I had the same problem, but I had success when I read the error file.<br><br>I'm using Python and subprocess.call. This method has some parameters and one is a file that receives the error message when the program fails. Furthermore the python official documentation (<a href="http://docs.python.org/library/subprocess.html">http://docs.python.org/library/subprocess.html</a>) there is the link <a href="http://developer.spikesource.com/wiki/index.php/How_to_invoke_subprocesses_from_Python">http://developer.spikesource.com/wiki/index.php/How_to_invoke_subprocesses_from_Python</a><br>
<br>However, it's necessary look for the words fatal or error in this file.<br><br>Unfortunately, my Python script has some classes and if I send to you, the code will be enormous, because I use these classes to manager the execution of others programs. Moreover, I can help you, if necessary.<br>
<br>I hope that this email helped you.<br><br>Cheers, <br><br>--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>
Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br">http://laips.sel.eesc.usp.br</a><br>Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218">http://lattes.cnpq.br/1025157978990218</a><br>
<br><br><div class="gmail_quote">On Mon, Jul 20, 2009 at 7:32 PM, Justin MacCallum <span dir="ltr"><<a href="mailto:justin.maccallum@me.com">justin.maccallum@me.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi All,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Cheers,<br>
Justin<br>
----<br>
<br>
Justin MacCallum<br>
Post Doctoral Fellow<br>
Department of Pharmaceutical Chemistry<br>
University of California San Francisco<br>
<br>
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