[gmx-users] only one cpu "works" in my linux cluster

liu xin zgxjlx at gmail.com
Mon Oct 8 14:51:12 CEST 2007

Dear GMXers

this is how I've done it so far:
grompp -f -c -p -o 12np.tpr -np 12
qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s
12np.tpr-np 12 )
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.

the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info:
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
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.
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?

This is the first time I build up a Linux Cluster on my own, ANY suggestions
are appreciated !

Xin Liu
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