On Monday, October 29, 2012 5:31:14 PM UTC, Christoph Junghans wrote: > Victor is right, most information can be found here: > > https://groups.google.com/d/topic/votca/bUYLg20mNyM/discussion > > > > If you are using thread-parallel gromacs on Linux everything should > > happen automatically, just request a full node in the top of your PBS > > script and execute csg_inverse without mpirun (because it is > > thread-parallel not mpi-parallel). > > > > Christoph > > > > 2012/10/28 Victor Ruehle <[email protected]>: > > > Hi, > > > > > > as long as you source your VOTCARC.bash/csh file (+ GMXRC) at the > > > beginning of the submit script to setup all the pathes, it should work > > > without any problems. If you had any other issue, please give a bit > > > more details. If it's about parallel runs (run analysis / md in > > > parallel), you can specify that in the settings.xml, see e.g. the > > > tasks option, there are quite a few related posts for that. > > > > > > Victor > > > > > > > > > 2012/10/28 Sudharsan <[email protected]>: > > >> Hello everyone, > > >> > > >> > > >> Is there a job script available for submitting csg_inverse in a pbs queue ? > > >> I am unable to create one. As the csg_inverse calls for many scripts like > > >> csg_call and etc., > > >> > > >> Thank you for your time. > > >> > > >> Sincerely, > > >> > > >> Sudharsan > > >> > > >> -- > > >> You received this message because you are subscribed to the Google Groups > > >> "votca" group. > > >> To view this discussion on the web visit > > >> https://groups.google.com/d/msg/votca/-/xdmOPfGwJPoJ. > > >> To post to this group, send email to [email protected]. > > >> To unsubscribe from this group, send email to > > >> [email protected]. > > >> For more options, visit this group at > > >> http://groups.google.com/group/votca?hl=en. > > > > > > -- > > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > > To post to this group, send email to [email protected]. > > > To unsubscribe from this group, send email to > > [email protected]. > > > For more options, visit this group at > > http://groups.google.com/group/votca?hl=en. > > > > > > > > > > > -- > > Christoph Junghans > > Web: http://www.compphys.de
Hi Christoph! It's all fine only if you are not running out of the max wall-time. In many cases that max is 24 hours, which is way too small for any serious system. So, the question must be, how to arrange running votca on an HPC cluster with self-resubmitting ability, for both/either votca and/or the simulation engine? Cheers Andrey -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
