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. Thanks, -Micholas =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: [email protected] <[email protected]> on behalf of Justin Lemkul <[email protected]> Sent: Tuesday, August 28, 2018 10:08 AM To: [email protected] 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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 [email protected] | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
