Comments (6)
kyleabeauchamp
commented on June 15, 2024
This is not immediately useful right now, as we don't use MDTraj here, but MDTraj might eventually support automatic HDF5 lossy and lossless compression. See https://github.com/rmcgibbo/mdtraj/issues/287
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jchodera
commented on June 15, 2024
Excellent idea! The MDTraj-powered HDF5 realization of the database could use this.
We probably want lossless compression for restart/checkpoint, but lossy compression is fine for trajectories written only for post-simulation health checks.
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Lnaden
commented on June 15, 2024
Handle in post yank 1.0
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Lnaden
commented on June 15, 2024
Do we think this can be closed now as #675 has added the checkpointing feature, or should we do more to reduce file sizes?
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andrrizzi
commented on June 15, 2024
Maybe we should keep this around and rename it to something like "Quantize floats to reduce file size"? The updated link to the mdtraj issue is mdtraj/mdtraj#287 (the one above gives a not found error).
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jchodera
commented on June 15, 2024
I believe #704 has greatly helped with reducing file sizes for the analysis file. We can reopen/revisit as needed.
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Related Issues (20)
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