Desmond

Owned by Indy Siva
Dec 10, 2015
4 min read

Desmond: Desmond is a software package developed at D.E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on parallel systems that is available as part of Schrodinger or as a stand-alone
package. It is the backend to the MD code in Schrodinger Software and uses Schrodinger force fields, hence it has advantages over NAMD in that the structure files do not have to be proteins

http://www.deshawresearch.com/

http://www.deshawresearch.com/downloads/download_desmond.cgi/

Installation Directory

Module file

module load desmond/3.0.3.1

Sample PBS script

#!/bin/bash -l
#PBS -m abe
### Mail to user
#PBS -M <YourEmail>@griffith.edu.au
#PBS -V
### Job name
#PBS -N  Desmond
#PBS -q workq
#PBS -l walltime=12:00:00
### Number of nodes:Number of CPUs:Number of threads per node
#PBS -l select=1:ncpus=1:mem=2gb:mpiprocs=1
###$PBS_NODEFILE is a node-list file created with select and mpiprocs options by PBS
###### The number of MPI processes available is mpiprocs * nodes (=NPROCS)
NPROCS=1
#PBS -j oe
# This job's working directory
echo Working directory is $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
source $HOME/.bashrc
module load desmond/3.0.3.1
#module list
echo "Starting job"
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
#echo This jobs runs on the following processors:
#echo `cat $PBS_NODEFILE`
/sw/openMPI/1.4.3-gnu/bin/mpirun -machinefile $PBS_NODEFILE -np $NPROCS  env PATH=$PATH  env LD_LIBRARY_PATH=$LD_LIBRARY_PATH desmond <inputdata>
echo "Done with job"

Build Prerequisites

Intel or AMD 32- or 64-bit platform
version 2.6.27 of the Linux kernel
the GNU lib C version 2.5
AMD, Intel i686 and x86_64 systems

Desmond requires several third-party software packages
======================================================

1. SCONS SCONS Open Source software construction tool (http://www.scons.org : Version 1.3, and 2.0 have been tested and are known
to work)

(we will try with scons --version scons-2.1.0)

It is a python runtime env..

module load python/2.7.1

which scons
/sw/python/2.7.1/bin/scons

2. GNU GCC only the specific version of GNU GCC (http://gcc.gnu.org) version 4.5.1 is supported

(In order to build GCC 4.5.1, you will also need to build and install several
other packages: GMP 4.3.2 (http://gmplib.org/), MPFR 2.4.2
(http://www.mpfr.org), and MPC 0.8.1 (http://www.multiprecision.org); again,
other versions of these software packages may work with GCC 4.5.1, but these
are the ones we have tested.)

(We will try with version: gcc version 4.4.5 20110214 (Red Hat 4.4.5-6) (GCC))

3. Open MPI
the only version of MPI supported is Open MPI 1.4.3
It is not necessary to compile Desmond to run in parallel, in fact Desmond
applications support parallel systems through the use of a dynamically loaded
plug-in and the default communicator built into the software will run
serially.

module load mpi/openMPI/1.4.3-gnu

4. Boost
Desmond requires version 1_45_0 or greater of the Boost library
(http://www.boost.org);

Several boost libraries are
used by Desmond on Linux systems: filesystem, boost.python, and optionally the
iostreams and the thread libraries.

module load boost/ser/1.4.8
OR
module load boost/mpi/1.4.8

5. Python
~~~~~~

Desmond supports only version 2.7.x of Python (http://www/python.org),
specifically version 2.7.1. You will need to install that version of Python
to build Desmond and execute Desmond Python scripts. Other versions of Python
will possibly work, but we have only tested Python 2.7.1; almost certainly
Python 3 will not work.

module load python/2.7.1

6. Numpy
~~~~~

Several Desmond Python scripts use version 1.5.0 of Numpy

module load python/2.7.1

7. ANTLR
~~~~~

The enhanced sampling Desmond extension requires the use of use of ANTLR
(http://www.antlr.org) version 3.1.3.

Python runtime env: module load python/2.7.1

8. VMD
~~~

This release of Desmond no longer requires that the user compile plugins for
VMD that enable reading and writing Desmond trajectories and DMS and Maestro
structure files. Such support is available natively in VMD 1.9.0 and later.

The VMD software is available from the Theoretical and Computational
Biophysics Group at the University of Illinois at Urbana-Champaign. Register
at http://www.ks.uiuc.edu/Research/vmd/alpha to have access to the alpha
versions.

module load vmd/1.9.1a17

Installation

  • Build Desmond

build Desmond using the following command line:

$ scons --user-conf=<conf file>

where <conf file> is a python script that customizes the SCONS build environment for your system. The $DESMOND_PREFIX/share directory contains a sample configuration file.

cd share
user-conf.sample.py user-conf.gowonda.py

vi user-conf.gowonda.py

At a minimum, to get a single node version of Desmond you will have to give the location of the Boost include and library
files. To build a multi-node MPI version, you will have to give the same path information for MPI. Similarly for Python.

Build Desmond with scons --user-config=share/user-conf.gowonda.py

changes that were made to share/user-conf.gowonda.py are:

cd /sw/desmond/3.0.3.1/Desmond-3.0.3.1
vi share/user-conf.gowonda.py

  diff  share/user-conf.gowonda.py share/user-conf.sample.py
58c58
<     boost_prefix =  '/sw/library/boost/1.4.8/openmpi'
---
>     boost_prefix =  '/proj/desres/root/Linux/x86_64/boost/1_45_0-21A/Release'
65c65
<     mpi_prefix = '/sw/openMPI/1.4.3-gnu'
---
>     mpi_prefix = '/proj/desres/root/Linux/x86_64/openmpi/1.5.3-23'
67c67
<     MPI_LDFLAGS = "-L%s/lib64 -Wl,-rpath,%s/lib64" % (mpi_prefix,mpi_prefix)
---
>     MPI_LDFLAGS = "-L%s/lib -Wl,-rpath,%s/lib" % (mpi_prefix,mpi_prefix)
71c71
<     WITH_INFINIBAND = 0
---
>     WITH_INFINIBAND = 1
79,80c79,80
<     python_prefix = '/sw/python/2.7.1-shared'
<     numpy_prefix = "/sw/python/2.7.1/lib/python2.7-shared/site-packages"
---
>     python_prefix = '/proj/desres/root/Linux/x86_64/Python/2.7.1-06A'
>     numpy_prefix = "/proj/desres/root/Linux/x86_64/numpy/1.5.0-28A/lib/python2.7/site-packages"
82c82
<     EXTRA_INCLUDE_PATH += ' %s/include/python2.7-shared' % python_prefix
---
>     EXTRA_INCLUDE_PATH += ' %s/include/python2.7' % python_prefix

cd /sw/desmond/3.0.3.1/src
module load python/2.7.1-shared
module load mpi/openMPI/1.4.3-gnu
module load boost/ser/1.4.8-python-shared
module load vmd/1.9.1a17
module load compilers/gcc-4.5.1
scons --user-config=share/user-conf.gowonda.py 2>&1 | tee build_log.txt

This builds.... :

g++ -o objs/Linux/x86_64/gcc-4.5.1/Release/unit-tests/ut_printfCutils -z origin -g -pthread -Wl,-rpath=\$ORIGIN/../lib -Wl,-rpath=\$ORIGIN/../../lib -Wl,-rpath=\$ORIGIN/../../../lib -Wl,-rpath=/sw/library/boost/1.4.8/openmpi/lib -Wl,-rpath=/sw/python/2.7.1-shared/lib -Wl,-rpath=/sw/python/2.7.1/lib/python2.7-shared/site-packages/numpy/core objs/Linux/x86_64/gcc-4.5.1/Release/other/printfutils/ut_printfCutils.os -Lobjs/Linux/x86_64/gcc-4.5.1/Release/lib -L/sw/library/boost/1.4.8/openmpi/lib -L/sw/python/2.7.1-shared/lib -L/sw/python/2.7.1/lib/python2.7-shared/site-packages/numpy/core -ldl -lpthread -lboost_filesystem -lboost_system -lboost_python -lpython2.7 -lDesmond
g++ -o objs/Linux/x86_64/gcc-4.5.1/Release/unit-tests/ut_printfutils -z origin -g -pthread -Wl,-rpath=\$ORIGIN/../lib -Wl,-rpath=\$ORIGIN/../../lib -Wl,-rpath=\$ORIGIN/../../../lib -Wl,-rpath=/sw/library/boost/1.4.8/openmpi/lib -Wl,-rpath=/sw/python/2.7.1-shared/lib -Wl,-rpath=/sw/python/2.7.1/lib/python2.7-shared/site-packages/numpy/core objs/Linux/x86_64/gcc-4.5.1/Release/other/printfutils/ut_printfutils.os -Lobjs/Linux/x86_64/gcc-4.5.1/Release/lib -L/sw/library/boost/1.4.8/openmpi/lib -L/sw/python/2.7.1-shared/lib -L/sw/python/2.7.1/lib/python2.7-shared/site-packages/numpy/core -ldl -lpthread -lboost_filesystem -lboost_system -lboost_python -lpython2.7 -lDesmond
scons: done building targets.
You have new mail in /var/spool/mail/root

After you have satisfied yourself that Desmond's simulator has built
correctly, you can install Desmond and its affiliated software by typing

  $ scons --user-conf=<conf file> install PREFIX=$INSTALL_PREFIX

e.g: 

scons --user-config=share/user-conf.gowonda.py install PREFIX=/sw/desmond/3.0.3.1 2>&1 | tee build_install_log.txt

  where INSTALL_PREFIX is the name of a directory where Desmond shoul

Manuals

Tutorial: http://df.arcs.org.au/quickshare/3f43f139fdcbf7a7/Desmond_Tutorial-0.6.pdf
User Guide: http://confluence.rcs.griffith.edu.au:8080/download/attachments/29458675/Desmond_Users_Guide-0.5.3.pdf