Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6

  • Compiler: GCC \(\boldsymbol{\ge}\) 7.4.

  • Requirements:

    • CHARM++ \(\boldsymbol{\ge}\) 6.8.2 with GCC 7.4.

    • CUDA 10.1 (Optional).

Build process

  1. Download NAMD from the official website, you should create an account and agree the license term.

  2. Decompress the tar file.

    tar xfz NAMD_2.13_Source.tar.gz
cd NAMD_2.13_Source

  3. Compile CHARM++.

    Charm++ [1] is a parallel object-oriented programming language based on C++ and developed in the Parallel Programming Laboratory at the University of Illinois at Urbana–Champaign. Charm++ is designed with the goal of enhancing programmer productivity by providing a high-level abstraction of a parallel program while at the same time delivering good performance on a wide variety of underlying hardware platforms.

    1. Decompress it (the namd source files contains the needed source files of CHARM).

      tar xf charm-6.8.2.tar
cd charm-6.8.2

    2. Compile it. The command structure is build <target> <version> <options> [charmc-options ...]

    ## To compile NAMD with CUDA
./build charm++ multicore-linux-x86_64 smp gcc --with-production

## To compile NAMD with MPI
./build charm++ mpi-linux-x86_64 mpicxx gcc --with-production

  4. Configure the compilation.

    ## To compile NAMD with CUDA
./config Linux-x86_64-g++ --charm-arch multicore-linux-x86_64 --with-cuda --cuda-prefix /path/to/cuda/10.1/

## To compile NAMD with MPI
./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64-mpicxx

  5. Compile NAMD.

    cd Linux-x86_64-g++
make -j 4

Module files

  • NAMD with CUDA

    2.13-gcc_CUDA
    #%Module1.0####################################################################
##
## module load namd/2.13-gcc_CUDA
##
## /share/apps/modules/namd/2.13-gcc_CUDA
## Written by Manuela Carrasco Pinzon
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using NAMD 2.13 with CUDA\
     	    \nin the shared directory /share/apps/namd/2.13/2.13-gcc_CUDA\
	    	   \nbuilded with GCC 7.4 and CUDA 10.1"
}

module-whatis "(Name________) namd"
module-whatis "(Version_____) 2.13-gcc_CUDA"
module-whatis "(Compilers___) gcc 7.4 and cuda 10.1"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/namd/2.13/2.13-gcc_CUDA/
set         version       2.13-gcc_CUDA
set         sys           x86_64-redhat-linux

conflict mafft
module load gcc/7.4.0
module load cuda/10.1


prepend-path	PATH			$topdir/bin

  • NAMD with MPI

    2.13-gcc_MPI
    #%Module1.0####################################################################
##
## module load namd/2.13-gcc_MPI
##
## /share/apps/modules/namd/2.13-gcc_MPI
## Written by Manuela Carrasco Pinzon
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using NAMD 2.13 with MPI\
     	    \nin the shared directory /share/apps/namd/2.13/2.13-gcc_MPI\
	    	   \nbuilded with GCC 7.4 and OpenMPI 1.10.7"
}

module-whatis "(Name________) namd"
module-whatis "(Version_____) 2.13-gcc_MPI"
module-whatis "(Compilers___) gcc 7.4 and OpenMPI 1.10.7"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/namd/2.13/2.13-gcc_MPI/
set         version       2.13-gcc_MPI
set         sys           x86_64-redhat-linux

conflict mafft
module load gcc/5.4.0
module load openmpi/1.10.7_gcc-5.4.0


prepend-path	PATH			$topdir/bin