<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear gmx-usres,</DIV>
<DIV>In our university we have a cluster containing 20 nodes each with 4 processors, which I want to use that for the simulation project.</DIV>
<DIV>As a test I submitted a run that I have tested it before in the Imperial College (London).</DIV>
<DIV>Here the structure of the cluster is so that I should specify on which nodes I want the simulation to be done.</DIV>
<DIV> </DIV>
<DIV>for this we have a folder (gromacs launcher), in which there are some files.</DIV>
<DIV>in the file (lamhosts.txt) the node numbers that I can have access to them, have been specified by the head of cluster.</DIV>
<DIV> </DIV>
<DIV>And in the file (hosts.txt) I can choose the nodes which I want to simulate my system with them, (I am resricted to use only the nodes that are listes in the lamhosts.txt).</DIV>
<DIV> </DIV>
<DIV>whan I want to use the grompp order, it wants me to specify the -np option(number of processors). For example I can have access to 12 processors (or 3 nodes).</DIV>
<DIV>I write these commands:</DIV>
<DIV> </DIV>
<DIV>/usr/local/gromacs/bin/grompp -c ~.gro -f ~.mdp -p ~.top -n ~.ndx -o topol.tpr -np 12</DIV>
<DIV>mpiexec /usr/local/gromacs/bin/mdrun -v -s topol.tpr -np 12</DIV>
<DIV> </DIV>
<DIV>I receive the error that I should include the server name in the list of nodes . I did it for both the lamhosts.txt and hosts.txt file.</DIV>
<DIV> </DIV>
<DIV>Then I should write number of processors <STRONG>13</STRONG> instead of <STRONG>12</STRONG>.</DIV>
<DIV>In this way the simulation goes very very slowly, as I see that if I run the simulation on one processor the speed is more satisfying !!!.</DIV>
<DIV> </DIV>
<DIV>I think this low speed is because of including the server in the processor list, and because the server is always busy with other jobs, the speed falls down.</DIV>
<DIV>Now:</DIV>
<DIV>1) Is the reason for low speed , including the server in the list?</DIV>
<DIV>2) is the way that let me not to include the server in the list of lamhosts.txt and hosts.txt?</DIV>
<DIV>It would be greatly appreciated if you guide me as I am completely confused !!!</DIV>
<DIV> </DIV>
<DIV>thanks in advance.</DIV>
<DIV>D. M</DIV>
<DIV> </DIV></td></tr></table><br>