[gmx-users] genbox + python bug?

[Mark Abraham]

On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo <marcelodepolo at gmail.com>
wrote:

> Hey,
>
> I have a python script running gmx commands (version 4.6.7) until the
> following:
>
>
>
> *if systype == 'system_1' or systype == 'system_2':    genboxcommand =
> "aprun -n 1 genbox_mpi -cs spc216.gro -cp " + prefix + ".min0.gro -p " +
> prefix + ".top -o " + prefix + ".wat.gro -maxsol " + str(water+ion) + ""
> os.system(genboxcommand)*
>
> And I get the following:
>
>
> *Invalid command line argument:--cp*
>
> As you can see, the -cp flag is correct at the command, but inside the
> script it is read as '--cp' for some reason. Also, other gmx commands run
> just fine before the crash. This might be a synergetic bug from python and
> genbox?
>
> Does anyone has a suggestion?
>

I'd actually suspect aprun of over-stepping its bounds - I seem to recall
some issue like this reported. Anyway, it is useless to run genbox with MPI
(and generally useless to do so in a workflow that needs to run mdrun on a
machine where aprun would be used, where your compute resources are lying
idle while genbox and friends do string processing and file I/O...), so I'd
either do my non-mdrun processing separately, or via a version of GROMACS
that is not compiled to run with MPI. Perhaps you can get away with just
running genbox_mpi on its own, YMMV.

Mark


> --
> Marcelo Depólo Polêto
> B.Sc. Biochemistry - University of Viçosa (Brazil)
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