Amber 8 Benchmarks

Notes:

You should not take any set of timings all that seriously. The values below are mainly useful to see generally how one machines performs against another, or how much (or little) parallel speedup we obtain for these systems. You should expect to get roughly similar performance on your Amber 8 installation with similar machines.
Unless otherwise noted, all of the results below are for pmemd, which is generally faster than sander. To run these yourself, set the TESTsander variable to "../../exe/pmemd" in the scripts in the subdirectories under $AMBEHROME/benchmarks.
We welcome additions or suggestions, and will continue to update this page from time to time. You may also want to consult other benchmarks:
- comparison of Amber, CHARMM and NAMD timings
- expanded PMEMD benchmarks for factor IX
- DNA benchmarks for the ABC project
- pmemd and sander on the Cray XD1
- pmemd on an opteron cluster (For dual core Opteron SMP see tables below.)
- pmemd on an Apple G5 cluster
Parallel speedups are generally highly dependent on the processor speed, and on the hardware and software details of the communications system.
The value of ps per day = 86.4/(seconds per step), for a time step of 1 fs. Double this value if you plan to use 2 fs time steps.
For some information about the Apple G5 systems, click here.
The 3.2 GHz Xeon benchmarks are from Bob Duke; details are here.
Note that pmemd has not been optimized for the SDSC "DataStar" machine, so it is possible that better results might be possible there.

     
     =============================================================================
     "jac" == Joint Amber/Charrm DHFR benchmark.  This is the protein DHFR,
     solvated with TIP3 water, in a periodic box.  There are 23,558 total atoms,
     and PME used with a direct space cutoff of 9 Ang.  This is the benchmark
     in benchmarks/jac subdirectory of the Amber 8 distribution.

     --------------------------------------------------------------------------------
     name   date      CPU              OS         compiler  npcu    ps per day
     --------------------------------------------------------------------------------

     bohr    2/04 2.0 Ghz PIV Xeon   RH 7.3         lf95     1         63

     loyd    4/04 2.4 Ghz PIV Xeon   RH 9           ifc8     1        123
                                                             2        210

    landau   4/04 3.0 Ghz PIV        RH9            ifc8     1        153

    unc/duke 4/04 3.2 GHz PIV Xeon  RH E3smp        ifc7     1        202
                                                             2        330

     g5test  7/04 2.0 Ghz G5         Mac OSX 10.3  xlf8.1    1        187
                                                             2        319
     
     nocona  9/04 3.4 Ghz Xeon_EM64T  Suse           ifc8    1        179

     yt      2/04 altix/itanium 1.3GHz linux       ifort8    1        269
                                                             2        465
                                                             4        892
                                                             8       1655
                                                            16       2949
                                                            32       4711
                                                            64       6216
     

     SGI     9/04 altix/itanium 1.5GHz linux       ifort8    1        349
             (details)                                       2        586
                                                             4       1131
                                                             8       2108
                                                            16       3781
                                                            32       6176
     

     bluefish 12/03 SGI Origin 3800                  f90     1       
                                                             2        115
                                                             4        229
                                                             8        440
                                                            16        827
                                                            32       1529

    SDSC     6/04 IBM Power4 P655+, 1.5 GHz          xlf     2        257
             "DataStar"                                      4        504
                                                             8        952
                                                            16       1799
                                                            32       3138
                                                            64       5310
                                                           128       6101
                                                           256       6288

    utah    7/04  1.3 GHz Opteron                 pathscale  1        115
                  myrinet, mpich-gm (sander!!)               2        231
                                                             4        424
                                                             8        752
                                                            16       1170
                                                            32       1464

                                                             
    Imperial 6/05 Dual Core Opteron 875 (2.2GHz)   PGI(6.0)  1        187 Kernel 2.6.7
                  4 x Dual Core = 8cpu SMP 16GB Ram          2        342
                  Numbers by Ian Gould (Imperial College)    4        650
                  (PME)                                      8       1181

                                                             1        187  Kernel 2.6.12
                                                             2        358
                                                             4        705
                                                             8       1237

     =============================================================================
	 "hb": This is a hemoglobin benchmark, also a protein solvated with TIP3
      water, in a periodic box.  There are 44,247 total atoms, and PME used 
      with a direct space cutoff of 8 Ang.  This 500-step test is in 
      amber8/benchmarks/hb; it uses a truncted octahedral box, and nrespa=2.
     
     --------------------------------------------------------------------------------
     name   date      CPU              OS         compiler  npcu    ps-per-day
     --------------------------------------------------------------------------------
     
     bohr    2/04 2.0 Ghz PIV Xeon   RH 7.3         ifc7     2        117

     g5test  7/04 2.0 Ghz G5         Mac OSX 10.3  xlf8.1    1        124
                                                             2        218
     
     yt      2/04 altix/itanium 1.3GHz linux       ifort8    1  
                                                             2        296
                                                             4       
                                                             8       1017
                                                            16       1841
                                                            32       2437
                                                            64       3636
     
    Imperial 6/05 Dual Core Opteron 875 (2.2GHz)   PGI(6.0)  1        127 Kernel 2.6.7
                  4 x Dual Core = 8cpu SMP 16GB Ram          2        227
                  Numbers by Ian Gould (Imperial College)    4        423
                  (PME)                                      8        783

                                                             1        127 Kernel 2.6.12
                                                             2        239
                                                             4        472
                                                             8        853

     =============================================================================
     "fix": This is a factor_ix benchmark, from Bob Duke, also a protein
     solvated with TIP3 water, in a periodic box.  There are 90,906 total atoms,
     and PME used with a direct space cutoff of 8 Ang.  This test is in 
     amber8/benchmarks/factor_ix.  This uses dt=0.0015, so the conversion is
     ps-per-day = 129.6/(time-per-step)
     
     --------------------------------------------------------------------------------
     name   date      CPU              OS         compiler  npcu   ps-per-day
     --------------------------------------------------------------------------------
     
     bohr    2/04 2.0 Ghz PIV Xeon   RH 7.3         ifc7     2         78

     unc/duke 4/04 3.2 GHz PIV Xeon  RH E3smp      ifc7      1         75
                                                             2        120

     g5test  7/04 2.0 Ghz G5         Mac OSX 10.3  xlf8.1    1         91
                                                                      155
     
     yt      2/04 altix/itanium 1.3GHz linux       ifort8    1        114
                                                             2        190
                                                             4        368
                                                             8        709
                                                            16       1304
                                                            32       2139
                                                            64       3256

    Imperial 6/05 Dual Core Opteron 875 (2.2GHz)   PGI(6.0)  1         88 Kernel 2.6.7
                  4 x Dual Core = 8cpu SMP 16GB Ram          2        158
                  Numbers by Ian Gould (Imperial College)    4        310
                  (PME)                                      8        534

                                                             1         88 Kernel 2.6.12
                                                             2        167
                                                             4        329
                                                             8        562

     =============================================================================
     "gb_mb" == Generalized Born myoglobin simulation.  This protein has 2492
     atoms, and is run with a 20 Ang. cutoff and a salt concentration of 0.2 M,
     with nrespa=4 (long range forces computed every 4 steps.)  This is the
     test case in the benchmarks/gb_mb subdirectory of the Amber 8 distribution.
     (These results are from sander, since pmemd does not do GB calculations.)
     
     --------------------------------------------------------------------------------
     node-name        CPU                 OS         compiler  npcu  ps-per-day
     --------------------------------------------------------------------------------
     
     yt      2/04 altix/itanium 1.3GHz linux       ifort8    1        129
                                                             2        252
                                                             4        502
                                                             8        985