[gmx-users] Attempting to scale gromacs mdrun_mpi

[NG HUI WEN]

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
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