Re: [gmx-users] genbox + python bug?
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.
Re: [gmx-users] genbox + python bug?
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.
[gmx-users] genbox + python bug?
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? -- 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.
