Upgrades pl_upgrades to match main branch changes. #438
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- much faster due to the use of threading and mp - also supports sharding
- much faster due to the use of threading and mp - also supports sharding
…openfold into setup-improvements
…ights only, without parsing a time step.
This adds workers=True to the Lightning seed_everything function which guarantees different random states across all processes in distributed training. Prior to that some processes on different GPUs with the same worker ID could share the same random state. Note that this will break reproducibility between runs prior to and after this change. Also removes the seed and supress_output modules that were not used anymore in OpenFold.
Without the break statement this function will fall back to setting the resolution to _reflns.d_resolution_high for most structures, which reflects the resolution limit in the raw data and not the final structure (see https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.d_resolution_high.html and https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_d_res_high.html).
Fix distributed seeding behavior
Fixed a small typo in permutation unit test docstring
An mpi lib file is missing from the currently selected docker image. More testing is needed to support mpi mode for the docker CI.
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