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).
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? 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.
