I have a question about the procedure for running a parallel
simulation on more than 12 processors using GROMACS 4.0.7.
I understand that partitioning the PME calculations and PP
calculations improves performance, and that there is an initial
automated "guess" at deciding how many processors to devote to PME vs.
PP calculations.
When I ran a simulation of a system on 16 processors, GROMACS
automatically devoted 6 processors to PMA calculations and 10 to PP
calculations. A 1 nsec simulation using 2 fs steps took only
marginally less time (5 h 12 m) as runningthe same simulation on 8
processors (6 h 45 m), without the separation of PME and PP
calculations and the following note was in the log file:
NOTE: 35.7 % performance was lost because the PME nodes
had more work to do than the PP nodes.
You might want to increase the number of PME nodes
or increase the cut-off and the grid spacing.
I reran the same simulation, this time including -npme 8 in the mdrun
call, and the simulation completed in 4 h 19 min, with the following
note in the log file:
NOTE: 16.8 % performance was lost because the PME nodes
had more work to do than the PP nodes.
You might want to increase the number of PME nodes
or increase the cut-off and the grid spacing.
So I conclude that I need to increase cut-off and grid spacing, since
this is recommended in the manual and in the paper describing the
GROMACS 4 algoithm changes.
Unfortunately
a) I am unclear on which parameters in the .mdp file represent cut-off
and grid spacing
and
b) When the manual says "For changing the electrostatics settings it
is useful to know the accuracy of the electrostatics remains nearly
constant when the Coulomb cut-off and the PME grid spacing are scaled
by the same factor."
Does this mean that cut-off and grid-spacing parameters need to be
changed by the same proportion?
I hope this is sufficiently specific a question - if not, let me knwo
what I need to be clearer on.
Thanks,
Warren Gallin
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