[gmx-developers] Gromacs developer resources - checkpointing

Paul bauer paul.bauer.q at gmail.com
Thu Mar 19 17:41:35 CET 2020

Hello Matthew,

great for getting involved in the project!
We are currently working on a long term project to move the 
checkpointing to a key-value-tree representation of different modules 
that contribute to the final checkpointing stage, so if you are 
interested in contributing there it will be awesome!

Right now there is not much low-level documentation for writing the 
checkpoint files (sorry ...), but in principle it is done by a hacked 
together XDR serializer that writes the individual fields defined in 
src/gromacs/fileio/checkpoint.* for the main simulation state and 
additional routines that might have been selected. The whole thing is 
still a bit messy, so that might cause a bit of confusion.

If you want to contribute, I would highly recommend to first cherry pick 
the other changes you did to the current master branch and verify that 
things still work as intended.
Then you could change the additional functionality to be derived from 
the MDModules interface, that will allow you to use the key-value-tree 
checkpointing style that is already implement for it.

Please don't hesitate to come back to us and open issues when needed on 
Redmine (or soon Gitlab).



On 19/03/2020 17:32, Matthew Alexandrakis wrote:
> Hello everyone,
> I am a Research Software Engineer at Queen Mary Univ. of London. I'm 
> trying to help a PhD researcher to fix the checkpointing system of 
> Gromacs. The PhD has extended stock Gromacs 2016.4 with additional 
> containers that would have to be added to the checkpointing.
> I would like to ask if there are any low-level developer resources or 
> documentation that delve more deeply on the subject of checkpointing? 
> Already available resources I found online just explain the usage of 
> checkpointing on a very high level.
> Thanks,
> Matthew

Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab

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