I would like to run one simulation in parallel so that it utilises all the available nodes and cores. For that, I have compiled gromacs with mpi enabled and also installed openmpi on my machine. I am using the following command: mpirun -np 4 mdrun_mpi -v -s *.tpr
When i use top command, I get: PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 22449 root 20 0 107m 59m 3152 R 25 2.9 0:05.42 mdrun_mpi 22450 root 20 0 107m 59m 3152 R 25 2.9 0:05.41 mdrun_mpi 22451 root 20 0 107m 59m 3152 R 25 2.9 0:05.41 mdrun_mpi 22452 root 20 0 107m 59m 3152 R 25 2.9 0:05.40 mdrun_mpi Similarly when i use mpirun -np 2 mdrun_mpi -v -s *.tpr, I get PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 22461 root 20 0 108m 59m 3248 R 50 3.0 5:58.64 mdrun_mpi 22462 root 20 0 108m 59m 3248 R 50 3.0 5:58.56 mdrun_mpi If I look at %CPU column, it is actually 100/(no. of processes) Why is all the cpu not 100% utilised? Also if I compare my performance, it is significantly hampered. Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
