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? 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.
