[gmx-users] What does it mean that particle decomposition does not support checkpointing?

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 10 00:07:01 CET 2013


Sorry, I don't remember the observation that led to my statement, but I
believed it to be true and since pretty much none of the developers still
use particle decomposition, nobody has corrected me! Your observations
suggest that checkpointing is working fine for you. You should be able to
prove it by using mdrun -reprod; do two runs from the same starting point,
one of which is in two parts via a checkpoint, and use gmxcheck to verify
identical results.


On Sun, Dec 8, 2013 at 1:18 PM, Andrew DeYoung <adeyoung at andrew.cmu.edu>wrote:

> Hi,
> I am a Gromacs user (I'm running version 4.5.5).  I am not _at all_ an
> experienced programmer, but I was looking through this redmine page about
> "mdrun features to deprecate for 5.0":
> http://redmine.gromacs.org/issues/1292
> Near the top of that page (for issue #1292), it mentions particle
> decomposition as a feature to deprecate for 5.0:
> "1) Particle decomposition
> Doesn't support checkpointing. Doesn't scale because it does not balance
> load. Removing it will simplify a lot of conditionally executed code paths.
> The main caveat is whether there are important algorithms whose
> implementations still require it (see below)."
> What does it mean that particle decomposition doesn't support
> checkpointing?
> I use particle decomposition for my Gromacs simulations (in version 4.5.5),
> and I also save checkpoints from mdrun every 15 minutes using the -cpo
> flag.
> The resulting .cpt files seem to work fine -- at least "on the surface"; I
> have not checked this in detail -- for doing a restart whenever my system
> crashes.
> As a test, I took the final checkpoint file of a run.  Then, using the -t
> flag in mdrun, I started a new simulation using that final checkpoint file.
> After that new simulation finished, I used trjconv -dump 0 to dump the
> first
> frame into a configuration file (in my case, a .g96 file).  I compared this
> to the coordinates in the checkpoint file (as read by gmxdump -cp
> checkpoint.cpt), and the coordinates in the dumped configuration and in the
> checkpoint were the same up to the 0.00001 nm decimal place (since .g96
> files and gmxdump output have different precision).
> So it seems that, at least in some ways, checkpointing is working even when
> particle decomposition is used.  If so, then what does it mean in the above
> redmine post that "particle decomposition doesn't support checkpointing"?
> If not, why does my very quick, superficial check described in the previous
> paragraph appear to be successful?
> Thanks so very much for your time!
> Andrew DeYoung
> Carnegie Mellon University
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