Hi,
On Wed, 4 Sep 2019 at 12:54, sunyeping <sunyep...@aliyun.com> wrote: > Dear everyone, > > I am trying to do simulation with a workstation with 72 core and 8 geforce > 1080 GPUs. > 72 cores, or just 36 cores each with two hyperthreads? (it matters because you might not want to share cores between simulations, which is what you'd get if you just assigned 9 hyperthreads per GPU and 1 GPU per simulation). > When I do not assign a certain GPU with the command: > gmx mdrun -v -deffnm md > all GPUs are used and but the utilization of each GPU is extremely low > (only 1-2 %), and the simulation will be finished after several months. > Yep. Too many workers for not enough work means everyone spends time more time coordinating than working. This is likely to improve in GROMACS 2020 (beta out shortly). In contrast, when I assign the simulation task to only one GPU: > gmx mdrun -v -gpu_id 0 -deffnm md > the GPU utilization can reach 60-70%, and the simulation can be finished > within a week. Even when I use only two GPU: > Utilization is only a proxy - what you actually want to measure is the rate of simulation ie. ns/day. gmx mdrun -v -gpu_id 0,2 -deffnm md > > the GPU utilizations are very low and the simulation is very slow. > That could be for a variety of reasons, which you could diagnose by looking at the performance report at the end of the log file, and comparing different runs. > I think I may missuse the GPU for gromacs simulation. Could you tell me > what is the correct way to use multiple GPUs? > If you're happy running multiple simulations, then the easiest thing to do is to use the existing multi-simulation support to do mpirun -np 8 gmx_mpi -multidir dir0 dir1 dir2 ... dir7 and let mdrun handle the details. Otherwise you have to get involved in assigning a subset of the CPU cores and GPUs to each job that both runs fast and does not conflict. See the documentation for GROMACS for the version you're running e.g. http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#running-mdrun-within-a-single-node . You probably want to check out this webinar tomorrow https://bioexcel.eu/webinar-more-bang-for-your-buck-improved-use-of-gpu-nodes-for-gromacs-2018-2019-09-05/ . Mark > Best regards > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.