How to compile NAMD

Instructions to compile NAMD:

Extract the package and go inside to extract charm

tar xf NAMD_2.11_Source.tar.gz
cd NAMD_2.11_Source
tar xf charm-6.7.0.tar
  • Download and install TCL and FFTW.

Please see the release notes for the appropriate version of these libraries. fftw

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

tcl

wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
tar xzf tcl*-linux-x86_64.tar.gz
mv tcl*-linux-x86_64 tcl

tcl threaded

wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
tar xzf tcl*-linux-x86_64-threaded.tar.gz
mv tcl*-linux-x86_64-threaded tcl-threaded
  • Build Charm++.

The build script has an interactive mode, you can also specify options in the command line as explained below.

cd charm-6.7.0
./build charm++ {arch} {C compiler} {Fortran compiler} {other options}

Example. Charm++ build for single-node configuration using gcc compilers with all production optimizations.

./build charm++ multicore-linux64 gcc --with-production
  • Build NAMD.

Make sure you're in the main NAMD directory, then configure and run make:

./config {namd-arch} --charm-arch {charm-arch} {opts}
cd {namd-arch}
make

Example. NAMD compilation for single-node configuration using gcc compilers with all production optimizations.

./config Linux-x86_64-g++ --charm-arch multicore-linux64-gcc
cd Linux-x86_64-g++
make -j8

References: http://www.nvidia.com/object/gpu-accelerated-applications-namd-installation.html

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