Dear Christoph, Where is this file or how can I use cg.inverse.gromacs.mdrun.opts? I use "find ~/votca/ -name cg.inverse.gromacs.mdrun.opts" command. There is only one related file, run_gromacs.sh.
Thank you. Best regards, Changwoon Jang On Fri, Jul 22, 2016 at 3:55 PM, Christoph Junghans <[email protected]> wrote: > 2016-07-22 13:09 GMT-06:00 Chang Woon Jang <[email protected]>: > > Dear Christoph, > > > > Thank you for your help. However, I have no problem with the similar > size of > > the system 1300 beads in 5.5x5.5x5.5 box with same parallel condition 16 > > cores. The main difference is the number of bead types (5 bead types > > previous, 7 bead types now-error). > It is the same cutoff? > > > > > How can I modify the mdrun option in votca? In the run.sh file, there is > > only a command "csg_inverse --options settings.xml". I would like to > include > > "-nt 1" in mdrun options. Which file should I take a look for including > this > > option? > Sure, you can add extra options for mdrun in cg.inverse.gromacs.mdrun.opts > > Christoph > > > > Thank you. > > > > Best regards, > > Changwoon Jang > > > > On Fri, Jul 22, 2016 at 12:54 PM, Christoph Junghans <[email protected] > > > > wrote: > >> > >> 2016-07-22 9:24 GMT-06:00 Chang Woon Jang <[email protected]>: > >> > Dear Christoph, > >> > > >> > I run mdrun by hand using "mdrun -v" in the last step (step_001). > >> > > >> > The following error comes out. > >> > > >> > ------------------------------------------------------- > >> > > >> > Program mdrun, VERSION 5.0.7-dev-20151003-1909f2f > >> > > >> > Source code file: > >> > > >> > > /home1/02271/huddack/votca_install/src/gromacs/src/gromacs/mdlib/domdec.c, > >> > line: 6902 > >> > > >> > > >> > Fatal error: > >> > > >> > There is no domain decomposition for 16 ranks that is compatible with > >> > the > >> > given box and a minimum cell size of 1.875 nm > >> > > >> > Change the number of ranks or mdrun option -rdd or -dds > >> > > >> > Look in the log file for details on the domain decomposition > >> > > >> > For more information and tips for troubleshooting, please check the > >> > GROMACS > >> > > >> > website at http://www.gromacs.org/Documentation/Errors > >> > > >> > ------------------------------------------------------- > >> > > >> > > >> > What does this mean for no domain decomposition for 16 ranks. I > actually > >> > do > >> > IBI in Stampede TACC using 16 processor. Does this mean that I need to > >> > reduce the number of process? Would you please give me some comments? > >> Yes, it seems your system is too small to get decomposed in 16 domain. > >> > >> As this is more a gromacs problem, you might want to ask on the > >> Gromacs Users list: [email protected] > >> > >> Christoph > >> > > >> > Thank you. > >> > > >> > Best regards, > >> > Changwoon Jang > >> > > >> > On Fri, Jul 22, 2016 at 10:57 AM, Christoph Junghans > >> > <[email protected]> > >> > wrote: > >> >> > >> >> 2016-07-22 7:46 GMT-06:00 Chang Woon Jang <[email protected]>: > >> >> > Dear Votca Users, > >> >> > > >> >> > > >> >> > I am trying to figure out an error message from IBI run. The error > >> >> > message > >> >> > is > >> >> These aren't errors! > >> >> > > >> >> > > >> >> > > >> >> > This run will generate roughly 152 Mb of data > >> >> > > >> >> > csg_get_property: No value for 'cg.inverse.gromacs.mdrun.command' > >> >> > found > >> >> > in > >> >> > > >> >> > > >> >> > > /work/02271/huddack/CGPROJECT/2_DGEBAJD230/4_CG_PRS_JD2000/tmp/settings_pressure.xml, > >> >> > trying > >> >> > /home1/02271/huddack/votca_install/share/votca/xml/csg_defaults.xml > >> >> > > >> >> > csg_get_property: value for 'cg.inverse.gromacs.mdrun.command' from > >> >> > > /home1/02271/huddack/votca_install/share/votca/xml/csg_defaults.xml: > >> >> > gmx > >> >> > mdrun > >> >> You didn't specify cg.inverse.gromacs.mdrun.command in your xml file > >> >> and hence the default ("gmx mdrun") is used. > >> >> > > >> >> > > >> >> > run_gromacs.sh: No walltime defined, so no time limitation given to > >> >> > gmx > >> >> > mdrun > >> >> Same here, you gave on walltime on the command line (csg_inverse's > >> >> --wall-time options) and hence no time limit is given to mdrun. > >> >> > >> >> > > >> >> > csg_get_property: No value for 'cg.inverse.gromacs.log' found in > >> >> > > >> >> > > >> >> > > /work/02271/huddack/CGPROJECT/2_DGEBAJD230/4_CG_PRS_JD2000/tmp/settings_pressure.xml, > >> >> > trying > >> >> > /home1/02271/huddack/votca_install/share/votca/xml/csg_defaults.xml > >> >> Same here, you did't specify cg.inverse.gromacs.log, so gromacs > output > >> >> is written to the default log file ("inverse.log"). > >> >> > > >> >> > > >> >> > > >> >> > When I have the same grumpp.mdp and different mapping scheme, it > >> >> > works > >> >> > fine. > >> >> > For example, I have 2 bead types of 3 beads in a molecule, and > >> >> > another > >> >> > molecule has 3 bead types of 5 beads. However, when I have 4 bead > >> >> > types > >> >> > of 7 > >> >> > beads, and another molecule has 3 bead types of 5 beads (this is > the > >> >> > same > >> >> > molecule), IBI run has the error above. > >> >> > > >> >> > I do not think that the mapping scheme would result in the error. > >> >> > Please > >> >> > give me some comments. > >> >> The actually error must be somewhere below the lines given above. > >> >> > >> >> My advice, go into the last step dir and run mdrun by hand to see > what > >> >> goes wrong. > >> >> > >> >> Christoph > >> >> > >> >> > > >> >> > Best regards, > >> >> > Changwoon Jang, > >> >> > > >> >> > -- > >> >> > You received this message because you are subscribed to the Google > >> >> > Groups > >> >> > "votca" group. > >> >> > To unsubscribe from this group and stop receiving emails from it, > >> >> > send > >> >> > an > >> >> > email to [email protected]. > >> >> > To post to this group, send email to [email protected]. > >> >> > Visit this group at https://groups.google.com/group/votca. > >> >> > For more options, visit https://groups.google.com/d/optout. > >> >> > >> >> > >> >> > >> >> -- > >> >> Christoph Junghans > >> >> Web: http://www.compphys.de > >> >> > >> >> -- > >> >> You received this message because you are subscribed to the Google > >> >> Groups > >> >> "votca" group. > >> >> To unsubscribe from this group and stop receiving emails from it, > send > >> >> an > >> >> email to [email protected]. > >> >> To post to this group, send email to [email protected]. > >> >> Visit this group at https://groups.google.com/group/votca. > >> >> For more options, visit https://groups.google.com/d/optout. > >> > > >> > > >> > > >> > > >> > -- > >> > Best regards, > >> > Changwoon Jang, > >> > > >> > Postdoctoral Research Fellow > >> > Department of Chemical & Biological Engineering, Drexel University > >> > 3141 Chestnut Street, Philadelphia, PA 19104 > >> > > >> > Voice: (662) 617-2267 > >> > E-mail: [email protected] > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "votca" group. > >> > To unsubscribe from this group and stop receiving emails from it, send > >> > an > >> > email to [email protected]. > >> > To post to this group, send email to [email protected]. > >> > Visit this group at https://groups.google.com/group/votca. > >> > For more options, visit https://groups.google.com/d/optout. > >> > >> > >> > >> -- > >> Christoph Junghans > >> Web: http://www.compphys.de > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups > >> "votca" group. > >> To unsubscribe from this group and stop receiving emails from it, send > an > >> email to [email protected]. > >> To post to this group, send email to [email protected]. > >> Visit this group at https://groups.google.com/group/votca. > >> For more options, visit https://groups.google.com/d/optout. > > > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to [email protected]. > > To post to this group, send email to [email protected]. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- Best regards, Changwoon Jang, Postdoctoral Research Fellow Department of Chemical & Biological Engineering, Drexel University 3141 Chestnut Street, Philadelphia, PA 19104 Voice: (662) 617-2267 E-mail: [email protected] -- You received this message because you are subscribed to the Google Groups "votca" group. 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