[gmx-users] parallel running

Jianguo Li ljggmx at yahoo.com.sg
Tue Mar 8 11:06:58 CET 2011

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. 


From: mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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 

Please let me know how can I run mdrun on all of CPUs of my cluster.
Thanks in advance

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