<div>Dear GMXers</div>
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<div>this is how I've done it so far:</div>
<div>grompp -f -c -p -o 12np.tpr -np 12</div>
<div>qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr -np 12 )</div>
<div>then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with "top", I find that there's only one cpu works with 12 processes! The other nodes are completely idle.</div>
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<div>the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info:</div>
<div>Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux</div>
<div>our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir.</div>
<div>I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else?</div>
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<div>This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated !</div>
<div> </div>
<div>Xin Liu</div>