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m (NAMD instructions)
m (NAMD instructions)
Line 36: Line 36:
  
 
This compile was tested on monk using default settings on Sept. 6, 2012.
 
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  
 
  tar xvfz NAMD_2.9_Source.tar.gz  
Line 55: Line 61:
 
  tar xvf charm-6.4.0.tar  
 
  tar xvf charm-6.4.0.tar  
 
  cd charm-6.4.0
 
  cd charm-6.4.0
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/sharcnet/intel/12.1.3/icc/composer_xe_2011_sp1.9.293/compiler/lib/intel64
 
 
  
 
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
cd mpi-linux-x86_64/tests/charm++/megatest
+
 
make pgm
+
mpirun -n 4 ./pgm
+
cd ../../../../..
+
  
  
Line 71: Line 72:
 
  cd Linux-x86_64-icc
 
  cd Linux-x86_64-icc
 
  make
 
  make
 +
 +
 +
Test charm:
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 +
From the directory charm is in,
 +
cd architecture_directory/tests/charm++/megatest
 +
make pgm
 +
mpirun -n 4 ./pgm

Revision as of 12:44, 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

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