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

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 31 2012 - 00:53:47 CST

Hi,
sorry if that reply isn't really helpful but I can't hold it:

Unbelievable! Where's the camera?

Axel is right, like always, you need to get a little more motivation to
understand what you are doing. IMHO you should better use a precompiled NAMD
from the Homepage, and then post the errors you might get. Although I can't
imagine what kind of errors can occur there, but let's see.

Good luck

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Axel Kohlmeyer
> Gesendet: Montag, 30. Januar 2012 19:25
> An: Shyno Mathew
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: Installing NAMD on a 64-bit linux (NVIDIA CUDA)
>
> On Mon, Jan 30, 2012 at 1:15 PM, Shyno Mathew <sm3334_at_columbia.edu>
> wrote:
> > Hi,
> > I have problems while compiling NAMD. Initially I tried installing
> version
> > 2.8: Linux-x86_64-CUDA (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.
>
> that is bad.
> the error message indicates that likely the mpirun you are using is
> not matching the MPI library that you are using.
> the same will happen to other programs including NAMD.
> you should resolve that first.
>
>
> > 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
>
> you cannot swap csh to bash.
> they have a different syntax.
>
>
> > 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.
>
> you need to follow the instructions
> more closely and find a (local) expert
> to explain the things to you that don't
> work (they have nothing to do with NAMD).
>
> compiling software requires at least a minimal
> understanding of the tools that you are using,
> and even more so, if you are ignoring or changing things.
>
> ..there ain't no escape from the blues...
>
> axel.
>
> > Sincerely,
> > Shyno Mathew
> > PhD student
> > Department of Chemical Engineering
> > Columbia University
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

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