AMBER Archive (2006)

Subject: AMBER: which time should I use to calculate the number of "ps/Day"

From: Zhihong Yu (computation_at_mail.nankai.edu.cn)
Date: Mon May 29 2006 - 04:32:26 CDT

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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