[gmx-developers] exit codes

Justin MacCallum justin.maccallum at me.com
Tue Jul 21 00:32:49 CEST 2009

Hi All,

I'm writing some scripts to automate setting up and running gromacs  
simulations and I have run into the minor problem in that sometimes  
the gromacs tools do not give a useful exit code. For example, calling  
any of the tools with an option that they don't understand (e.g.  
"editconf -xxxxx ...")  gives a return code of zero. I haven't checked  
thoroughly to see in what situations the exit code is set, but ideally  
the command line tools should have an exit code of zero if everything  
completed successfully and non-zero if something went wrong. Checking  
the exit code is much simpler than trying to search for error strings  
in the standard output.

I looked at the code, but I'm not very familiar with gromacs internals  
and I couldn't figure out why this wasn't working correctly. This is  
with the latest git running on OS X 10.5. I'm using subprocess.Popen  
in python to execute the gromacs tools.


Justin MacCallum
Post Doctoral Fellow
Department of Pharmaceutical Chemistry
University of California San Francisco

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