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== NAMD instructions == | == NAMD instructions == | ||
| − | + | Preliminaries: | |
| − | + | ||
| − | + | ||
| + | module unload openmpi | ||
| + | module load openmpi/intel/1.7.4 | ||
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/sharcnet/intel/12.1.3/icc/composer_xe_2011_sp1.9.293/compiler/lib/intel64 | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/sharcnet/intel/12.1.3/icc/composer_xe_2011_sp1.9.293/compiler/lib/intel64 | ||
| + | OpenMPI 1.7.4 is compiled with CUDA support. Environment variable is needed to locate all the libraries at runtime. | ||
| + | Get all the required source files: | ||
tar xvfz NAMD_2.9_Source.tar.gz | tar xvfz NAMD_2.9_Source.tar.gz | ||
| Line 57: | Line 59: | ||
mv tcl8.5.9-linux-x86_64 tcl | mv tcl8.5.9-linux-x86_64 tcl | ||
mv tcl8.5.9-linux-x86_64-threaded tcl-threaded | mv tcl8.5.9-linux-x86_64-threaded tcl-threaded | ||
| − | Compile | + | |
| + | Compile charm, choosing which parallelization is to be used (threaded, MPI, MPI-SMP): | ||
tar xvf charm-6.4.0.tar | tar xvf charm-6.4.0.tar | ||
cd charm-6.4.0 | cd charm-6.4.0 | ||
| − | Compile charm - MPI build | + | Compile charm - MPI build: |
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared --with-production | env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared --with-production | ||
| + | Compile charm - MPI-SMP build: | ||
| + | env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 smp --no-build-shared --with-production | ||
| + | Compile charm - threaded build: | ||
| + | ./build charm++ multicore-linux64 --no-build-shared --with-production | ||
| Line 74: | Line 81: | ||
| − | Test charm: | + | Test charm if needed: |
From the directory charm is in, | From the directory charm is in, | ||
Revision as of 12:50, 27 February 2014
Pawel Pomorski
High Performance Computing Programming Specialist
University of Waterloo
Software which I help maintain
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NAMD instructions
Preliminaries:
module unload openmpi module load openmpi/intel/1.7.4 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/sharcnet/intel/12.1.3/icc/composer_xe_2011_sp1.9.293/compiler/lib/intel64
OpenMPI 1.7.4 is compiled with CUDA support. Environment variable is needed to locate all the libraries at runtime.
Get all the required source files:
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 charm, choosing which parallelization is to be used (threaded, MPI, MPI-SMP):
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
Compile charm - MPI-SMP build:
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 smp --no-build-shared --with-production
Compile charm - threaded build:
./build charm++ multicore-linux64 --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 if needed:
From the directory charm is in,
cd architecture_directory/tests/charm++/megatest make pgm mpirun -n 4 ./pgm