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Use SOA format for mechanism data #2027

Merged
merged 373 commits into from
Jun 5, 2023
Merged

Use SOA format for mechanism data #2027

merged 373 commits into from
Jun 5, 2023

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olupton
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@olupton olupton commented Oct 17, 2022 •
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Introduce new SOA data structures for NEURON model data. So far:

  • Nodes: area, voltages and matrix equation data (d, a, b, rhs).
  • Mechanisms: floating point data (i.e. RANGE variables)

are migrated to use the new neuron::container::soa<...> format.

Status:

  • The CI on this PR is normally passing
  • Internal BBP CI is normally passing
  • ModelDB CI is normally passing without suspicious diffs

Dependencies:

This builds on #1929 (which was not merged) and incorporates ideas from https://github.com/neuronsimulator/data-structure-design.

@olupton olupton changed the base branch from olupton/data-structures to master October 27, 2022 08:32
olupton
olupton commented Nov 1, 2022
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@olupton olupton force-pushed the olupton/data-structures-including-mechanisms branch 2 times, most recently from 3f121e0 to b51f37f Compare November 1, 2022 12:14
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Minor improvements from #2027 (#2051)
53f87a1 
* Bump submodule past iv#45.
* PyObject_HEAD contains an ;
* drop nrn_isdouble
* drop unused memory pool code
@olupton olupton force-pushed the olupton/data-structures-including-mechanisms branch from ac0450f to 88cf7b6 Compare November 1, 2022 21:07
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codecov-commenter commented Nov 2, 2022 •
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Codecov Report

Merging #2027 (2b44298) into master (b4ade55) will increase coverage by 1.38%.
The diff coverage is 92.02%.

❗ Current head 2b44298 differs from pull request most recent head e23d8d8. Consider uploading reports for the commit e23d8d8 to get more accurate results

@@            Coverage Diff             @@
##           master    #2027      +/-   ##
==========================================
+ Coverage   58.77%   60.15%   +1.38%     
==========================================
  Files         623      642      +19     
  Lines      119597   121134    +1537     
==========================================
+ Hits        70288    72872    +2584     
+ Misses      49309    48262    -1047
Impacted Files Coverage Δ
...re/lib/python/neuron/tests/utils/capture_stdout.py 0.00% <0.00%> (ø)
src/ivoc/oc2iv.h 50.00% <ø> (ø)
src/ivoc/symdir.cpp 0.00% <0.00%> (ø)
src/ivoc/xmenu.h 68.00% <ø> (+2.61%) ⬆️
src/nmodl/netrec_discon.cpp 62.31% <ø> (ø)
src/nrncvode/netcvode.h 100.00% <ø> (ø)
src/nrncvode/vrecitem.h 65.51% <ø> (ø)
src/nrniv/arraypool.h 96.10% <ø> (-3.90%) ⬇️
src/nrniv/bbsavestate.h 50.00% <ø> (ø)
src/nrniv/glinerec.h 0.00% <ø> (-35.72%) ⬇️
... and 118 more

... and 9 files with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

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@alexsavulescu alexsavulescu force-pushed the olupton/data-structures-including-mechanisms branch from d41678e to 63e20bc Compare November 8, 2022 16:14
@olupton olupton force-pushed the olupton/data-structures-including-mechanisms branch 3 times, most recently from a4e9fac to ce1bade Compare November 9, 2022 18:09
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@olupton olupton force-pushed the olupton/data-structures-including-mechanisms branch from 73e3340 to cd03677 Compare November 11, 2022 21:35
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@olupton olupton force-pushed the olupton/data-structures-including-mechanisms branch from 7ded4ab to 4ac4e2b Compare November 21, 2022 16:15
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@olupton olupton force-pushed the olupton/data-structures-including-mechanisms branch from 380e7c3 to 2b44298 Compare June 5, 2023 11:11
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✔️ 2b44298 -> Azure artifacts URL

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github-actions bot commented Jun 5, 2023

NEURON ModelDB CI: launching for 2b44298 via its drop url

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NEURON ModelDB CI: 2b44298 -> download reports from here

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✔️ e23d8d8 -> Azure artifacts URL

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Logfiles from GitLab pipeline #128960 (:white_check_mark:) have been uploaded here!

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@olupton olupton merged commit 6c529a4 into master Jun 5, 2023
@olupton olupton deleted the olupton/data-structures-including-mechanisms branch June 5, 2023 16:54
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@olupton olupton mentioned this pull request Jun 14, 2023
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@olupton
Use modern SoA helpers for fast_imem data (#2381)
7c36a8f 
These data were already in SoA format, but bringing them into
the ecosystem introduced in #2027 removes the final usage of
some old pointer-updating logic, which in any case required
contortions in Python scripts to get things to work. This can be
removed because the new data_handle<T> component can
now handle referring to i_membrane_ values.

To enable this, add support to neuron::container::soa<...> for
fields that can be toggled active/inactive at runtime, and add
new tests covering this.

Also drop set_area and set_v for uniformity.
@olupton olupton mentioned this pull request Jun 19, 2023
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@alexsavulescu alexsavulescu alexsavulescu approved these changes

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