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.
