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(NAMD instructions: update to CUDA 5.5)
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Configure NAMD and compile (with CUDA support enabled)
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/4.1/cudatoolkit_4.1.28_linux_64_rhel6
  ./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
  cd Linux-x86_64-icc

Revision as of 13:07, 20 February 2014

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.

tar xvfz NAMD_2.9_Source.tar.gz 
cd NAMD_2.9_Source

Compile and test charm (export LD_LIBRARY_PATH is needed to find library at runtime)

tar xvf charm-6.4.0.tar 
cd charm-6.4.0
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared --with-production
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/sharcnet/intel/12.1.3/icc/composer_xe_2011_sp1.9.293/compiler/lib/intel64
cd mpi-linux-x86_64/tests/charm++/megatest
make pgm
mpirun -n 4 ./pgm
cd ../../../../..

Download and install precompiled TCL and FFTW libraries: (working in NAMD source directory)

 tar xzf fftw-linux-x86_64.tar.gz
 mv linux-x86_64 fftw
 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

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