[gmx-users] Speeding things up

[Borys Szefczyk]

Dear Gromacs Users,

I am was wondering if I would be able tweak my simulation to run it
a bit faster. According to the chapter 3.17 of the manual, I have setup
the cut-offs and Fourier grid spacing so that the PME load is around 25%.
However, Gromacs still complains in the log file about the performance
loss due to the load imballance:

    D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 49748.7
 av. #atoms communicated per step for LINCS:  2 x 4755.5

 Average load imbalance: 29.1 %
 Part of the total run time spent waiting due to load imbalance: 17.1 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 %

NOTE: 17.1 % performance was lost due to load imbalance
      in the domain decomposition.


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing:         Nodes     Number     G-Cycles    Seconds     %
-----------------------------------------------------------------------
 Domain decomp.         8       5001      418.999      167.6     0.4
 Comm. coord.           8      50001      312.233      124.9     0.3
 Neighbor search        8       5001    11297.211     4518.7    12.0
 Force                  8      50001    55518.686    22206.4    58.7
 Wait + Comm. F         8      50001      761.632      304.6     0.8
 PME mesh               8      50001    24141.436     9656.1    25.5
 Write traj.            8        105        3.990        1.6     0.0
 Update                 8      50001      407.860      163.1     0.4
 Constraints            8      50001     1229.791      491.9     1.3
 Comm. energies         8      50001      230.156       92.1     0.2
 Rest                   8                 182.584       73.0     0.2
-----------------------------------------------------------------------
 Total                  8               94504.578    37800.0   100.0

        Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:   4725.000   4725.000    100.0
                       1h18:45

Is there something I could do about it? I should probably mention
that my system is composed of a slab of molecules and a protein on top
of it, in a cubic box, so there is a lot of vacuum around. I understand
that Gromacs should take care to optimize the domain decomposition
(I use the default parameters for DD). The job is running on 8 cores
of a single machine.

I would appreciate suggestions,
Borys Szefczyk

-- 
                 REQUIMTE,  &  Molecular Modelling & Quantum Chemistry Group,
  Department of Chemistry,  &  Institute of Physical & Theoretical Chemistry,
       Faculty of Science,  &  Wroclaw University of Technology
       University of Porto  &  http://ichfit.ch.pwr.wroc.pl/people/szefczyk