AMBER Archive (2005)

Subject: AMBER: Interpreting Amber8 Benchmark Results

From: Nikhil Kelshikar \(nkelshik\) (nkelshik_at_cisco.com)
Date: Wed Aug 31 2005 - 12:07:24 CDT

Hello,

This is a newbie question and might have been covered elsewhere on this
list but I have searched and couldn't find the information I am looking
for. Any help I can get or a pointer to webpage will be helpful.

I am trying to run Amber8 on EM64T with Intel Compilers. I have never
done this before and needed help to understand how to interpret the
benchmark data. The primary purpose of the benchmarks is to understand
how using different interconnects such as GbE, InfiniBand, 10 GigE may
affect the application performance.

- What number should I be looking at from the benchmark summary report
(attached).?

- What tests are more relevant to a customer who may be looking to
purchase a cluster to running Amber as a primary application?

I am simply using the benchmarks included with the software for these
tests.

Regards,
Nikhil
 
./factor_ix/bench.fix.out

|>>>>>>>>PROFILE of Average TIMES>>>>>>>>>
| Read coords time 0.06 ( 0.02% of Total)
| Build the list 12.87 (91.86% of List )
| Other 1.14 ( 8.14% of List )
| List time 14.01 ( 9.12% of Nonbo)
| Short_ene time 82.50 (92.96% of Direc)
| Other 6.25 ( 7.04% of Direc)
| Direct Ewald time 88.75 (63.53% of Ewald)
| Adjust Ewald time 0.70 ( 0.50% of Ewald)
| Fill Bspline coeffs 2.87 ( 8.71% of Recip)
| Fill charge grid 4.64 (14.10% of Recip)
| Scalar sum 3.21 ( 9.77% of Recip)
| Grad sum 6.84 (20.79% of Recip)
| FFT communication ti 5.39 (37.29% of FFT t)
| Other 9.06 (62.71% of FFT t)
| FFT time 14.45 (43.94% of Recip)
| Other 0.88 ( 2.68% of Recip)
| Recip Ewald time 32.89 (23.55% of Ewald)
| Force Adjust 15.26 (10.93% of Ewald)
| Virial junk 1.49 ( 1.07% of Ewald)
| Start sycnronization 0.58 ( 0.42% of Ewald)
| Ewald time 139.68 (90.88% of Nonbo)
| Nonbond force 153.70 (96.66% of Force)
| Bond/Angle/Dihedral 0.59 ( 0.37% of Force)
| FRC Collect time 3.90 ( 2.45% of Force)
| Other 0.81 ( 0.51% of Force)
| Force time 159.00 (96.43% of Runmd)
| Shake time 1.28 ( 0.78% of Runmd)
| Verlet update time 1.29 ( 0.78% of Runmd)
| CRD distribute time 3.31 ( 2.01% of Runmd)
| Other 0.01 ( 0.01% of Runmd)
| Runmd Time 164.89 (73.21% of Total)
| Other 60.29 (26.77% of Total)
| Total time 225.24 (100.0% of ALL )
 
Nikhil Kelshikar
Server Virtualization Business Unit
W: (408) 853-7733
M: (813) 789-8353


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