[gmx-users] query regarding replica exchange

[Sanku M]

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 
allocated .




________________________________
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.

Mark

> -- Josh
>
> On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote:
>> Hi,
>>
>>
>>    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.
>>
>>
>> Sanku
>>
>>
>>
>>
>>
>>
>>
>>
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110525/42212dcc/attachment.html>