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Improves IO performance for the report readers#104
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sergiorg-hpc merged 6 commits intomasterfrom Oct 20, 2020
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> IO:
* Loop through rows (timesteps) instead of columns (node_ids).
- Changes from tsteps * node_ids reads, to tsteps reads (i.e.,
constant time in terms of IO, regardless of node_ids reqs.).
* Read all node_ids in a buffer every timestep, between min and max
offsets of node_ids requested.
> Memory
* Allocate buffer before passing to HighFive to avoid extra and
unnecessary memory allocations before reading.
* Change data structure of node_ids/offsets from vector to map
for faster search (from n^2 to nlogn).
* In soma reports, assign values directly to return buffer instead
of std::copy/memcpy.
> New features and others:
* Add support for strided reads, allowing to reduce the amount of
timesteps (e.g., 1 by default, 2 for every 2 timesteps, etc.).
* Eliminate duplicated code, avoid calling HDF5 metadata in every
iteration, updated unit tests, and other minor changes.
alkino
previously approved these changes
Oct 9, 2020
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Really nice way to improve things |
matz-e
previously approved these changes
Oct 9, 2020
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matz-e
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matz-e
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Great! Some nitpicks about the docs… if that's intentional, please ignore.
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@jorblancoa and I went through all the comments and suggestions, and integrated everything (specially Jorge, thanks for the effort). Thanks for all the great feedback! If no one has any additional comments, we are ready to close the PR and merge the changes! |
alkino
previously approved these changes
Oct 19, 2020
mgeplf
reviewed
Oct 19, 2020
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Changes
IO:
constant time in terms of IO, regardless of node_ids reqs.).
offsets of node_ids requested.
Memory:
unnecessary memory allocations before reading.
for faster search (from n^2 to nlogn).
of std::copy/memcpy.
New features and others:
timesteps (e.g., 1 by default, 2 for every 2 timesteps, etc.).
iteration, updated unit tests, and other minor changes.
Important note
Performance evaluations and other related discussions can be obtained here:
https://bbpteam.epfl.ch/project/issues/browse/REP-60
https://bbpteam.epfl.ch/project/issues/browse/BLPY-217