parallel LeafletFinder

[orbeckst]

Parallel version of the MDAnalysis.analysis.leaflet.LeafletFinder algorithm from @iparask (see upcoming paper https://arxiv.org/abs/1801.07630).

[iparask]

Hello @orbeckst ,

I see that the base class parallelizes over the frames a trajectory has. Our parallel implementation of the LeafletFinder parallelized the execution over a single frame.

I will use the most effecient case based on what we did for the paper, but I may have to override the core functionality of the based class and parallelize for a single frame and create multiple Dask DAGs to execute over the frames.

Is that something you think will be usefull or do you prefer to keep the core functionality as is?

[orbeckst]

The current framework might well be too limiting. I'm happy to consider other approaches! It should present the same user interface but implementation details can differ.

…

-- Oliver Beckstein email: orbeckst@gmail.com

Am Aug 30, 2018 um 07:45 schrieb Ioannis Paraskevakos ***@***.***>: Hello @orbeckst , I see that the base class parallelizes over the frames a trajectory has. Our parallel implementation of the LeafletFinder parallelized the execution over a single frame. I will use the most effecient case based on what we did for the paper, but I may have to override the core functionality of the based class and parallelize for a single frame and create multiple Dask DAGs to execute over the frames. Is that something you think will be usefull or do you prefer to keep the core functionality as is? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[orbeckst]

@iparask can you link to the code that you used for the paper?

[iparask]

Sorry for replying this late, but here is the code link.

Please feel free to open tickets for discussion and any bugs that you may find if you want to run it.