[gmx-users] Re: loab imbalance

[lina]

> The first time I did not notice that 16 cpus are twice as slow as 8.
> Are you really sure you did not mix things up?
> The other way around the timings would make perfect sense.
> If not, there is a problem with your 16 cpu simulation.
> 
> What load imbalance is reported for the 8 cpu run?
> 
> Berk
> 

Sorry, recently so sleepy, so I mixed up with the 8cpus and 16 cpus in
the last email. no doubt that the 16 cpus fast. Seems 8 cpus no
problems. 
 
    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 70598.6
 av. #atoms communicated per step for LINCS:  2 x 952.6

 Average load imbalance: 1500.0 %
 Part of the total run time spent waiting due to load imbalance: 187.5 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
X 0 % Y 
0 %

NOTE: 187.5 % 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.        16    1000000   121878.350    36533.7     4.4
 Comm. coord.          16    5000001   247646.114    74233.2     8.9
 Neighbor search       16    1000001  1002091.741   300382.2    35.9
 Force                 16    5000001   919401.942   275595.5    32.9
 Wait + Comm. F        16    5000001   299888.017    89893.0    10.7
 Write traj.           16       2001      249.523       74.8     0.0
 Update                16    5000001    20258.672     6072.6     0.7
 Constraints           16    5000001   105721.492    31690.6     3.8
 Comm. energies        16    5000001    51653.353    15483.4     1.9
 Rest                  16               22395.593     6713.2     0.8
-----------------------------------------------------------------------
 Total                 16             2791184.797   836672.0   100.0
-----------------------------------------------------------------------

	Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:  52292.000  52292.000    100.0
                       14h31:32
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    523.244     19.720     16.523      1.453
Finished mdrun on node 0 Tue Apr  6 05:09:47 2010
\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\(below is
8cpu's md.log)

    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 46783.6
 av. #atoms communicated per step for LINCS:  2 x 664.8

 Average load imbalance: 9.8 %
 Part of the total run time spent waiting due to load imbalance: 3.5 %


     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    1000000    69839.474    20934.6     2.7
 Comm. coord.           8    5000001   162704.625    48771.3     6.3
 Neighbor search        8    1000001   982919.098   294633.3    38.2
 Force                  8    5000001   917463.617   275012.8    35.6
 Wait + Comm. F         8    5000001   273548.449    81997.1    10.6
 Update                 8    5000001    20465.372     6134.6     0.8
 Constraints            8    5000001    96414.222    28900.5     3.7
 Comm. energies         8    5000001    28884.158     8658.1     1.1
 Rest                   8            9223372036.855 2764736802.2
358286.2
-----------------------------------------------------------------------
 Total                  8             2574303.046   771656.0   100.0
-----------------------------------------------------------------------

	Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:  96457.000  96457.000    100.0
                       1d02h47:37
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    283.696     10.701      8.957      2.679
Finished mdrun on node 0 Mon Apr  5 01:36:18 2010

Thanks and regards,

lina