[gmx-users] Heterogeneous GPU cluster question?

Smith, Micholas D. smithmd at ornl.gov
Tue Aug 28 16:31:22 CEST 2018

Dear users (and developers),

My sys. admin. is exploring purchasing some more GPU nodes for our cluster and was curious if we could get away with running GROMACS on a cluster that has two different types of GPUs, i.e. 70% of the nodes have 2 p100 gpus while 30% have volta (both have 2 gpu's per node).? 

I've been looking through the mailing list, but haven't bumped into this situation before. 

My inclination was to just purchase the "older" p100 since that is what all of the nodes are currently sporting, but thought I would ask to see if anyone has tried this kind of set-up before.



Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, August 28, 2018 10:08 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] rerun doesn't calculate Coulomb & LJ interactions between groups

On 8/28/18 10:04 AM, Irem Altan wrote:
> Hi,
> I ran some umbrella sampling simulations on GPUs. I want to get the Coulomb and LJ energy between certain groups (chain A - chain B, chain A - solvent, etc.) , so I ran rerun:
> gmx mdrun -rerun umbrella1.xtc -nb cpu -v -deffnm umbrella1
> However, when I run gmx energy on the output .edr file:
> gmx energy -f umbrella1.edr -o umbrella1_ener.xvg
> I only get 50 terms listed, as opposed to ~90 that contains things like "LJ-SR:SOL-Chain_A". What am I missing?
> The executable is created with the following command:
> gmx grompp -f umbrella.mdp -c conf1.gro -p topol.top -n index.ndx -maxwarn 1 -o umbrella1.tpr
> where chain A, chain B, and SOL are defined in index.ndx.

The contents of index.ndx are irrelevant unless you've actually specific
which energygrps you want to define (in the .mdp file). Also, why are
you using -maxwarn 1? This should almost never be done.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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