out > #PBS -e gromacs.err > > cd /globaltmp/xz/job_name > grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr > mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job > > All nodes of my cluster consist of 12 CPU. When I'm using just 1 node on > that cluster I have no problems with running of my jobs but when I try to > use more than one nodes I've obtain error ( the example is attached in the > gromacs.err file as well as mmd.mdp of that system). Another outcome of > such multi-node simulation is that my job has been started but no > calculation were done ( the name_of_my_job.log file was empty and no update > of .trr file was seen ). Commonly this error occurs when I uses many nodes > (8-10) Finally sometimes I've obtain some errors with the PME order ( this > time I've used 3 nodes). The exactly error differs when I varry the number > of nodes. > > > Could you tell me whats wrong could be with my cluster? > > Thanks for help > > James > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
