[gmx-users] Segmentation fault with gromacs executables

[Mark Abraham]

On 26/04/2010 2:45 PM, Sikandar Mashayak wrote:
> Hi
>
> I am facing this strange problem of segmentation fault while executing
> mpi-enabled gromacs executables on remote server.
>
> I source GMXRC, so that I can access executables from any directory
> without specifying full path of gromacs/bin. And when I execute, say
> grompp, I get segmentation fault.

Use "which grompp" and/or "echo $PATH" just before they execute to be 
sure which version you're getting.

> But when I use the same command by specifying full path
> /home/.../gromacs/bin/grompp , it executes without any issues!!

It sounds like some kind of dynamic linking issue. Perhaps 
LD_LIBRARY_PATH or LD_RUN_PATH needs to be configured differently.

Talk to your system admins - this issue will very likely not be specific 
to GROMACS.

Mark