[gmx-users] Checkpointing

Mark Abraham mark.abraham at anu.edu.au
Wed Feb 3 00:18:54 CET 2010

----- Original Message -----
From: Jack Shultz <js at drugdiscoveryathome.com>
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users <gmx-users at gromacs.org>, Andrey Voronkov <av at 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.


> 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list