I have compiled amber8 (including pmemd) successfully on my redhat 9.0 linux cluster using ifort 9.0, the computing nodes of cluster are composed of Xeon (IA-32, dual cpu, 3.06 GHz) through Myrinet network. After I made benckmarks on "jac" and "factor_ix" system, I found that the efficiency of my sander and pmemd looks not very good, especially for Parallel efficiency (defined as: speedup/CPU), the following is my benchmark data:
for jac:
sander:
CPU Ps/Day speedup Parallel efficiency
1 113 1.00 100.00%
2 192 1.70 85.00%
4 332 2.94 73.45%
8 588 5.20 65.04%
16 719 6.36 39.76%
pmemd:
CPU Ps/Day speedup Parallel efficiency
1 158.57 1.00 100.00%
2 259.55 1.64 81.84%
4 480.03 3.03 75.68%
8 853.59 5.38 67.29%
16 1077.31 6.79 42.46%
for factor_ix:
sander:
CPU Ps/Day speedup Parallel efficiency
1 50.28 1.00 100.00%
2 82.44 1.64 81.98%
4 139.03 2.77 69.13%
8 194.70 3.87 48.40%
pmemd:
CPU Ps/Day speedup Parallel efficiency
1 77.14 1.00 100.00%
2 144.57 1.87 93.70%
4 226.14 2.93 73.29%
8 284.58 3.69 46.12%
Compared with amber website's data (pmemd, Intel Xeon x86_64, 3.4 GHz, 1cpu, jac, 179 ps/day), I think my 159 ps/day is normal and acceptable, But compared with datas on "
http://coffee.sdsc.edu/amber_sdsc/", my parallel efficiency descended rapidly with increasing CPUs, I think maybe I need some optimization on parallel sander or pmemd, did somebody has similar cases and give me some advice? thanks a lot!
BTW, for sander, my configure command is: ./configure -mpi -p4 ifort
for pmemd, the command is: ./new_configure linux_p4 ifort mpich_gm
sincerely yours, zhihong
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Received on Wed May 17 2006 - 06:07:07 PDT
