How to install and run NAMD

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How to install and run NAMD

Postby shainer on Tue Dec 14, 2010 11:10 pm

Download NAMD 2.7b3 at: http://www.ks.uiuc.edu/Development/Down ... eName=NAMD
Download the ApoA1 benchmark from: http://www.ks.uiuc.edu/Research/namd/ut ... oa1.tar.gz
Download FFTW from: http://www.fftw.org/
Download TCL from: http://www.tcl.tk/

Extract NAMD
% tar xvfz NAMD_2.7b3_Source

Extract Charm, FFTW, TCL into the NAMD source directory, and rename FFTW and TCL after they are extracted.
% cd NAMD_2.7b3_Source
% tar xvf charm-6.2.1.tar
% tar xvfz tcl-linux-x86_64.tar.gz
% mv linux-x86_64 tcl
% tar xvfz fftw-linux-x86_64.tar.gz
% mv linux-x86_64 fftw
Build Charm from mvapich2-1.5
% cd charm-6.2.1
% env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared --with-production

Build NAMD with MPI support
% cd /path/to/NAMD_2.7b3_Source
% ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
% cd Linux-x86_64-g++
% make

Extract and run the ApoA1 benchmark with mvapich2-1.5:
% tar xvfz apoa1.tar.gz
% mpdboot ~/hostfile –n <number_of_host>
% charmrun –n <np> ./namd2 apoa1/apoa1.namd2
% mpdallexit
shainer
 
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Joined: Thu Jun 11, 2009 8:31 pm

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