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m (NAMD instructions)
m (NAMD instructions)
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== NAMD instructions ==
 
== NAMD instructions ==
  
This compile was tested on monk using default settings on Sept. 6, 2012.
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Preliminaries:
 
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It appears setting this environment variable is needed to make the executables find all the libraries at runtime:
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 +
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.
  
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Get all the required source files:
  
 
  tar xvfz NAMD_2.9_Source.tar.gz  
 
  tar xvfz NAMD_2.9_Source.tar.gz  
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   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 and test charm (export LD_LIBRARY_PATH is needed to find libcilkrts.so.5 library at runtime)
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 +
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.
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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
  
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Compile charm - MPI-SMP build:
 +
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 smp --no-build-shared --with-production
  
 +
Compile charm - threaded build:
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./build charm++ multicore-linux64 --no-build-shared  --with-production
  
  
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Test charm:
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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

User:Ppomorsk/Workspace

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