[gmx-users] Segmentaion fault error- installing gromacs-3.3.1 on MacOSX

Ibrahim M. Moustafa I.moustafa at psu.edu
Sat Dec 2 03:15:18 CET 2006

Hi gmx-users,

    I have a little problem with gromacs-3.3.1 installed on a Mac-OSX.
After installation (either building the package myself as instructed, 
or using a binary form GROMACS web site) I could not run any program 
with just typing the name on the xterm!
for example, issuing "pdb2gmx" command line gives an error message 
"segmentation fault". However, typing the whole path name 
"$GMXBIN/pdb2gmx or any other modules " works fine.
The variables for GROMACS are configured after the installation. My 
.cshrc sources from the GMXRC.csh and the variables are defined; the 
PATH includes the $GMXBIN also.
For the moment, I'm using alias to define the whole path for GROMACS 
programs to run; though, this a bit annoying.

    I posted this problem in CCL and M.L. Dodson, replied with some 
explanation for this weird problem:

  " Ahh... Think I have it.  Looking at the source code on my BSD Unix
box, I see in src/gmxlib/copyrite.c the following:

void CopyRight(FILE *out,char *szProgram)
   /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
    * name of a file. Otherwise, we won't be able to find the library dir.
#define NCR (int)asize(CopyrightText)
#define NGPL (int)asize(GPLText)

   char buf[256],tmpstr[1024];

   char *ptr;

   int i;


So I was right, it does use argv[0] for something: finding its
library directory."

   I wonder if there is a quick fix for this in the code, so I can 
run the programs by just typing the name without need for the whole path!

   A question here: if Dodson is right, why the programer wrote the 
code this way! is there any advantage?

P.S. I have no previous experience with GROMACS


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