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.
