1.1 Run NAMD

MPI version was compiled with TCL or FFTW, since Charm++ MPI network layer performs better than the verbs layer, and Intel Omni-Path networks are incompatible with the pre-built ibverbs NAMD binaries.

NAMD MPI binaries may be launched with mpiexec:

• setenv MPI_DSM_VERBOSE 1
• setenv MPI_MEMMAP_OFF true
• mpiexec_mpt -np $npr namd2 conf

1.2 Compile NAMD

The following is the building process.

• tar xzf NAMD_2.13_Source.tar.gz
• cd NAMD_2.13_Source
• tar xf charm-6.8.2.tar
• Build and test the Charm++/Converse library (MPI version):
  • cd charm-6.8.2
  • env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
  • cd mpi-linux-x86_64/tests/charm++/megatest
  • make pgm
  • mpiexec -n 4 ./pgm (run as any other MPI program on your cluster)
  • cd ../../../../..
• Download and install TCL and FFTW libraries: (cd to NAMD_2.13_Source if you’re not already there)
  • wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
  • tar xzf fftw-linux-x86_64.tar.gz
  • mv linux-x86_64 fftw
  • wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
  • wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
  • tar xzf tcl8.5.9-linux-x86_64.tar.gz
  • tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
  • mv tcl8.5.9-linux-x86_64 tcl
  • mv tcl8.5.9-linux-x86_64-threaded tcl-threaded
• Set up build directory and compile:
  • MPI version: ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
  • cd Linux-x86_64-g++
  • gmake -j4 (which should run faster than make)