NAMD2 on Apoa1 Benchmark

NAMD is a high performance dynamic molecular simulation tool based on Charm++ - a parallel, object-oriented C++ language. The purpose of this personal web page is to collect performance data on various platforms which are available to me.
For more ApoA1 performance data, please refer to our official website NAMD benchmark website.
 

Benchmark -  ApoA1

 92,224 atoms, 12A cutoff + PME every 4 steps, periodic
 

Speedup plots: (details see below)


 

Efficiency Plots:

sciclone.wm.edu - SUN Cluster
 

              tornado subcluster: Ultra60   360MHz,  512M RAM + NET-Myrinet
 
Num of Processors Benchmark time (seconds) Speedup
1 33.7965 1
2 17.9638 1.8814
4 8.8628 3.813
8 4.5367 7.450
16 2.2641 14.927
32 1.1631 29.057
40 (dual) 1.0086 33.508
50 (dual) 0.8896 37.991
64 (dual) 0.7703 43.874

 
  •   5/2/2001  net-sol-cc
    •               tornado subcluster: Ultra60   360MHz, 512M RAM +  Fast Ethernet 100Mbps
     
    Num of Processors Benchmark time (seconds) Speedup
    1 32.8455 1
    2 17.9969 1.82
    4 9.3737 3.504
    8 5.0287 6.5316
    16 2.8953 11.3444
    32 1.5515 21.170
    64 (dual) 1.0818 30.362
  •   5/12/2001  mpi-sol-cc
    •               tornado subcluster: Ultra60   360MHz, 512M RAM +  MPI Fast Ethernet 100Mbps
     
    Num of Processors Benchmark time (seconds) Speedup
    1 32.0946 1
    2 17.9229 1.7907
    4 9.23568 3.475
    8 4.85474 6.611
    16 2.811 11.4175
    32 1.49466 21.4728
    64 (dual) 1.05429 30.4419
                  typhoon subcluster: Ultra5   333MHz , 256M RAM + Fast Ethernet 100Mbps
     
    Num of Processors Benchmark time (seconds) Speedup
    1 38.8477 1
    2 21.2397 1.83
    4 10.8398 3.58
    8 5.632 6.9
    16 3.1301 12.41
    32 1.7586 22.09
    64 (dual) 1.0474 37.09

    turing.cs.uiuc.edu - Linux Cluster
     

                  Pentium III 1GHz, Myrinet
     
    Num of Processors Benchmark time (seconds) Speedup
    1 25.522 1
    2 13.7904 1.85
    4 6.90724 3.695
    8 3.54727 7.195
    16 1.81432 14.067
    32 0.942782 27.071
    40 0.748272 34.107918
    56 0.572339 44.592453
                  Pentium III 1GHz, Myrinet
     
    Num of Processors Benchmark time (seconds) Speedup
    1 25.4689 1
    2 14.3185 1.779
    4 7.52838 3.383
    8 3.91705 6.50
    16 2.00998 12.671
    32 1.10001 23.153

    modi4.ncsa.uiuc.edu - Origin2000

    Num of Processors Benchmark time (seconds) Speedup
    1 29.1015 1
    2 15.5919 1.86645
    4 7.67323 3.7926
    8 3.8618 7.5357
    16 1.98066 14.6928
    32 0.99519 29.242155
    64 0.520184 55.9446
    126 0.294418 98.84416

    titan.ncsa.uiuc.edu - Linux IA64 Cluster

                 Linux IA64 733MHz Dual Processors, 2MB Cache, 1G RAM + Myrinet
     
    Num of Processors Benchmark time (seconds) Speedup
    1 16.1123 1
    2 8.53735 1.8873
    4 4.23542 3.80418
    8 2.1306 7.5623
    16 1.09861 14.666
    32 (dual) 0.603945 26.678
                 Linux IA64 733MHz Dual Processors, 2MB Cache, 1G RAM
     
    Num of Processors Benchmark time (seconds) Speedup
    1 16.0763 1
    2 8.77759 1.8315
    4 4.67599 3.438
    8 2.48267 6.4754
    16 1.66839 9.6358
    32 (dual) 1.33104 12.078

     

    t3e.psc.edu - T3E

    Num of Processors Benchmark time (seconds) Speedup
    1 - 1
    2 - -
    4 - -
    8 6.83832 -
    16 3.44687 -
    32 1.7543 -
    64 0.910296 -
    128 0.476213 -
    256 0.324025