Model import: parallelize computation of derivatives

[dweindl]

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

[codecov]

Codecov Report

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

@@             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

[dweindl]

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

[dweindl]

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

[FFroehlich]

👍 neat !

[sonarqubecloud]

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0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

70.0% Coverage
0.0% Duplication