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? 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.
