Thanks for the insights, Mark. It was a 'aprun' issue. When I remove it from the command, everything worked out.
-- Marcelo 2015-03-13 14:10 GMT-03:00 Mark Abraham <mark.j.abra...@gmail.com>: > On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo <marcelodep...@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) > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.