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

[jimkress_58]

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

openmpi-default-hostfile

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

http://www.open-mpi.org/

Jim


-----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

Hi,
 


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