Dear Gromacs Users!<br><br><br>I have some problems with running my simulation on multi-modes station wich use open_MPI<br><br>I've launch my jobs by means of that script. The below example of running work on 1 node ( 12 cpu).<br>
<br>#!/bin/sh<br>#PBS -N gromacs<br>#PBS -l nodes=1:red:ppn=12<br>#PBS -V<br>#PBS -o gromacs.out<br>#PBS -e gromacs.err<br><br>cd /globaltmp/xz/job_name<br>grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o job.tpr<br>
mpiexec -np 12 mdrun_mpi_d.openmpi -v -deffnm job<br><br>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. <br>
<br><br>Could you tell me whats wrong could be with my cluster?<br><br>Thanks for help<br><br>James<br>