MD simulation of HAdV3 hexon homotrimer in water

总体系：368,286 atoms Gromacs 4.5.3 软件包64 bit

第一阶段：从1 cores增加到32 cores

第二阶段：从8个节点(64 cores)到24个节点(192 cores)进行统计

曙光高性能集群系统 Intel(R) Xeon(R) CPU E5430 @ 2.66GHz

结论：

Gromacs4.5的并行效率很高，在约30万个原子的模拟体系计算中，一直到192个核心也没有出现效能平台，并行效率一直是线性增长（再多的核心数没有尝试），这也可能与体系的大小有关，体系越大，核心数就越多越好。对于一定大小的的体系，理论上当核心数达到一定规模的时候会出现效能平台期。

_________________________________________________________

1 cores:

NODE (s) Real (s) (%)
Time: 318.370 318.414 100.0
5:18
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 42.231 2.689 0.093 258.585

gcq#127: "It's Not Your Fault" (Pulp Fiction)

__________________________________________________________

2 cores:
Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 126.752 126.752 100.0
2:06
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 99.875 6.352 0.219 109.345
__________________________________________________________

3 cores:
Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 124.612 124.612 100.0
2:04
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 145.687 9.264 0.320 74.923
__________________________________________________________

4 cores:
Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 98.066 98.066 100.0
1:38
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 201.129 12.791 0.442 54.264
__________________________________________________________

5 cores:
Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 949.204 949.204 100.0
15:49
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 227.260 14.451 0.501 47.922
__________________________________________________________

6 cores:
Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 95.109 95.109 100.0
1:35
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 265.130 16.859 0.583 41.152
__________________________________________________________

8 cores:
Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 125.620 125.620 100.0
2:05
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 338.097 21.504 0.744 32.250

gcq#96: "Proceed, With Fingers Crossed" (TeX)
__________________________________________________________

12 cores:
Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 76.288 76.288 100.0
1:16
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 515.582 32.780 1.135 21.149

gcq#54: "And It Goes a Little Something Like This" (Tag Team)
__________________________________________________________

16 cores:
Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 313.087 313.087 100.0
5:13
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 656.646 41.762 1.447 16.591

gcq#151: "I Ripped the Cord Right Out Of the Phone" (Capt. Beefheart)
__________________________________________________________
64 cores：5 x 4 x 2
NODE (s) Real (s) (%)
Time: 61.191 61.191 100.0
1:01
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 2470.244 156.950 5.425 4.424

gcq#44: "You Try to Run the Universe" (Tricky)

__________________________________________________________
80 cores：5 x 2 x 5

NODE (s) Real (s) (%)
Time: 56.262 56.262 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 2799.056 177.866 6.146 3.905

gcq#308: "I believe in miracles cause I'm one" (The Ramones)

__________________________________________________________

96 cores：8 x 4 x 2
NODE (s) Real (s) (%)
Time: 58.090 58.090 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 3333.504 211.844 7.321 3.278

gcq#61: "Would You Like to Be the Monster Tonight ?" (Captain Beefheart)

__________________________________________________________
112 cores：8 x 3 x 3
NODE (s) Real (s) (%)
Time: 76.179 76.179 100.0
1:16
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 3731.124 237.090 8.191 2.930

gcq#314: "Don't You Wish You Never Met Her, Dirty Blue Gene?" (Captain Beefheart)

__________________________________________________________
144 cores：8 x 6 x 2
NODE (s) Real (s) (%)
Time: 50.006 50.006 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 4675.533 297.155 10.267 2.338

gcq#58: "I Could Take You Home and Abuse You" (Magnapop)

__________________________________________________________
160 cores：4 x 9 x 3
NODE (s) Real (s) (%)
Time: 54.993 54.993 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 4709.033 299.315 10.341 2.321

gcq#336: "Ohne Arbeit wird das Leben Oede" (Wir Sind Helden)

__________________________________________________________
176 cores：8 x 3 x 5
NODE (s) Real (s) (%)
Time: 40.981 40.981 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 5108.852 324.781 11.220 2.139

gcq#62: "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)

__________________________________________________________
192 cores：8 x 8 x 2
NODE (s) Real (s) (%)
Time: 42.517 42.517 100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 5924.472 376.706 13.010 1.845

gcq#230: "Encountered Subspace Anomaly" (Star Trek)
__________________________________________________________