Installing NAMD on a 64-bit linux (NVIDIA CUDA)

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Mon Jan 30 2012 - 12:15:15 CST

Hi,
I have problems while compiling NAMD. Initially I tried installing version
2.8: Linux-x86_64-CUDA<http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1161>(NVIDIA
CUDA acceleration) as my machine has NVIDIA with CUDA.
Since I got errors, I tried re-installing NAMD from the source code. I
followed the instructions for 64-bit linux workstations.
Still I get the following errors :
1. During the Build and test the Charm++/Converse library (MPI version):
  "mpirun -n 4 ./pgm"

/pgm: error while loading shared libraries: libmpi_cxx.so.0: cannot open
shared object file: No such file or directory
./pgm: error while loading shared libraries: libmpi_cxx.so.0: cannot open
shared object file: No such file or directory
./pgm: error while loading shared libraries: libmpi_cxx.so.0: cannot open
shared object file: No such file or directory
./pgm: error while loading shared libraries: libmpi_cxx.so.0: cannot open
shared object file: No such file or directory

i ignored this and moved on.
2. during compilation
./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
initial error: bash: ./config: /bin/csh: bad interpreter: No such file or
directory
#changed csh to bash
then i got a bunch of errors!

./config: line 2: goto: command not found
./config: line 3: syntax:: command not found

This script will create a build directory for NAMD.

Usage: config [<build_dir>/]<arch>[.comment] [options]

Options (most defaults are set in arch subdirectory):
 --charm-base <Charm++ base build directory containing src>
   (defaults to ./charm-6.3.2 or ./charm)
 --charm-arch <subdirectory of Charm++ base build directory>
  (such as mpi-linux-x86_64-mpicxx or multicore-linux64)
 --charm-opts <options to pass to charmc (quote list)>
 --with-tcl (default) --without-tcl
 --tcl-prefix <directory containing Tcl lib and include>
  (defaults to ./tcl or ~/tcl)
 --with-fftw (default) --without-fftw
 --fftw-prefix <directory containing FFTW 2.1.3 lib and include>
   (defaults to ./fftw or ~/fftw)
 --cxx <C++ compiler command>
 --cxx-opts <C++ compiler options (quote list)>
 --cxx-noalias-opts <C++ compiler options (quote list)>
 --cxx-thread-opts <C++ compiler options (quote list)>
 --cc <C compiler command>
 --cc-opts <C compiler options (quote list)>
 --with-debug (sets all opts to -g)
 --arch-suffix <suffix for NAMD platform printed at startup>
  (the following are experimental features)
 --without-memopt (default) --with-memopt
 --without-cuda (default) --with-cuda
  (do NOT use CUDA-enabled Charm++, NAMD does not need it)
 --cuda-prefix <directory containing CUDA bin, lib, and include>
./config: line 38: syntax error near unexpected token ``uname -s`'
./config: line 38: ` switch ( `uname -s` )'

I am not sure if I need to modify config. Any help will be really
appreciated.

Sincerely,
Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University

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