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.
