Pawel Pomorski
High Performance Computing Programming Specialist
University of Waterloo
Software which I help maintain
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NAMD instructions
This compile was tested on monk using default settings on Sept. 6, 2012.
It appears setting this environment variable is needed to make the executables find all the libraries at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/sharcnet/intel/12.1.3/icc/composer_xe_2011_sp1.9.293/compiler/lib/intel64
tar xvfz NAMD_2.9_Source.tar.gz cd NAMD_2.9_Source
Download and install precompiled TCL and FFTW libraries: (working in NAMD source directory)
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
Compile and test charm (export LD_LIBRARY_PATH is needed to find libcilkrts.so.5 library at runtime)
tar xvf charm-6.4.0.tar cd charm-6.4.0
Compile charm - MPI build.
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared --with-production
Configure NAMD and compile (with CUDA support enabled)
./config Linux-x86_64-icc --charm-arch mpi-linux-x86_64 --with-cuda --cuda-prefix /opt/sharcnet/cuda/5.5.22/toolkit/ cd Linux-x86_64-icc make
Test charm:
From the directory charm is in,
cd architecture_directory/tests/charm++/megatest make pgm mpirun -n 4 ./pgm