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Pawel Pomorski

High Performance Computing Programming Specialist

University of Waterloo

User:Ppomorsk/Workspace

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