Cray XD1 pmemd and sander benchmarks

CRAY XD1 PMEMD AND SANDER BENCHMARKS, 4/18/05

Following are some explicit solvent pme md simulation benchmarks for the 
Cray XD1 at NIEHS.  This machine has 24 cpu's in two chassis with a RapidArray
interconnect. The cpu's are 2.4 GHz dual Opterons with 1 MB of cache.  All disk
i/o was to network-attached storage over gigabit ethernet.  This is not a
significant bottleneck for the number of processors used here.  PMEMD and SANDER
were compiled using pgf90, version 5.2-4.  A total of 20 cpu's were available
for benchmarking.

Special Notations:

NP2 - This indicates that a Sander 8 value could not be obtained for a given
      configuration because the number of processors used is "not a power of
      two".  Sander 8 places this restriction on parallelization, presumably
      as an efficiency measure, but it can prevent you from using a number of
      processors that would get you the best throughput at an acceptable CPU
      efficiency.

NA - Not applicable.

141154 Atoms, Constant Volume Molecular Dynamics (Reverse Transcriptase)
              cutoff = 8.0 angstrom, timestep = 0.0015 psec,
              orthogonal unit cell

#procs | PMEMD 8             | SANDER 8         
       | psec/day scaling(%) | psec/day scaling(%)
       |                     |
   1   |   58        NA      |   47        NA
   2   |  117       100      |   94       100
   4   |  227        97      |  173        92
   8   |  424        90      |  328        88
  12   |  632        90      |  NP2       NP2
  16   |  778        83      |  550        73
  20   | 1005        86      |  NP2       NP2

 90906 Atoms, Constant Volume Molecular Dynamics (Factor IX),
              cutoff = 8.0 angstrom, timestep = 0.0015 psec,
              orthogonal unit cell

#procs | PMEMD 8             | SANDER 8         
       | psec/day scaling(%) | psec/day scaling(%)
       |                     |
   1   |   94        NA      |   73        NA
   2   |  179       100      |  152       100
   4   |  353        99      |  270        89
   8   |  660        92      |  484        80
  12   | 1016        95      |  NP2       NP2
  16   | 1316        92      |  864        71
  20   | 1590        89      |  NP2       NP2

 90906 Atoms, Constant Pressure Molecular Dynamics (Factor IX)
              cutoff = 8.0 angstrom, timestep = 0.0015 psec,
              orthogonal unit cell

#procs | PMEMD 8             | SANDER 8         
       | psec/day scaling(%) | psec/day scaling(%)
       |                     |
   1   |   93        NA      |   74        NA
   2   |  183       100      |  151       100
   4   |  354        97      |  285        94
   8   |  650        89      |  498        82
  12   | 1005        92      |  NP2       NP2
  16   | 1271        87      |  900        74
  20   | 1525        83      |  NP2       NP2

 44247 Atoms, Constant Volume Molecular Dynamics (Hemoglobin)
              cutoff = 8.0 angstrom, timestep = 0.001 psec
              truncated octahedron unit cell, constrained coordinates

#procs | PMEMD 8             | SANDER 8         
       | psec/day scaling(%) | psec/day scaling(%)
       |                     |
   1   |  114        NA      |   98        NA
   2   |  216       100      |  190       100
   4   |  408        94      |  358        94
   8   |  789        91      |  638        84
  12   | 1192        92      |  NP2       NP2
  16   | 1557        90      | 1101        72
  20   | 1878        87      |  NP2       NP2

 44247 Atoms, Constant Pressure Molecular Dynamics (Hemoglobin)
              cutoff = 8.0 angstrom, timestep = 0.001 psec
              truncated octahedron unit cell, constrained coordinates

#procs | PMEMD 8             | SANDER 8         
       | psec/day scaling(%) | psec/day scaling(%)
       |                     |
   1   |  111        NA      |   98        NA
   2   |  200       100      |  188       100
   4   |  381        95      |  350        93
   8   |  796        99      |  586        78
  12   | 1137        95      |  NP2       NP2
  16   | 1516        95      |  999        66
  20   | 1781        89      |  NP2       NP2

 23558 Atoms, Constant Volume Molecular Dynamics (JAC Benchmark)
              cutoff = 9.0 angstrom, timestep = 0.001 psec,
              orthogonal unit cell

#procs | PMEMD 8             | SANDER 8         
       | psec/day scaling(%) | psec/day scaling(%)
       |                     |
   1   |  204        NA      |  173        NA
   2   |  389       100      |  340       100
   4   |  771        99      |  657        97
   8   | 1490        96      | 1230        90
  12   | 2215        95      |  NP2       NP2
  16   | 2880        93      | 2134        78
  20   | 3323        85      |  NP2       NP2


Bob Duke
NIEHS and
UNC-Chapel Hill Chemistry Dept.