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.