AMBER Archive (2004)

Subject: AMBER: pmemd speedup and interactions

From: Lubos Vrbka (
Date: Wed Mar 31 2004 - 03:27:21 CST

hi guys,

can the speedup for pmemd be dependent on the type of interactions that
are present in my system?

this is on linux xeon cluster (2 cpu per node), pmemd 3.1, mpich
compiled with -comm=shared.

i've the box of triangulated waters (SPCE) only.

the time needed for finishing my test job (in hours, 1 million steps,
constant pressure):
1 proc 3:30
2 proc (shmem) 2:35
2 proc (shmem + hyperthread) 2:02
4 proc (shmem + p4) 1:42
4 proc (shmem + p4 + hyperthread) 2:15

so there's speed increase, but for the last case (8 processes on 4
processors), it's bad. i think the problem shouldn't be in
hyperthreading, since shmem with it works fine (note that in this case
i've only one pmemd binary for both shmem and p4 thanks to -comm=shared
switch to mpich)

for 3.0.1 and 3.1 versions compiled against mpich without -comm=shared
(i.e. separate binaries for p4 and shmem, i can see similar numbers...
this is interesting, since my colleague told me that he gets best
results for the last case - so i thought it could be studied system

where could the problem be? do you have any ideas?


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