Hi, I have been playing with the "mdrun_mpi" command in gromacs 4.0.7 to try out parallel processing. Unfortunately, the results I got did not show any significant improvement in simulation time. Below is the command I issued: mpirun -np x mdrun_mpi -deffnm where x is the number of processors being used. >From the machine output, it seemed that the work had indeed been distributed >to multiple processors e.g. -np 10: NNODES=10, MYRANK=5, HOSTNAME=beowulf NODEID=4 argc=3 NNODES=10, MYRANK=1, HOSTNAME=beowulf NNODES=10, MYRANK=2, HOSTNAME=beowulf NODEID=1 argc=3 NODEID=9 argc=3 NODEID=5 argc=3 NNODES=10, MYRANK=3, HOSTNAME=beowulf NNODES=10, MYRANK=7, HOSTNAME=beowulf NNODES=10, MYRANK=8, HOSTNAME=beowulf NODEID=8 argc=3 NODEID=2 argc=3 NODEID=6 argc=3 NODEID=3 argc=3 NODEID=7 argc=3 Making 2D domain decomposition 5 x 1 x 2 starting mdrun 'PROTEIN' 1000 steps, 2.0 ps. The simulation system consists of 100581 atoms, the duration is 2ps (1000 steps). results obtained are as followed: number of CPUs Simulation time 1 13m28s 2 6m31s 3 7m33s 4 6m47s 5 7m48s 6 6m55s 7 7m36s 8 6m58s 9 7m15s 10 7m01s 15 7m27s 20 7m15s 30 7m42s Significant improvement in simulation time was only observed from -np 1 to 2. As almost all (except -np = 1) complaint about load imbalance and PP:PME imbalance (the latter was seen especially in those with larger -np value), I tried to increase the pme nodes by adding a -npme flag and entered a bigger number but the results either showed no improvement or worsened. As I am new to gromacs, there might be some things that I'd missed out/done incorrectly. Would really appreciate some input to this. Many thanks in advance!! HW << Email has been scanned for viruses by UNMC email management service >>
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