[gmx-users] Segmentation fault with gromacs executables

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 26 07:56:51 CEST 2010

On 26/04/2010 3:44 PM, Mark Abraham wrote:
> 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.

Of course, there's no need to execute grompp on the remote - only mdrun 
is MPI-aware, so you could/should do your preparation on your local 
machine, and merely run the MPI-enabled mdrun on the remote.


>> 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
> Mark

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