You don't use qsub or bsub? usually you should submit a script file containing the gromacs command, then bsub/qsub will allocate the required resource to your job.
Jianguo ________________________________ From: mohsen ramezanpour <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Tuesday, 8 March 2011 17:26:19 Subject: [gmx-users] parallel running Dear All I want to run gromacs in parallel on cluster.for this I follow below steps: 1-I connect to a node with ssh comand,fro example: ssh compute-o-1 2-cd scratch 3-grompp -f md.mdp -c input.gro -o output.tpr -p topol.top -n index.ndx 4- nohup mpirun -np 8 mdrun -deffnm output & The result is running mdrun on one node(compute-0-1) (on its 4 CPUs) Besides when I used the following command I get an executeable Error: mpirun -np 8 mdrun_mpi -deffnm output & The Error is related to mdrun_mpi I think is related to my cluster,because both of above commands work in my laptop Please let me know how can I run mdrun on all of CPUs of my cluster. Thanks in advance Mohsen
-- 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
