[gmx-users] query regarding replica exchange
msanku65 at yahoo.com
Thu May 26 04:01:41 CEST 2011
I was wondering if I try to run PBS script in a cluster, how can I get to
generate the hostfile as I do not know in advance which machines will be
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, May 25, 2011 7:16:44 PM
Subject: Re: [gmx-users] query regarding replica exchange
On 26/05/2011 8:50 AM, Joshua L. Phillips wrote:
> You will need a file formatted like the following:
> node0 slots=4 max_slots=4
> node1 slots=4 max_slots=4
> node9 slots=4 max_slots=4
> You will then need to use the -hostfile option to supply the filename to
> either mpiexec or mpirun (not mdrun).
Indeed. Details will vary with the nature of the MPI installation - but
it's an MPI issue, not a GROMACS issue. The only relevant detail is that
you wish every pair of cores assigned to a replica to be on the same
machine. The above approach will generally achieve that.
> -- Josh
> On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote:
>> I am planning to run replica exchange simulation using gromacs
>> 4.0.7 . I have read the manual about REMD. Only thing I wanted to know
>> is that how I can specify the name of host-machines where I am
>> planning to run the simulations.
>> I have 10 different quad-core computers each intra-connected with the
>> other each running OPENMPI. I want to run 20 replica each using 2
>> cores in parallel.
>> So, I was wondering whether I have to create any file containing the
>> names of those machines . If so, can someone give an example of format
>> of the file which contain those names ? Finally, what keyword I should
>> use in mdrun to specify that file for running replica exchange.
>> Also, I am not using any PBS for submitting jobs.
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