I will try it without the checkpointing flags. If that fails, maybe I'll introduce some python into this integration. Check if the checkpoint already exists.
On Tue, Feb 2, 2010 at 6:18 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > > > ----- Original Message ----- > From: Jack Shultz <j...@drugdiscoveryathome.com> > Date: Wednesday, February 3, 2010 2:36 > Subject: [gmx-users] Checkpointing > To: Discussion list for GROMACS users <gmx-users@gromacs.org>, Andrey > Voronkov <a...@drugdiscoveryathome.com> > >> We have mdrun integrated into our distributed computing project. When >> your users suspend or close the manger it checkpoints, so when they >> open again it continues mdrun where it left off. However, when users >> reboot, it starts from the beginning. We are using this command line >> to execute the work. >> >> mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt - >> deffnm md) > > If you're using this input line always, then you're getting what you're > asking for - an mdrun that begins from the state in md.cpt. Since you're > never updating that, it doesn't change. > > Try not stipulating different -cpo and -cpi and see what the native coping > mechanism is. Otherwise, you'll have to write a bunch of scripting logic to > decide which .cpt to use each restart. > > Mark > >> I have a seperate checkpoint for output so after this simulation we >> can extend the workunit. Should we try using this append option? >> >> Checkpoints containing the complete state of the system are >> written at >> regular intervals (option -cpt) to the file -cpo, unless option -cpt >> is set to -1. A simulation can be continued by reading the full state >> from file with option -cpi. This option is intelligent in the >> way that >> if no checkpoint file is found, Gromacs just assumes a normal >> run and >> starts from the first step of the tpr file. >> >> With checkpointing you can also use the option -append to just >> continue writing to the previous output files. This is not >> enabled by >> default since it is potentially dangerous if you move files, but if >> you just leave all your files in place and restart mdrun with exactly >> the same command (with options -cpi and -append) the result will be >> the same as from a single run. The contents will be binary identical >> (unless you use dynamic load balancing), but for technical reasons >> there might be some extra energy frames when using checkpointing >> (necessary for restarts without appending). >> >> >> >> >> -- >> Jack >> >> http://drugdiscoveryathome.com >> http://hydrogenathome.org >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php