AMBER Archive (2008)

Subject: AMBER: amber 10: sander and pmemd performance

From: Vlad Cojocaru (
Date: Fri Jul 25 2008 - 04:57:45 CDT

Dear ambers,

I have compiled AMBER10 with the intel compilers ifort and icc (10.1)
with 2 different mpi libs: v1= version with mpich2 1.0.7; v2 = version
with openmpi 1.2.6 (MKL were used in both). All MPI versions were
compiled with the same compilers as the AMBER package. Netcdf support
was included in all compilations.

I tested these compilations on a 60K atoms system on 4 cores of an AMD
opteron machine with 2 double core CPUs (OS: Debian Linux) . After this
I compared with one older compilation of AMBER9 with gcc 4.1 (gfortran)
and openmpi 1.2.5 (v3) . I used both NPT and NVE ensemble for testing.

To my surprise there is little difference in performance between v1 and
v2 compilations of AMBER 10 and the old compilation of AMBER 9 with gcc.
The new sander.MPI is just about 6-8 % faster while the new pmemd is
just about the same speed. Interestingly, the v2 compilation
(intel+openmpi) was slightly faster than v1 (compiled with mpich2).
Also, a different compilation using pgi 7.1 and openmpi 1.2.5 is very
similar in performance with the intel ones.

In general sander.MPI runs 0.155 to 0.165 ns per day of NPT simulation
while pmemd runs 0.24 to 0.25 ns/day of NPT simulation and 0.245 to
0.2670 ns/day of NVE simulation . All simulations have a time step of 1fs.

I would like to ask you if according to your experience these
performance parameters are what one would expect on such a machine? I
was hoping that the intel compilers would compile significantly faster
executables (around 15-20 %) comparing to gfortran but this is not the
case (or maybe the increase in performance comes with higher CPU counts
?). Is there something one can play with during the compilation with the
intel compilers to increase performance ? There are several messages int
he AMBER archives suggesting that the intel compilers provide faster
executables ....

Best wishes

Dr. Vlad Cojocaru

EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg

Tel: ++49-6221-533266 Fax: ++49-6221-533298


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