shaileshp51/centre

A tool for configurational entropy from MD simulation data

ABOUT

The CENTRE is a parallel and scalable tool for estimating Configurational entropy from MD simulation data using Information Theoretic methods:

• Mutual Information Expansion (MIE),
• Maximum Information Spanning Tree (MIST),
• Approximate Mutual Information Expansion (or Neighbor Approximated MIE i.e. A-MIE),
• Neighbor Approximated Maximum Information Spanning Tree (A-MIST).

This program accepts BOND/ANGLE/TORSION (BAT) format trajectory of the system for which the entropy is to be computed. An auxilary program cart2bat.py shipped with pycentre (https://github.com/shaileshp51/pycentre) python package can be used to generate a BAT format file from topology and trajectory files generated using popular Molecular Dynamics programs e.g. AMBER, NAMD, CHARMM, ACEMD, GROMACS.

DEPENDENCIES

NetCDF C Library version >= 4.6, with support for NETCDF4, NC_64BIT_OFFSET and NC_UBYTE.

NetCDF library can be installed using following commands on ubuntu based Linux Distributions based on Ubuntu 18.04 or higher.

        sudo apt install netcdf-bin libnetcdf11 libnetcdf-dev libhdf5-10 libhdf5-dev

NetCDF library source-code distribution can be ontained from following http://github.com/Unidata/netcdf-c and build following instructions provided on

INSTALL

Extract the distribution tar file using

tar -xvf centre-v0.1.2-b.tar.bz

change directory to the extracted directory centre-0.1.0 cd centre-0.1.0

On LINUX

Check the location of netcdf include and library file. In some of the Linux Distributions, these files are no longer installed in default locations i.e. /usr/local/include and /usr/local/lib respectively. However, the configuration searches for them in default location and fails. In such a case, try finding the locations of these files using command:

nc-config --all

It should print the detials of netcdf configuration on your system as below:

This netCDF 4.7.3 has been built with the following features: 

  --cc            -> /usr/bin/cc
  --cflags        -> -I/usr/include -I/usr/include/hdf5/serial
  --libs          -> -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf
  --static        -> -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl
  
  ... many more lines

As above we see the include files are are in /usr/include and lib file in /usr/lib/x86_64-linux-gnu. If so is the case please add

LDFLAGS="-L/usr/lib/x86_64-linux-gnu"

after --prefix option on on the ./configure command below.

Do an OpenMP thread based parallel build

./configure --prefix=`pwd`
make install

This step will create a file centre_OMP in bin folder, check with

ls bin/centre_OMP

Do an MPI based proecess+thread based hybrid parallel build. This build requires mpi headers and mpic++ processor capable to compile c++11 code

./configure --enable-mpi --prefix=`pwd`
make install

This step will create a file centre_OMPMPI in bin folder, check with

ls bin/centre_OMPMPI

On macOS

On macOS using clang++ compiler Do an OpenMP thread based parallel build

./configure --prefix=`pwd` CXX="clang++"
make install LIBS=-lomp

This step will create a file centre_OMP in bin folder, check with

ls bin/centre_OMP

Do an MPI based proecess+thread based hybrid parallel build. This build requires mpi headers and mpic++ processor capable to compile c++11 code

export OMPI_CXX=clang++
./configure --enable-mpi --prefix=`pwd`
make install LIBS=-lomp

This step will create a file centre_OMPMPI in bin folder, check with ls bin/centre_OMPMPI

USAGE

USAGE: 
centre_OMP [OPTION] -i <input-file>
Optional arguments for the CENTRE v0.1.2-b
    -h  --help       print this help message and exit
    -s  --sample     print a sample input file with description of parameters and exit
    -c  --cite       print citation details and exit
    -O               overwite any already existing files in output directory

Running MPI+OMP hybrid build

USAGE: 
mpirun -n $NUM_PROC centre_OMPMPI [OPTION] -i <input-file>
Optional arguments for the CENTRE v0.1.2-b
    -h  --help       print this help message and exit
    -s  --sample     print a sample input file with description of parameters and exit
    -c  --cite       print citation details and exit
    -O               overwite any already existing files in output directory

TERMS & CONDITIONS

CENTRE Copyright (C) 2020 Shailesh Kumar Panday This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License version 3 as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.