----- 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-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 -- 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
