found it. http://www.gromacs.org/Documentation/Acceleration_and_parallelization
GPUs are assigned to PP ranks within the same physical node in a sequential order, that is GPU 0 to the (thread-)MPI rank 0, GPU 1 to rank 1. In order to manually specify which GPU(s) to be used by mdrun, the respective device ID(s) can be passed with the -gpu_id XYZ command line option or with the GMX_GPU_ID=XYZ environment variable. Here, XYZ is a sequence of digits representing the numeric ID-s of available GPUs (the numbering starts from 0) . The environment variable is particularly useful when running on multiple compute nodes with different GPU configurations. Taking the above example of 8-core machine with two compatible GPUs, we can manually specify the GPUs and get the same launch configuration as in the above examples by: mdrun -ntmpi 2 -ntomp 4 -gpu_id 01 On Wed, Sep 24, 2014 at 10:49 AM, Johnny Lu <johnny.lu...@gmail.com> wrote: > Actually i am trying to find the answer to the same question now. > > manual 4.6.7/appendix D/mdrun > says > > -gpu_id > string > List of GPU device id-s to use, specifies the per-node PP rank to GPU > mapping > > On Tue, Sep 23, 2014 at 11:07 PM, Siva Dasetty <sdas...@g.clemson.edu> > wrote: > >> Thank you Lu for the reply. >> >> As I have mentioned in the post, I have already tried those options but it >> didn't work. Kindly please let me know if you have anymore suggestions. >> >> Thank you, >> >> On Tue, Sep 23, 2014 at 8:41 PM, Johnny Lu <johnny.lu...@gmail.com> >> wrote: >> >> > Try -nt, -ntmpi, -ntomp, -np (one at a time) ? >> > I forget about what I tried now.... But I just stop the mdrun, and then >> > read the log file. >> > Also can look for the mdrun page in the offical manual (pdf) and try >> this >> > page: >> > >> > >> http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun?highlight=mdrun >> > >> > >> > On Mon, Sep 22, 2014 at 6:46 PM, Siva Dasetty <sdas...@g.clemson.edu> >> > wrote: >> > >> > > Dear All, >> > > >> > > I am trying to run NPT simulations using GROMACS version 5.0.1 of a >> > system >> > > of size 140k atoms (protein+water systems) with 2 or more GPU's >> > > (model=k20); 8 cores (or more); and 1 or more nodes. I am trying to >> > > understand how to run simulations using multiple gpus on more than one >> > > node. I get the following errors/output when I run the simulation >> using >> > > the following commands:- >> > > >> > > Note: time-step used = 2 fs and total number of steps = 20000 >> > > >> > > First 4 cases are using single GPU and cases 5-8 are using 2 GPU's. >> > > >> > > 1. 1 node, 8 cpus, 1 gpu >> > > export OMP_NUM_THREADS = 8 >> > > command used- mdrun -s topol.tpr -gpu_id 0 >> > > Speed - 5.8 ns/day >> > > >> > > 2. 1 node, 8 cpus, 1 gpu >> > > export OMP_NUM_THREADS = 16 >> > > command used- mdrun -s topol.tpr -gpu_id 0 >> > > Speed - 4.7 ns/day >> > > >> > > 3. 1 node, 8cpus, 1gpu >> > > mdrun -s topol.tpr -ntomp 8 -gpu_id 0 >> > > Speed- 5.876 ns/day >> > > >> > > 4. 1 node, 8cpus, 1gpu >> > > mdrun -s topol.tpr -ntomp 16 -gpu_id 0 >> > > Fatal Error: Environment variable OMP_NUM_THREADS (8) and the number >> of >> > > threads requested on the command line (16) have different values. >> Either >> > > omit one, or set them both >> > > to the same value. >> > > >> > > Question for 3 and 4 : Do I need to always use OMP_NUM_THREADS or is >> > there >> > > a way ntomp overwrites the environment settings? >> > > >> > > >> > > 5. 1 node, 8cpus , 2gpus >> > > export OMP_NUM_THREADS = 8 >> > > mpirun -np 2 mdrun -s topol.tpr -pin on -gpu_id 01 >> > > Speed - 4.044 ns/day >> > > >> > > 6. 2 nodes, 8cpus , 2 gpus >> > > export OMP_NUM_THREADS = 8 >> > > mpirun -np 2 mdrun -s topol.tpr -pin on -gpu_id 01 >> > > Speed - 3.0 ns/day >> > > >> > > Are the commands that I used for 5 and 6 correct? >> > > >> > > 7. I also used (1node, 8 cpus, 2 gpus) >> > > mdrun -s topol.tpr -ntmpi 2 -ntomp 8 -gpu_id 01 >> > > but this time I get a fatal error: thread mpi's are requested but >> gromacs >> > > is not compiled with thread MPI. >> > > >> > > Question: Isn't thread MPI enabled by default? >> > > >> > > 8. Finally, I recompiled Gromacs without OpenMP and re-ran case 1 but >> > this >> > > time there is a fatal error "More than 1 OpenMP thread requested, but >> > > Gromacs was compiled without OpenMP support." >> > > command : mdrun -s topol.tpr (no environment settings) -gpu_id 0 >> > > Question: Here again, I assumed thread MPI is enabled by default and I >> > > think Gromacs still assumes OpenMp thread settings. Am i doing >> something >> > > wrong here? >> > > >> > > Thanks in advance for your help >> > > >> > > -- >> > > Siva >> > > -- >> > > 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. >> > >> >> >> >> -- >> Siva >> -- >> 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.