AMBER Archive (2006)

Subject: AMBER: parallel computation time vs serial computation time

From: Cenk Andac (
Date: Thu Dec 14 2006 - 05:17:28 CST

Dear Amber community,

I have installed amber9 sometime ago on a Dual-Core PentiumD 3.4 GHz PC computer (that is, 1 node with two physical CPUs) opearting under Linux SUSE v10.0 . To the best of my knowledge, the serial and parallel versions of sander passed all tests...I installed sander.MPI using MPICH2 and ifort9.0. As far as I know, I set up library and binary paths corerctly for mpich2.
In addition to the test experiments provided by amber9, I have conducted two minimization experiments for a small ligand, one with serial sander and the other with sander.mpi (mpiexec -n 2 sander.mpi -O -i in -o out -p prmtop -c incrd -r out.incrd). I do not know if it would be a useful info here, but I activated mpich2 by typing mpd on another console.

Now, looking at the sander outputs for parallel and serial routines, I see no difference between the time to complete these experiments. Both (parallel and serial) routines took about ~ 50 secs to reach 500 steps of minimization.
I am just wondering if this is the way it should be on a single node regardless of the number of CPUs. I mean can sander.serial really run both CPUs on one node or there is something else that I am missing here? or it is just that somewhat only one CPU is activated in both routines. In that sense, I would say there is something wrong with mpich2 settings and I can not figure it out what it is at this moment.
In another test, this time I excuted sander.mpi without mpiexec option and I got exactly the same timing result (~50 secs).
Can anyone please shed some light on the timing results that I got for paralel and serial sander routines. I am a little bit confused here...
best regards,


   Cenk Andac, M.S., Ph.D. Student
 School of Pharmacy at
 Gazi University-Ankara Turkiye
  Address: Bandirma Sok. No:6
 Etiler, Ankara, 06330 Turkey
 Cell: +90-(536)-4813012

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