AMBER Archive (2009)

Subject: Re: [AMBER] Verlet update time in explicit water Replica Exchange MD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Nov 25 2009 - 11:38:24 CST

Hmmm,
I am not a replica exchange expert, but I am presuming the master nodes
might be writing to disk? Could it be that if you have the former master
arrangement, you are writing to disk for some of the copies over an nfs
share? This can be really bad, especially if the nfs share is either
heavily loaded, or uses the same interconnect as mpi. I am just guessing
here, as this is sander, and replica exchange, neither of which I do all
that much with...
Regards - Bob Duke
----- Original Message -----
From: "Da-Wei Li" <lidawei_at_gmail.com>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Wednesday, November 25, 2009 12:28 PM
Subject: Re: [AMBER] Verlet update time in explicit water Replica Exchange
MD

> Hi,
>
> Just another update. If I re-arrange the MPI machine file to let the
> master processors of each group to be on the same node, everything
> will be fine. I have no idea why this happens.
>
> have a nice day.
>
> dawei
>
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>

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