Hi, Those commands are listed in the user guide, please look there :-)
Mark On Fri., 13 Dec. 2019, 10:10 Pragati Sharma, <pragati2...@gmail.com> wrote: > Hi Paul, > > The option -pme gpu works when I give pme order = 4 in mdp file instead of > 3. but it gives me an increase of 6-7 ns/day. > > @Dave M : I am also getting same observation. "If I run just one > simulation, I get almost double performance compared to when I run two > simulations in two GPUs as follows. > > mdrun -ntomp 12 -gpu_id 0 -nb gpu > mdrun -ntomp 12 -gpu_id 1 -nb gpu > > I am seeing various benchmarks, and the performance should not reduce to > half with two simulations. > > I need a command line with mdrun for maximal use of CPU and gpu. > > > > > > > > > > > > > > On Fri, Dec 13, 2019 at 1:14 PM Dave M <dave.gro...@gmail.com> wrote: > > > Hi Paul, > > > > I just jumped in this discussion. But I am wondering is > > CUDA_VISIBLE_DEVICES equivalent to providing gpu_id in mdrun? > > Also, my multiple simulations run slower in the same node with multiple > > gpus. e.g. in a node with 4 GPU and 64 CPU > > mpirun -np 1 mdrun -ntomp 24 -gpu_id 0 -pin on > > mpirun -np 1 mdrun -ntomp 24 -gpu_id 2 -pin on > > > > If I run just one simulation I get almost double performance (with same > > command as above). > > > > Dave > > > > On Thu, Dec 12, 2019 at 11:22 PM Paul bauer <paul.baue...@gmail.com> > > wrote: > > > > > Hello, > > > > > > the error you are getting in the end means that your simulation likely > > > does not use PME, or uses it in a way that is not implemented to run on > > > the GPU. > > > You can still run the nonbonded calculations on the GPU, just remove > the > > > -pme gpu flag. > > > > > > For running different simulations on your GPUs, you need to set the > > > environment variable CUDA_VISIBLE_DEVICES so that each simulation only > > > sees on of the available GPUs. > > > > > > Cheers > > > > > > Paul > > > > > > On 13/12/2019 06:22, Pragati Sharma wrote: > > > > Hello all, > > > > > > > > I am running a polymer melt with 100000 atoms, 2 fs time step, PME, > on > > a > > > > workstation with specifications: > > > > > > > > 2X Intel Xeon 6128 3.4 2666 MHz 6-core CPU > > > > 2X16B DDR4 RAM > > > > 2XRTX 2080Ti 11 GB > > > > > > > > I have installed *GPU and thread_mpi *enabled gromacs 2019.0 version > > > using: > > > > > > > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > > > *-DGMX_THREAD_MPI=ON > > > > -DGMX_GPU=ON* > > > > > > > > While running a single job with below command, I am getting a > > performance > > > > of *65 ns/day. * > > > > > > > > *gmx_tmpi mdrun -v -s t1.tpr -c t1.pdb -gpu_id 0 -ntmpi 1 -ntomp 24* > > > > > > > > *Q. However I want to run two different simulations at a time using > CPU > > > > cores and one GPU for each, Can somebody help me with mdrun command > > (what > > > > combination of ntmpi and ntomp) I should use to run two simulations > > with > > > > efficient utilization of CPU cores and 1 GPU each.* > > > > > > > > *Q.* I have also tried utilising GPU for PME calculations using -pme > > GPU, > > > > as in the command > > > > > > > > gmx_tmpi mdrun -v -s t1.tpr -c t1.pdb -ntmpi 1 -ntomp 24 -gputasks > 01* > > > -nb > > > > gpu -pme gpu* > > > > > > > > but i get the below error, > > > > > > > > > > > > *"Feature not implemented:The input simulation did not use PME in a > way > > > > that is supported on the GPU."* > > > > > > > > why is this error coming? Should I put extra attributes while > compiling > > > > gromacs. > > > > > > > > Thanks > > > > > > > > > -- > > > Paul Bauer, PhD > > > GROMACS Release Manager > > > KTH Stockholm, SciLifeLab > > > 0046737308594 > > > > > > -- > > > 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? 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