Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

On Tue, Jul 30, 2019 at 3:29 PM Carlos Navarro wrote: > > Hi all, > First of all, thanks for all your valuable inputs!!. > I tried Szilárd suggestion (multi simulations) with the following commands > (using a single node): > > EXE="mpirun -np 4 gmx_mpi mdrun " > > cd $WORKDIR0 > #$DO_PARALLEL >

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Hi all, First of all, thanks for all your valuable inputs!!. I tried Szilárd suggestion (multi simulations) with the following commands (using a single node): EXE="mpirun -np 4 gmx_mpi mdrun " cd $WORKDIR0 #$DO_PARALLEL $EXE -s 4q.tpr -deffnm 4q -dlb yes -resethway -multidir 1 2 3 4 And I

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Hi, Yes and the -nmpi I copied from Carlos's post is ineffective - use -ntmpi Mark On Mon., 29 Jul. 2019, 15:15 Justin Lemkul, wrote: > > > On 7/29/19 8:46 AM, Carlos Navarro wrote: > > Hi Mark, > > I tried that before, but unfortunately in that case (removing —gres=gpu:1 > > and including

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Carlos, You can accomplish the same using the multi-simulation feature of mdrun and avoid having to manually manage the placement of runs, e.g. instead of the above you just write gmx mdrun_mpi -np N -multidir $WORKDIR1 $WORKDIR2 $WORKDIR3 ... For more details see

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

On 7/29/19 8:46 AM, Carlos Navarro wrote: Hi Mark, I tried that before, but unfortunately in that case (removing —gres=gpu:1 and including in each line the -gpu_id flag) for some reason the jobs are run one at a time (one after the other), so I can’t use properly the whole node. You need to

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Hi Mark, I tried that before, but unfortunately in that case (removing —gres=gpu:1 and including in each line the -gpu_id flag) for some reason the jobs are run one at a time (one after the other), so I can’t use properly the whole node. —— Carlos Navarro Retamal Bioinformatic Engineering.

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Hi, When you use DO_PARALLEL=" srun --exclusive -n 1 --gres=gpu:1 " then the environment seems to make sure only one GPU is visible. (The log files report only finding one GPU.) But it's probably the same GPU in each case, with three remaining idle. I would suggest not using --gres unless you

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Hi Szilárd, To answer your questions: **are you trying to run multiple simulations concurrently on the same node or are you trying to strong-scale? I'm trying to run multiple simulations on the same node at the same time. ** what are you simulating? Regular and CompEl simulations ** can you

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Hi, It is not clear to me how are you trying to set up your runs, so please provide some details: - are you trying to run multiple simulations concurrently on the same node or are you trying to strong-scale? - what are you simulating? - can you provide log files of the runs? Cheers, -- Szilárd

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

No one can give me an idea of what can be happening? Or how I can solve it? Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile E: