[gmx-users] using_gromacs_with_openmpi

Hossein H haji309 at gmail.com
Wed Apr 22 21:59:58 CEST 2015

Dear GROMACS users and developers

I've compiled GROMACS 4.5.5 with gcc and *enable-mpi* option for a small
cluster e.g 4 nodes on 1GbE network
The code was compiled without problem and i can use it in sequential and
parallel mode (using mpirun command), but the performance over the network
is very poor. indeed i can run the jobs on one nodes faster than 4 nodes.

because each nodes has 4 cores, i run jobs over network using following

> mpirun -np 16 --host node01,node02,node03,node04 mdrun -deffnm input -v

Someone has any idea why the performance is so poor?

Thanks in advance

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