[gmx-users] GROMACS 4.6v - Myrinet2000

Hrachya Astsatryan hrach at sci.am
Mon Apr 8 08:28:19 CEST 2013

Dear all,

We have installed the latest version of Gromacs (version 4.6) on our 
cluster by the following step:

  * cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/backup/sicnas/gromacs

The interconnection of the cluster is Myrinet2000 and the driver is MX 
(and mpich 1.3.1).

The job scripts (see below) and different simulations show that there is 
no adequate performance (usually it should be 2-3 time more).

Could you, pls. help us to overcome the problem in order to get better 

With regards,

#PBS -l nodes=8:ppn=2
##PBS -l walltime=360:00
#PBS -q armcluster
#PBS -e 33mM_16_new.err
#PBS -o 33mM_16_new.log
## Specify the shell to be bash
#PBS -S /bin/bash


/opt/mpi/bin/mpirun -machinefile /backup/sicnas/npt101/machine -np 16 
/backup/sicnas/gromacs/bin/mdrun_mpi -s /backup/sicnas/npt101/topol.tpr -v

Hrachya Astsatryan
Head of HPC Laboratory,
Institute for Informatics and Automation Problems,
National Academy of Sciences of the Republic of Armenia
1, P. Sevak str., Yerevan 0014, Armenia
t: 374 10 284780
f: 374 10 285812
e: hrach at sci.am
skype: tighra

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