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[coordinates] handle default_chunksize gracefully. #1251
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PCA, TICA and VAMP have dynamic dimension methods, so we need to handle this when accessing the method to compute the desired number of time steps for the chunk size. The chunksize argument in the api is also passed when no data is passed.
When we pass a too large chunksize to read_as_traj function of mdtraj, this would overflow memory. So we truncate it.
Codecov Report
@@ Coverage Diff @@
## devel #1251 +/- ##
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+ Coverage 91.19% 91.2% +<.01%
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Files 219 219
Lines 23646 23709 +63
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+ Hits 21565 21624 +59
- Misses 2081 2085 +4
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[coordinates/lagged iterator] skip over trajectories that are shorter…
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PCA, TICA and VAMP have dynamic dimension methods, so we need to handle
this when accessing the method to compute the desired number of time
steps for the chunk size.
The chunksize argument in the api is also passed when no data is passed.
For the FeatureReader we need to cap the passed chunksize, because we are using low-level reading routines of mdtraj.
@euhruska I'd be happy if you can run a test with your massive data set. I have tested it locally on some huge data set, but the more tests we run, the more problems we can possibly detect. Thank you in advance!
Fixes #1250