<br><br><div class="gmail_quote">On Tue, Mar 8, 2011 at 1:36 PM, Jianguo Li <span dir="ltr"><<a href="mailto:ljggmx@yahoo.com.sg">ljggmx@yahoo.com.sg</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><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></div></div></div>
</blockquote><div><br>No,What is these?How can I prepare and use them?<br>Thanks in advance<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><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;">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 face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> mohsen ramezanpour <<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>><br>
<b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><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><div><div></div><div class="h5"><br>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>
</div></div></div></div>
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