Re: [gmx-users] simulation on 2 gpus

On Fri, Sep 6, 2019 at 3:47 PM Stefano Guglielmo wrote: > > Hi Szilard, > > thanks for suggestions. > > > As for the strange crash, the workstation works fine using only cpu; the > problem seems to be related to gpu usage, when both cards are used for 200 > W over 250 (more or less) the

Re: [gmx-users] simulation on 2 gpus

Hi Szilard, thanks for suggestions. As for the strange crash, the workstation works fine using only cpu; the problem seems to be related to gpu usage, when both cards are used for 200 W over 250 (more or less) the workstation turns off. It is not about PSU (even in the "offending" case we are

Re: [gmx-users] simulation on 2 gpus

Hi Stefano, On Tue, Aug 20, 2019 at 3:29 PM Stefano Guglielmo wrote: > > Dear Szilard, > > thanks for the very clear answer. > Following your suggestion I tried to run without DD; for the same system I > run two simulations on two gpus: > > gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28

Re: [gmx-users] simulation on 2 gpus

Dear Szilard, thanks for the very clear answer. Following your suggestion I tried to run without DD; for the same system I run two simulations on two gpus: gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 -gputasks 00 -pin on -pinoffset 0 -pinstride 1 gmx mdrun -deffnm run2 -nb

Re: [gmx-users] simulation on 2 gpus

On Mon, Aug 5, 2019 at 5:00 PM Stefano Guglielmo wrote: > > Dear Paul, > thanks for suggestions. Following them I managed to run 91 ns/day for the > system I referred to in my previous post with the configuration: > gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 -gputasks >

Re: [gmx-users] simulation on 2 gpus

Dear Paul, thanks for suggestions. Following them I managed to run 91 ns/day for the system I referred to in my previous post with the configuration: gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 4 -ntmpi 7 -npme 1 -gputasks 111 -pin on (still 28 threads seems to be the best choice) and 56

Re: [gmx-users] simulation on 2 gpus

Stefano, Here is a typical run fpr minimization mdrun -deffnm grofile. -nn gpu and for other runs for a 32 core gmx -deffnm grofile.nvt -nb gpu -pme gpu -ntomp 8 -ntmpi 8 -npme 1 -gputasks -pin on Depending on the molecular system/model -ntomp -4 -ntmpi 16 may

Re: [gmx-users] simulation on 2 gpus

I run the same system and setup but no nvlink. Maestro runs both gpus at 100 percent. Gromacs typically 50 --60 percent can do 600ns/d on 2 atoms PB > On Jul 25, 2019, at 9:30 PM, Kevin Boyd wrote: > > Hi, > > I've done a lot of research/experimentation on this, so I can maybe get you >

Re: [gmx-users] simulation on 2 gpus

other > > unsubset of yet-unallocated CPU/GPU). Also, could you elaborate on the > > drawbacks of the MPI compilation that you hinted at? > > Gregory > > > > From: Kevin Boyd<mailto:kevin.b...@uconn.edu> > > Sent: Thursday, July 25, 2019 10:31 PM &g

Re: [gmx-users] simulation on 2 gpus

les on how to start multiple runs at different times (e.g., > allocate a > > subset of CPU/GPU to one run, and start another run later using another > > unsubset of yet-unallocated CPU/GPU). Also, could you elaborate on the > > drawbacks of the MPI compilation that you h

Re: [gmx-users] simulation on 2 gpus

Thursday, July 25, 2019 10:31 PM > To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> > Subject: Re: [gmx-users] simulation on 2 gpus > > Hi, > > I've done a lot of research/experimentation on this, so I can maybe get you > started - if anyone has any questions abou

Re: [gmx-users] simulation on 2 gpus

..@uconn.edu> > Sent: Thursday, July 25, 2019 10:31 PM > To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> > Subject: Re: [gmx-users] simulation on 2 gpus > > Hi, > > I've done a lot of research/experimentation on this, so I can maybe get you > started - i

Re: [gmx-users] simulation on 2 gpus

on the drawbacks of the MPI compilation that you hinted at? Gregory From: Kevin Boyd<mailto:kevin.b...@uconn.edu> Sent: Thursday, July 25, 2019 10:31 PM To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> Subject: Re: [gmx-users] simulation on 2 gpus Hi, I've done a lot

Re: [gmx-users] simulation on 2 gpus

Hi, I've done a lot of research/experimentation on this, so I can maybe get you started - if anyone has any questions about the essay to follow, feel free to email me personally, and I'll link it to the email thread if it ends up being pertinent. First, there's some more internet resources to

[gmx-users] simulation on 2 gpus

Dear all, I am trying to run simulation with Gromacs 2019.2 on a workstation with an amd Threadripper cpu (32 core, 64 threads, 128 GB RAM and with two rtx 2080 ti with nvlink bridge. I read user's guide section regarding performance and I am exploring some possibile combinations of cpu/gpu work