[gmx-users] very low speed in simulation !( need for help)

delara aghaie d_aghaie at yahoo.com
Tue May 18 09:35:49 CEST 2010

Dear gmx-usres,
In our university we have a cluster containing 20 nodes each with 4 processors, which I want to use that for the simulation project.
As a test I submitted a run that I have tested it before in the Imperial College (London).
Here the structure of the cluster is so that I should specify on which nodes I want the simulation to be done.
for this we have a folder (gromacs launcher), in which there are some files.
in the file (lamhosts.txt) the node numbers that I can have access to them, have been specified by the head of cluster.
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).
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).
I write these commands:
/usr/local/gromacs/bin/grompp -c ~.gro -f ~.mdp -p ~.top -n ~.ndx -o topol.tpr -np 12
mpiexec /usr/local/gromacs/bin/mdrun -v -s topol.tpr -np 12
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.
Then I should write number of processors 13 instead of 12.
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 !!!.
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.
1) Is the reason for low speed , including the server in the list?
2) is the way that let me not to include the server in the list  of lamhosts.txt and hosts.txt?
It would be greatly appreciated if you guide me as I am completely confused !!!
thanks in advance.
D. M

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