[gmx-users] Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed

jimkress_58 jimkress_58 at kressworks.org
Fri Jun 12 13:04:59 CEST 2009

Hostfile should look like:

master slots=4 max-slots=4
compute-0-0 slots=4 max-slots=4
compute-0-1 slots=4 max-slots=4
compute-0-2 slots=4 max-slots=4
compute-0-3 slots=4 max-slots=4
compute-0-4 slots=4 max-slots=4
compute-0-5 slots=4 max-slots=4
compute-0-6 slots=4 max-slots=4

so its format is:

node name, #cpus or cores you want to use on that node, maximum number of
cpus or cores on that node.

You can locate


file and put this info in it or you can create your own file (say hfile),
put it in some directory and then run

mpirun -np 8 -hostfile hfile mdrun ...

see the openMPI web site for more info



-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Thamu
Sent: Thursday, June 11, 2009 10:54 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed


	i am using openmpi, how to build hostfile and where keep that file

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