AMBER 8 PMEMD Benchmark Done During RECOMB04 Meeting

If you are looking for current AMBER 8 PMEMD benchmark, please visit here

I always want to do some AMBER 8 benchmark on Apple's G5 machines, but apparently there is no G5 nearby, *sigh*.

Recently I got a chance to access powermac G5 (sponsored by Apple) in the RECOMB04. I wasn't able to run sander on those G5 email console because my old binaries still need IBM's dynamic libraries. Later I finally found the way to build static binary (Yes, I already tried "-Wl,-static".) with xlf 8.1beta on my powerbook. Here is how:

1. mkdir /opt/ibmcmp/lib_save/
2. mv /opt/ibmcmp/lib/*.dylib /opt/ibmcmp/lib_save/
3. echo "int mjhsiehkickme(){}" > test.c
4. xlc -c test.c -o test.o
5. ar rvs test.a test.o; ranlib test.a
6. mv test.a /opt/ibmcmp/lib/libxlomp_ser.a
7. Then you now can make a static binary with xlf.

By the way, remember to add this to your shell's environment variables:
setenv XLFRTEOPTS "namelist=old:xrf_messages=no"

I only tested it on jac and gb_mb because there were too many people eager to use these consoles and I still haven't gotten a chance to use it again.

=============================================================================
  "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
-------------------------------------------------------------------------------
RECOMB04  3/31   1.8 Ghz G5   MacOS X 10.3   IBM XLF 8.1b  1       138 (sander)
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1b  1        25 (sander)
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1b  1        26 (pmemd)

============================================================================
  "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.
-------------------------------------------------------------------------------
  node-name        CPU                 OS         compiler  npcu  ps-per-day
-------------------------------------------------------------------------------
RECOMB04  3/31   1.8 Ghz G5   MacOS X 10.3   IBM XLF 8.1b  1       184
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1b  1        23

============================================================================
  "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
-------------------------------------------------------------------------------
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1b  1        10

============================================================================
   "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
-------------------------------------------------------------------------------
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1   1        16