[gmx-developers] Gromacs developer resources - checkpointing

cblau cblau at gwdg.de
Fri Mar 20 09:30:56 CET 2020

Hello Matthew,

Great that you want to work on checkpointing - this had been a 
long-standing issue.

Following up on what Paul wrote - there is currently some reshaping of 
the checkpoining infrastructure underway, e.g., here
(and very soon on gitlab)

It might be good to coordinate your efforts with Pascal Merz who 
requires changes in checkpoint structure to move on with work on the 
modular simulator.

Your contributions and the ones of the research project you're involved 
in will be most fruitful if based on the current gromacs version - this 
is where we can help you push things forward.


On 2020-03-19 17:41, Paul bauer wrote:
> 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).
> Cheers
> Paul
> 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
> 0046737308594

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