Thanks for the clarification! Christoph
2016-07-25 14:34 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > It is my misunderstanding during finding ways to solve the domain > decomposition error on Stampede. Gromacs suggests optimizing the DD grids > and choosing the proper ranks. When standalone mode is ok, I thought that > log file might give me some clue about that. Therefore, I looked at the log > file saying that csg_stat --nt 8 ... > > I guessed that this may be a way to solve the error. That is why I asked it. > > However, I found the answer after I tried few numbers for "mdrun -nt > option". > > <mdrun> > <opts>-nt number</opts> > <mdrun> > > > Gromacs manual: "With thread-MPI there are additional options -nt, which > sets the total number of threads." > > The IBI is running now. > > Thank you for your kind answers. > > Best regards, > Changwoon Jang > > > > > > On Mon, Jul 25, 2016 at 4:09 PM, Christoph Junghans <[email protected]> > wrote: >> >> Can you explain, what the issue with csg_stat was please? Is there an >> error? >> >> 2016-07-25 12:25 GMT-06:00 Chang Woon Jang <[email protected]>: >> > Dear Christoph, >> > >> > Thank you for your reply. Does it mean that I need to set up the >> > following like >> > >> > <simulation> >> > <tasks>--nt number</tasks> >> > </simulation> >> > >> > in the <gromacs> in xml file? >> Ok, "cg.inverse.simulation.tasks" means >> <cg> >> <inverse> >> <simulation> >> <tasks>8</tasks> >> </simulation> >> </inverse> >> </cg> >> but make sure to put it in existing blocks! >> >> Christoph >> >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > >> > >> > >> > On Mon, Jul 25, 2016 at 1:42 PM, Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> 2016-07-25 9:59 GMT-06:00 Chang Woon Jang <[email protected]>: >> >> > Dear Votca Users, >> >> > >> >> > I would like to solve the gromacs domain decomposition error on >> >> > parallel >> >> > machine. I have asked Gromacs Users about the error. The final >> >> > conclusion is >> >> > to choose the proper number of ranks. The option "-nt 27" needs to be >> >> > included in setting file. I have tried the following options. >> >> > >> >> > <mdrun> >> >> > <opts>-nt 27</opts> >> >> > </mdrun> >> >> > >> >> > However, it does not influence the domain decomposition. >> >> > >> >> > >> >> > >> >> > I have tested standalone mode in my local machine. It works well. I >> >> > have >> >> > looked at inverse.log file. It says "Running critical command >> >> > 'csg_stat >> >> > --nt >> >> > 8 --options /home/tmp/settings.xml --top topol.tpr --trj traj.xtc >> >> > --begin 10 >> >> > --first-frame 0'. I think this is the key issue. >> >> What is exactly is the issue with csg_stat and 8 threads? >> >> csg_stat should work with all number of threads, otherwise please >> >> report an issue: >> >> <https://github.com/votca/csg/issues> >> >> >> >> > >> >> > Therefore, how can I change csg_stat --nt "numbers" via setting.xml >> >> > file? >> >> You can limit the number of threads using the xml option >> >> "cg.inverse.simulation.tasks"! >> >> >> >> Christoph >> >> > >> >> > Thank you. >> >> > >> >> > >> >> > 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. > > -- > 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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