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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)