<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">You don't use qsub or bsub? <br>usually you should submit a script file containing the gromacs command, then bsub/qsub will allocate the required resource to your job. <br>Jianguo<br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> mohsen ramezanpour <ramezanpour.mohsen@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Tuesday, 8 March 2011 17:26:19<br><b><span style="font-weight: bold;">Subject:</span></b> [gmx-users] parallel running<br></font><br><meta
http-equiv="x-dns-prefetch-control" content="off">Dear All<br><br>I want to run gromacs in parallel on cluster.for this I follow below steps:<br>1-I connect to a node with ssh comand,fro example: ssh compute-o-1<br>2-cd scratch <br>3-grompp -f md.mdp -c input.gro -o output.tpr -p topol.top -n index.ndx<br>
4- nohup mpirun -np 8 mdrun -deffnm output &<br><br>The result is running mdrun on one node(compute-0-1) (on its 4 CPUs)<br>Besides when I used the following command I get an executeable Error:<br>mpirun -np 8 mdrun_mpi -deffnm output &<br>
<br>The Error is related to mdrun_mpi <br>I think is related to my cluster,because both of above commands work in my laptop<br><br>Please let me know how can I run mdrun on all of CPUs of my cluster.<br>Thanks in advance<br>
Mohsen<br>
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