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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