[gmx-users] Clusters

[Szilárd Páll]

On Tue, Apr 14, 2015 at 2:45 AM, Lucas Dadalt Morero <ldm_w at hotmail.com> wrote:
> Sorry, it's 8 cores. Network is good.

Good for what? I was hoping to hear that it's e.g IB QDR. Otherwise
it's unlikely that you'll scale to all nodes.

> The hardware setup is ok, I just want to know how to perform a gromacs simulation using all the nodes..

Compile with MPI and run just like you'd run any MPI application. See
if it scales at all on your network, if it does you can try tweaking
the performance (e.g. PP-PME ratio, mutiple OpenMP threads per rank,
nstlist, etc.)
I suggest you check out that following page:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization

--
Szilárd

>
>
> Lucas
>
>> Date: Tue, 14 Apr 2015 02:06:49 +0200
>> From: pall.szilard at gmail.com
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Clusters
>>
>> What network do you have? Unless it's fast (that is low latency) you
>> won't be able to run across nodes. Are you sure about 9 cores, that
>> number seems strange?
>> --
>> Szilárd
>>
>>
>> On Mon, Apr 13, 2015 at 11:52 PM, Lucas Dadalt Morero <ldm_w at hotmail.com> wrote:
>> > Are there any tutorial or tips to use cluster in Gromacs?
>> > I have 5 nodes  with 9 cores each node and want use all them in one simulation, is that possible?
>> > I've read something about gromacs MPI but I don't know how to use.
>> > Can someone suggest some text or some tutorial for me?
>> >
>> > Thanks in advance,
>> > Lucas
>> >
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