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Model import: parallelize computation of derivatives #1740

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merged 3 commits into from Mar 25, 2022
Merged

Model import: parallelize computation of derivatives #1740

merged 3 commits into from Mar 25, 2022

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dweindl
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@dweindl dweindl commented Mar 24, 2022 •
edited

Allows to compute derivatives in parallel (using multiprocessing). Disabled by default. Enable by setting environment variable AMICI_IMPORT_NPROCS to the number of processes to use. For smaller models, the multiprocessing overhead dominates, therefore, this is only advisable to use for larger models (import time of ⪆ 5min).

Closes #1739

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codecov bot commented Mar 24, 2022 •
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Codecov Report

Merging #1740 (09085b5) into develop (f60957b) will increase coverage by 9.28%.
The diff coverage is 70.00%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #1740      +/-   ##
===========================================
+ Coverage    68.58%   77.86%   +9.28%     
===========================================
  Files           29       73      +44     
  Lines         4132    11372    +7240     
===========================================
+ Hits          2834     8855    +6021     
- Misses        1298     2517    +1219
Flag Coverage Δ
cpp 74.76% <ø> (?)
petab 62.51% <70.00%> (-0.01%) ⬇️
python 68.19% <70.00%> (?)
sbmlsuite 87.94% <70.00%> (-0.14%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
python/amici/ode_export.py 92.30% <70.00%> (+4.71%) ⬆️
src/exception.cpp 74.19% <0.00%> (ø)
include/amici/sundials_linsol_wrapper.h 100.00% <0.00%> (ø)
src/abstract_model.cpp 4.06% <0.00%> (ø)
src/rdata.cpp 93.76% <0.00%> (ø)
src/forwardproblem.cpp 90.64% <0.00%> (ø)
src/simulation_parameters.cpp 71.42% <0.00%> (ø)
src/backwardproblem.cpp 63.73% <0.00%> (ø)
ThirdParty/gsl/gsl/gsl-lite.hpp 95.34% <0.00%> (ø)
src/edata.cpp 88.05% <0.00%> (ø)
... and 50 more

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dweindl commented Mar 24, 2022

Tested with https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/tree/master/Benchmark-Models/Chen_MSB2009 on 8 core CPU, model import without compilation:

n_procs walltime m:ss
1 4:25.61
2 4:14.30
4 3:39.20
8 3:37.07

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dweindl commented Mar 24, 2022 •
edited

Tested with https://github.com/ICB-DCM/CS_Signalling_ERBB_RAS_AKT/tree/master/FroehlichKes2018/PEtab:

    n_procs=1 - walltime (m:ss): 25:05.64
    n_procs=2 - walltime (m:ss): 23:25.90
    n_procs=8 - walltime (m:ss): 17:29.66

@dweindl dweindl marked this pull request as ready for review March 24, 2022 10:54
@dweindl dweindl requested a review from FFroehlich March 25, 2022 08:01
@dweindl dweindl linked an issue Mar 25, 2022 that may be closed by this pull request
Model import: parallelize computation of derivatives #1739
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FFroehlich
FFroehlich approved these changes Mar 25, 2022
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👍 neat !

@dweindl dweindl merged commit c095b00 into develop Mar 25, 2022
@dweindl dweindl deleted the feature_1739_par_jac branch March 25, 2022 15:02
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sonarcloud bot commented Mar 25, 2022

SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

70.0% 70.0% Coverage
0.0% 0.0% Duplication

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@FFroehlich FFroehlich FFroehlich approved these changes

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Model import: parallelize computation of derivatives
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