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.
