Parallelize matrix simplification #1778

dweindl · 2022-04-08T22:05:51Z

Allow for optional parallelization of sympy matrix simplification using multiprocessing. Number of processes is controlled via environment variable AMICI_IMPORT_NPROCS.

This only helps for larger models and may slow down import of smaller models slightly.

Benchmarking (only code generation; derivatives computed sequentially in both cases):

1 process: 2:26:19 (h:mm:ss) (100%)
4 processes: 1:53:01 (h:mm:ss) (78%)

codecov · 2022-04-08T22:17:53Z

Codecov Report

Merging #1778 (53b5785) into develop (717851b) will decrease coverage by 10.15%.
The diff coverage is 33.33%.

@@             Coverage Diff              @@
##           develop    #1778       +/-   ##
============================================
- Coverage    76.33%   66.17%   -10.16%     
============================================
  Files           74       30       -44     
  Lines        12836     4722     -8114     
============================================
- Hits          9798     3125     -6673     
+ Misses        3038     1597     -1441

Flag	Coverage Δ
cpp	`?`
petab	`59.30% <38.88%> (-0.11%)`	⬇️
python	`?`

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

Impacted Files	Coverage Δ
python/amici/sbml_import.py	`89.42% <ø> (-4.40%)`	⬇️
python/amici/ode_export.py	`88.71% <33.33%> (-4.20%)`	⬇️
python/amici/bngl_import.py	`0.00% <0.00%> (-100.00%)`	⬇️
python/amici/pandas.py	`11.62% <0.00%> (-86.63%)`	⬇️
python/amici/conserved_quantities_demartino.py	`0.00% <0.00%> (-65.56%)`	⬇️
python/amici/testing.py	`0.00% <0.00%> (-50.00%)`	⬇️
python/amici/swig_wrappers.py	`59.32% <0.00%> (-35.60%)`	⬇️
python/amici/import_utils.py	`52.79% <0.00%> (-34.79%)`	⬇️
python/amici/pysb_import.py	`60.47% <0.00%> (-34.14%)`	⬇️
python/amici/numpy.py	`65.21% <0.00%> (-17.40%)`	⬇️
... and 53 more