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.
