Installing Demond on a 64-bit AMD Opteron Cluster running CentOS 5 Linux
Desmond is a software package developed at D.E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on parallel systems. Desmond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions.
You'll need to contact D.E. Shaw Research directly to obtain a copy of the academic version. Download and extract to a sensible location (e.g.,
/usr/local/src/DESMOND/Desmond-version), and begin the non-trivial install process.
Note the following from the
Unfortunately, the Desmond software distribution is not provided in a form that lends itself to easy compilation and installation. The reason for this is that internally DESRES uses a custom build environment that we have not been able to make available in this release, though it may be available later.
We have also not yet found time to create a more conventional build environment based on generally available tools (for example, the GNU autotools system). It is possible that this will be done for a future release of the software.
They're not kidding either. But rather than massive editing of the GNU Makefile, let's try to get around heavy editing of the file by establishing prefixes.
module load openmpi-gcc/1.3.2
module load gcc/4.1.2
module load python/2.5.1-gcc
module load boost/1.37.0-gcc
make -f GNUmakefile MPI=openmpi PYTHON_PREFIX=/usr/local/python/2.5.1-gcc OPENMPI_PREFIX=/usr/local/openmpi/1.3.2-gcc BOOST_PREFIX=/usr/local/boost/1.37.0-gcc VMD_PREFIX=/usr/local/vmd/1.8
.6 NUMPY_PREFIX=/usr/local/python/2.6.1-gcc BOOST_SERIALIZATION=boost_serialization-gcc41-mt BOOST_IOSTREAMS=boost_iostreams-gcc41-mt BOOST_INCL=/usr/local/boost/1.37.0-gcc/include/boost-1
_37/ PYTHON_INCL=/usr/local/python/2.5.1-gcc/include/python2.6 PYTHON_VERSION=2.5.1 BOOST_SUFFIX=-gcc41-mt
This build process will create the necessary files under
objs/Linux/x86_64/gcc-4.1.2. Change to that directory and copy the files to the appropriate directory (
cp -r /usr/local/desmond/188.8.131.52/) and create the appropriate module files.