[gmx-users] parallel running
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
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
3-grompp -f md.mdp -c input.gro -o output.tpr -p topol.top
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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