To add : I am running simulations on institute cluster with 8 nodes (2 cores each). Please suggest me the way so that I can run one simulation on all available nodes, cores and threads. Thanks in advance.
On Mon, Oct 7, 2013 at 1:55 PM, pratibha kapoor <kapoorpratib...@gmail.com>wrote: > 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
