2016-07-22 14:03 GMT-06:00 Chang Woon Jang <[email protected]>: > 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. Here is an example: <https://github.com/votca/csg-tutorials/blob/master/methanol-water/X_0.938/simplex/settings.xml#L106>
Christoph > > > 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. > 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. 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