[AMBER-Developers] Parallel Cpptraj with Openmp

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 6 Jul 2011 17:52:00 -0400

Hi All,

Just as a heads up, I've started to parallelize some of the more CPU
intensive calculations in cpptraj using OpenMP. Currently the
'closest', 'surf', and 'mask' (when selecting by distance) actions are
OpenMP parallelized.

OpenMP is currently not part of the regular Cpptraj build in
AmberTools, but it can be compiled using the built-in configure script
located in $AMBERHOME/AmberTools/src/cpptraj, e.g.

cd $AMBERHOME/AmberTools/src/cpptraj
./configure -openmp gnu [--with-netcdf=$AMBERHOME]
make clean; make install

This will put the cpptraj binary in
$AMBERHOME/AmberTools/src/cpptraj/bin. One could also manually edit
the $AMBERHOME/AmberTools/src/config.h file to include the appropriate
flags (-fopenmp for gnu, -openmp for intel). I've tested it with both
gnu and intel compilers, seems to work fine. You will only need the
'--with-netcdf=' option if your system doesn't have netcdf libs
already installed.

If you get a chance to try it and have any questions or comments, let me know!


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Received on Wed Jul 06 2011 - 15:00:04 PDT
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