So you mean something like -cpi state.cpt -cpo state.cpt ? If so, I'll try this approach again. I had a little trouble doing it this way previously. I think I had trouble with the extension scripts doing it this way.
On Tue, Feb 2, 2010 at 11:56 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 03/02/10 15:44, Jack Shultz wrote: >> >> I will try it without the checkpointing flags. > > That's not quite what I said. I suggested not using *different* filenames > for -cpo and -cpi. What you want is the output file from a former run to > transparently become the input file for the subsequent one, and I expect > GROMACS will handle this for you if you let it. Try some things and see. > > Mark > >> 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 >>> >> >> >> > -- > 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
