use the total time (52.79).
HOWEVER it looks like you are spending mode time
in data distribution than calculation- you might be using too many
CPUs. try doing benchmarks with different numbers of processors.
more is not always better.
Zhihong Yu wrote:
>Dear all,
>
> I've done the benchmark of JAC system for parallel pmed (Amber9), the list of timings at the end of out file is as follow, then which time should I use to calculate the number of "ps/Day" ? 52.79, 29.90 or 57? thanks very much!
>
>
>--------------------------------------------------------------------------------
> 5. TIMINGS
>--------------------------------------------------------------------------------
>
>| NonSetup CPU Time in Major Routines, Average for All Tasks:
>|
>| Routine Sec %
>| ------------------------------
>| DataDistrib 36.37 68.90
>| Nonbond 15.67 29.69
>| Bond 0.00 0.01
>| Angle 0.03 0.05
>| Dihedral 0.12 0.23
>| Shake 0.15 0.29
>| RunMD 0.41 0.78
>| Other 0.03 0.05
>| ------------------------------
>| Total 52.79
>
>| PME Nonbond Pairlist CPU Time, Average for All Tasks:
>|
>| Routine Sec %
>| ---------------------------------
>| Set Up Cit 0.20 0.38
>| Build List 0.75 1.42
>| ---------------------------------
>| Total 0.95 1.81
>
>| PME Direct Force CPU Time, Average for All Tasks:
>|
>| Routine Sec %
>| ---------------------------------
>| NonBonded Calc 9.98 18.90
>| Exclude Masked 0.22 0.41
>| Other 1.06 2.01
>| ---------------------------------
>| Total 11.26 21.33
>
>| PME Reciprocal Force CPU Time, Average for All Tasks:
>|
>| Routine Sec %
>| ---------------------------------
>| 1D bspline 0.20 0.38
>| Grid Charges 0.36 0.69
>| Scalar Sum 0.23 0.43
>| Gradient Sum 0.45 0.84
>| FFT 2.22 4.21
>| ---------------------------------
>| Total 3.46 6.56
>
>| PME Load Balancing CPU Time, Average for All Tasks:
>|
>| Routine Sec %
>| ------------------------------------
>| Atom Reassign 0.02 0.03
>| Image Reassign 0.09 0.18
>| FFT Slab Reassign 1.33 2.52
>| ------------------------------------
>| Total 1.44 2.73
>
>| Master Setup CPU time: 0.59 seconds
>| Master NonSetup CPU time: 29.31 seconds
>| Master Total CPU time: 29.90 seconds 0.01 hours
>
>| Master Setup wall time: 3 seconds
>| Master NonSetup wall time: 54 seconds
>| Master Total wall time: 57 seconds 0.02 hours
>
>
>
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Received on Wed May 31 2006 - 00:11:56 PDT
