[gmx-users] problem with cluster

Pietro Lopriore p.lopriore at it.ibm.com
Wed Apr 13 16:00:30 CEST 2005

Dear Nguyen,
we had a similar problem in our cluster (powerPC based).
a) the following is an example

grompp –f grompp.mdp –c conf.gro –p topol.top –po mdout.mdp –shuffle –sort
–np <nr. processors>

mpirun c0, 2, 7 –ssi rpi gm
/usr/local/gromacs/powerpc64-unknown-linux-gnu/bin/mdrun –s topol.tpr –o
traj.trr –c confout.gro –e ener.edr –g md.log

In this case, specifying 0,2 and 7 means that the mdrun runs on processors
0, 2 and 7 as specified in the mpi machine file (We have a two-ways
cluster; node 1:  processors 0 and 1; node 2: processors 2 and 3,

b) We had a similar problem but it could be due to too many things. We had
problems with the CSM software launching ghost processes around. Swithcin
it off everything went fine (check the SYS usage of the memory). But it
could be also due to other things like networking or any other application
running on the cluster.

Hope this helps,


Pietro Lopriore
EMEA South Region Technical Sales Support
IBM Healthcare and Life Sciences Industry
IBM Life Sciences Internet site: http://www.ibm.com/solutions/lifesciences
IBM Computational Biology Center:

             Nguyen Hoang                                                  
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             uni-frankfurt.de>         gmx-users at gromacs.org               
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                                       [gmx-users] problem with cluster    
             04/13/2005 03:09                                              
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Dear All,

we have a new cluster consists of 11 Intel cpus with hyperthreading. I
have some problems with running gromacs on this cluster:

a) When I submit a job, it is distributed at random on 2 cpus (I asked for
2 cpus). How can I run the job on specific cpus?

b) The cpus which run the mdrun program alway work with about 40% of
power. How can I increase the power of the cpus?

Thank you very much in advance for any hint.


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