Comments (2)
The problem is that ParallelAnalysisBase._dask_helper()
needs to be pickled by dask. But it is a bound method of ParallelAnalysisBase
so that method (or rather, the class that was derived from it, e.g. RMSD
) also needs to be pickled. If this class contains anything that cannot be pickled, the whole pickle fails. In particular, there is ParallelAnalysisBase._trajectory
, which contains the Reader from the universe (not the universe itself, which is currently no picklable). Almost all readers are picklable, except the ChainReader, because it contains a Generator:
_ChainReader__chained_trajectories_iter': <generator object ChainReader._chained_iterator at 0x7f1c19716468>
Ideally, pickling _dask_helper()
would not need to pickle the enclosing class. However, a short term fix should be to make the ChainReader picklable.
from pmda.
ChainReader should work once PR MDAnalysis/mdanalysis#2723 is merged.
from pmda.
Related Issues (20)
- Parallelize select_atoms by coordinates HOT 7
- Turn ParallelAnalysisBase into dask custom collection HOT 3
- make_balanced_slices should raise error when n_blocks are larger than n_frames HOT 1
- Travis breaks due to new pytest 6.0.0 HOT 4
- np.hstack should not be used in _conclude
- Travis breaks due to matplotlib 3.3
- Bad Performance of Parallelization with On-the-fly Transformation HOT 10
- MAINT: Switch from Travis to Github actions as CI provider HOT 1
- Error when running `AnalysisFromFunction()` on more processes than frames HOT 3
- test compatibility with MDAnalysis 2.0.0
- Printing of hydrogen bonding analysis results using mdanalysis HOT 2
- sitemap.xml contains broken links
- drop Python 2.7 support HOT 5
- test if PMDA runs on Windows HOT 1
- pmda.density not compatible to MDA 2.0.0 HOT 1
- Any performance comparison between dask and multprocessing? HOT 2
- Uniform analysis results with MDA HOT 1
- AttributeError: Atom has no attribute indices. Do you mean index HOT 2
- Pip and conda distributions don't have H-Bond Analysis
- Incompatible with Numpy 1.24.1
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