2016-01-21 19:17 GMT-07:00 Christoph Junghans <[email protected]>: > Hi Joshua, > > 2016-01-21 13:05 GMT-07:00 'Joshua Brown' via Developers <[email protected]>: >> Hi, >> >> I have been looking through the manual and trying to understand if VOTCA is >> setup to run on high performance computers but have not been unable to find >> anything. I understand that the MD simulations and the Quantum Chemical >> software packages used by VOTCA are HPC compatible but was wondering about >> the program as a whole? > I can only speak for votca-csg, which mainly makes use of the fact > that the MD program runs in parallel. > You can set cg.inverse.gromacs.command (or cg.inverse.lammps.command) > in the xml settings file to something like "mpirun ..." to get that. > > In addition csg_stat makes use of threads for parallelization. The > options is called cg.inverse.simulation.tasks in the xml file which's > default is "auto" meaning use all cores. > > csg_inverse can be run inside a submit script of a queuing system, > combined with the tricks from above. I usually use the following lines > csg_inverse --wall-time SEK --options settings.xml > [ $? -eq 0 ] && [ ! -f done ] && qsub SUBMIT_SCRIPT > where SEK are the wall-clock time in seconds and SUBMIT_SCRIPT is the > script itself. > If the MD engine support wall-clock timing (like gromacs) it will > handed through. I forgot to mention that votca-csg does checkpointing after each iteration step, which can be uses for restarting after crash or re-submitting after wall-clock time is up. In addition, it creates restart point in each iteration step after computationally heavy parts, like the MD simulation and the rdf calculation, so even if an iteration step cannot be finished for some reason it doesn't have to be re-done completely. Let I said above, when using gromacs, the remaining wall-clock time will be handed through to mdrun and hence triggers some checkpoint mechanism (by default every 15min) in there, so with gromacs you can even run iterations step, where one step takes longer than the wall-clock time.
Christoph > > I hoped that helped, > > Christoph > > > > > >> >> Thanks for your time, >> > > > -- > Christoph Junghans > Web: http://www.compphys.de -- 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.
