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
  

[1]	Wikipedia contributors. (2019a, September 11). Charm++. Retrieved December 11, 2019, from https://en.wikipedia.org/wiki/Charm%2B%2B