A sampler study

In this notebook, we perform a short study of how various samplers implemented in pyPESTO perform.

The pipeline

First, we show a typical workflow, fully integrating the samplers with a PEtab problem, using a toy example of a conversion reaction.

[1]:
import pypesto
import pypesto.petab
import pypesto.optimize as optimize
import pypesto.sample as sample
import pypesto.visualize as visualize
import petab

# import to petab
petab_problem = petab.Problem.from_yaml(
    "conversion_reaction/conversion_reaction.yaml")
# import to pypesto
importer = pypesto.petab.PetabImporter(petab_problem)
# create problem
problem = importer.create_problem()
2021-03-15 08:50:22.614 - amici.petab_import - INFO - Importing model ...
2021-03-15 08:50:22.617 - amici.petab_import - INFO - Model name is 'conversion_reaction_0'.
Writing model code to '/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0'.
2021-03-15 08:50:22.619 - amici.petab_import - INFO - Species: 2
2021-03-15 08:50:22.619 - amici.petab_import - INFO - Global parameters: 2
2021-03-15 08:50:22.620 - amici.petab_import - INFO - Reactions: 2
2021-03-15 08:50:22.629 - amici.petab_import - INFO - Observables: 1
2021-03-15 08:50:22.632 - amici.petab_import - INFO - Sigmas: 1
2021-03-15 08:50:22.635 - amici.petab_import - DEBUG - Adding output parameters to model: OrderedDict()
2021-03-15 08:50:22.636 - amici.petab_import - DEBUG - Adding initial assignments for []
2021-03-15 08:50:22.637 - amici.petab_import - DEBUG - Condition table: (1, 0)
2021-03-15 08:50:22.637 - amici.petab_import - DEBUG - Fixed parameters are []
2021-03-15 08:50:22.638 - amici.petab_import - INFO - Overall fixed parameters: 0
2021-03-15 08:50:22.639 - amici.petab_import - INFO - Variable parameters: 2
2021-03-15 08:50:22.655 - amici.sbml_import - INFO - Finished gathering local SBML symbols       ++ (3.76E-03s)
2021-03-15 08:50:22.660 - amici.sbml_import - INFO - Finished processing SBML parameters         ++ (1.52E-04s)
2021-03-15 08:50:22.665 - amici.sbml_import - INFO - Finished processing SBML compartments       ++ (2.55E-04s)
2021-03-15 08:50:22.674 - amici.sbml_import - INFO - Finished processing SBML species initials  +++ (2.79E-04s)
2021-03-15 08:50:22.679 - amici.sbml_import - INFO - Finished processing SBML rate rules        +++ (3.09E-05s)
2021-03-15 08:50:22.680 - amici.sbml_import - INFO - Finished processing SBML species            ++ (9.89E-03s)
2021-03-15 08:50:22.688 - amici.sbml_import - INFO - Finished processing SBML reactions          ++ (1.64E-03s)
2021-03-15 08:50:22.693 - amici.sbml_import - INFO - Finished processing SBML rules              ++ (2.03E-04s)
2021-03-15 08:50:22.698 - amici.sbml_import - INFO - Finished processing SBML initial assignments++ (7.04E-05s)
2021-03-15 08:50:22.704 - amici.sbml_import - INFO - Finished processing SBML species references ++ (2.42E-04s)
2021-03-15 08:50:22.704 - amici.sbml_import - INFO - Finished importing SBML                      + (5.85E-02s)
2021-03-15 08:50:22.758 - amici.sbml_import - INFO - Finished processing SBML observables         + (4.68E-02s)
2021-03-15 08:50:22.772 - amici.ode_export - INFO - Finished running smart_multiply              ++ (1.29E-03s)
2021-03-15 08:50:22.785 - amici.ode_export - INFO - Finished simplifying w                      +++ (1.97E-03s)
2021-03-15 08:50:22.785 - amici.ode_export - INFO - Finished computing w                         ++ (7.49E-03s)
2021-03-15 08:50:22.788 - amici.ode_export - INFO - Finished importing SbmlImporter               + (2.05E-02s)
2021-03-15 08:50:22.810 - amici.ode_export - INFO - Finished simplifying Jy                    ++++ (6.82E-03s)
2021-03-15 08:50:22.810 - amici.ode_export - INFO - Finished computing Jy                       +++ (1.05E-02s)
2021-03-15 08:50:22.832 - amici.ode_export - INFO - Finished writing Jy.cpp                      ++ (3.50E-02s)
2021-03-15 08:50:22.854 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (1.02E-02s)
2021-03-15 08:50:22.863 - amici.ode_export - INFO - Finished simplifying dJydsigmay            ++++ (3.55E-03s)
2021-03-15 08:50:22.863 - amici.ode_export - INFO - Finished computing dJydsigmay               +++ (2.29E-02s)
2021-03-15 08:50:22.867 - amici.ode_export - INFO - Finished writing dJydsigmay.cpp              ++ (3.04E-02s)
2021-03-15 08:50:22.884 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (5.70E-03s)
2021-03-15 08:50:22.895 - amici.ode_export - INFO - Finished simplifying dJydy                 ++++ (5.63E-03s)
2021-03-15 08:50:22.897 - amici.ode_export - INFO - Finished computing dJydy                    +++ (2.16E-02s)
2021-03-15 08:50:22.904 - amici.ode_export - INFO - Finished writing dJydy.cpp                   ++ (3.23E-02s)
2021-03-15 08:50:22.921 - amici.ode_export - INFO - Finished simplifying root                  ++++ (7.09E-05s)
2021-03-15 08:50:22.922 - amici.ode_export - INFO - Finished computing root                     +++ (6.78E-03s)
2021-03-15 08:50:22.923 - amici.ode_export - INFO - Finished writing root.cpp                    ++ (1.28E-02s)
2021-03-15 08:50:22.944 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (3.90E-03s)
2021-03-15 08:50:22.953 - amici.ode_export - INFO - Finished simplifying dwdp                  ++++ (1.53E-03s)
2021-03-15 08:50:22.956 - amici.ode_export - INFO - Finished computing dwdp                     +++ (2.09E-02s)
2021-03-15 08:50:22.964 - amici.ode_export - INFO - Finished writing dwdp.cpp                    ++ (3.48E-02s)
2021-03-15 08:50:22.991 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (4.88E-03s)
2021-03-15 08:50:22.997 - amici.ode_export - INFO - Finished simplifying dwdx                  ++++ (1.64E-03s)
2021-03-15 08:50:23.000 - amici.ode_export - INFO - Finished computing dwdx                     +++ (2.08E-02s)
2021-03-15 08:50:23.006 - amici.ode_export - INFO - Finished writing dwdx.cpp                    ++ (3.27E-02s)
2021-03-15 08:50:23.022 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (1.28E-04s)
2021-03-15 08:50:23.028 - amici.ode_export - INFO - Finished simplifying dwdw                  ++++ (8.05E-05s)
2021-03-15 08:50:23.029 - amici.ode_export - INFO - Finished computing dwdw                     +++ (1.16E-02s)
2021-03-15 08:50:23.032 - amici.ode_export - INFO - Finished writing dwdw.cpp                    ++ (2.06E-02s)
2021-03-15 08:50:23.056 - amici.ode_export - INFO - Finished simplifying xdot                  ++++ (2.48E-03s)
2021-03-15 08:50:23.057 - amici.ode_export - INFO - Finished computing xdot                     +++ (1.02E-02s)
2021-03-15 08:50:23.066 - amici.ode_export - INFO - Finished writing dxdotdw.cpp                 ++ (2.14E-02s)
2021-03-15 08:50:23.089 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (2.54E-03s)
2021-03-15 08:50:23.100 - amici.ode_export - INFO - Finished simplifying dxdotdx_explicit      ++++ (1.42E-04s)
2021-03-15 08:50:23.102 - amici.ode_export - INFO - Finished computing dxdotdx_explicit         +++ (2.35E-02s)
2021-03-15 08:50:23.104 - amici.ode_export - INFO - Finished writing dxdotdx_explicit.cpp        ++ (3.17E-02s)
2021-03-15 08:50:23.133 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (2.19E-04s)
2021-03-15 08:50:23.142 - amici.ode_export - INFO - Finished simplifying dxdotdp_explicit      ++++ (1.24E-04s)
2021-03-15 08:50:23.143 - amici.ode_export - INFO - Finished computing dxdotdp_explicit         +++ (1.97E-02s)
2021-03-15 08:50:23.146 - amici.ode_export - INFO - Finished writing dxdotdp_explicit.cpp        ++ (3.14E-02s)
2021-03-15 08:50:23.179 - amici.ode_export - INFO - Finished simplifying y                   ++++++ (4.50E-05s)
2021-03-15 08:50:23.179 - amici.ode_export - INFO - Finished computing y                      +++++ (4.03E-03s)
2021-03-15 08:50:23.188 - amici.ode_export - INFO - Finished running smart_jacobian           +++++ (8.90E-04s)
2021-03-15 08:50:23.194 - amici.ode_export - INFO - Finished simplifying dydx                 +++++ (6.74E-05s)
2021-03-15 08:50:23.195 - amici.ode_export - INFO - Finished computing dydx                    ++++ (2.33E-02s)
2021-03-15 08:50:23.211 - amici.ode_export - INFO - Finished running smart_jacobian           +++++ (1.15E-04s)
2021-03-15 08:50:23.218 - amici.ode_export - INFO - Finished simplifying dydw                 +++++ (9.86E-05s)
2021-03-15 08:50:23.219 - amici.ode_export - INFO - Finished computing dydw                    ++++ (1.33E-02s)
2021-03-15 08:50:23.225 - amici.ode_export - INFO - Finished simplifying dydx                  ++++ (8.66E-05s)
2021-03-15 08:50:23.226 - amici.ode_export - INFO - Finished computing dydx                     +++ (5.92E-02s)
2021-03-15 08:50:23.230 - amici.ode_export - INFO - Finished writing dydx.cpp                    ++ (6.91E-02s)
2021-03-15 08:50:23.249 - amici.ode_export - INFO - Finished running smart_jacobian           +++++ (1.44E-04s)
2021-03-15 08:50:23.256 - amici.ode_export - INFO - Finished simplifying dydp                 +++++ (6.76E-05s)
2021-03-15 08:50:23.257 - amici.ode_export - INFO - Finished computing dydp                    ++++ (1.17E-02s)
2021-03-15 08:50:23.262 - amici.ode_export - INFO - Finished simplifying dydp                  ++++ (6.56E-05s)
2021-03-15 08:50:23.262 - amici.ode_export - INFO - Finished computing dydp                     +++ (2.19E-02s)
2021-03-15 08:50:23.263 - amici.ode_export - INFO - Finished writing dydp.cpp                    ++ (2.69E-02s)
2021-03-15 08:50:23.278 - amici.ode_export - INFO - Finished simplifying sigmay               +++++ (4.36E-05s)
2021-03-15 08:50:23.278 - amici.ode_export - INFO - Finished computing sigmay                  ++++ (3.84E-03s)
2021-03-15 08:50:23.283 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (2.24E-04s)
2021-03-15 08:50:23.288 - amici.ode_export - INFO - Finished simplifying dsigmaydp             ++++ (6.41E-05s)
2021-03-15 08:50:23.289 - amici.ode_export - INFO - Finished computing dsigmaydp                +++ (1.77E-02s)
2021-03-15 08:50:23.290 - amici.ode_export - INFO - Finished writing dsigmaydp.cpp               ++ (2.23E-02s)
2021-03-15 08:50:23.299 - amici.ode_export - INFO - Finished writing sigmay.cpp                  ++ (1.19E-03s)
2021-03-15 08:50:23.308 - amici.ode_export - INFO - Finished computing stau                     +++ (1.14E-04s)
2021-03-15 08:50:23.309 - amici.ode_export - INFO - Finished writing stau.cpp                    ++ (4.80E-03s)
2021-03-15 08:50:23.317 - amici.ode_export - INFO - Finished computing deltasx                  +++ (1.12E-04s)
2021-03-15 08:50:23.318 - amici.ode_export - INFO - Finished writing deltasx.cpp                 ++ (4.36E-03s)
2021-03-15 08:50:23.324 - amici.ode_export - INFO - Finished writing w.cpp                       ++ (1.32E-03s)
2021-03-15 08:50:23.336 - amici.ode_export - INFO - Finished simplifying x0                    ++++ (4.87E-05s)
2021-03-15 08:50:23.337 - amici.ode_export - INFO - Finished computing x0                       +++ (4.14E-03s)
2021-03-15 08:50:23.339 - amici.ode_export - INFO - Finished writing x0.cpp                      ++ (9.07E-03s)
2021-03-15 08:50:23.351 - amici.ode_export - INFO - Finished simplifying x0_fixedParameters    ++++ (3.09E-05s)
2021-03-15 08:50:23.352 - amici.ode_export - INFO - Finished computing x0_fixedParameters       +++ (4.07E-03s)
2021-03-15 08:50:23.353 - amici.ode_export - INFO - Finished writing x0_fixedParameters.cpp      ++ (9.17E-03s)
2021-03-15 08:50:23.364 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (2.02E-04s)
2021-03-15 08:50:23.369 - amici.ode_export - INFO - Finished simplifying sx0                   ++++ (8.59E-05s)
2021-03-15 08:50:23.370 - amici.ode_export - INFO - Finished computing sx0                      +++ (9.57E-03s)
2021-03-15 08:50:23.371 - amici.ode_export - INFO - Finished writing sx0.cpp                     ++ (1.38E-02s)
2021-03-15 08:50:23.383 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (4.07E-05s)
2021-03-15 08:50:23.390 - amici.ode_export - INFO - Finished running smart_jacobian            ++++ (6.25E-05s)
2021-03-15 08:50:23.396 - amici.ode_export - INFO - Finished simplifying sx0_fixedParameters   ++++ (4.51E-05s)
2021-03-15 08:50:23.397 - amici.ode_export - INFO - Finished computing sx0_fixedParameters      +++ (1.78E-02s)
2021-03-15 08:50:23.398 - amici.ode_export - INFO - Finished writing sx0_fixedParameters.cpp     ++ (2.25E-02s)
2021-03-15 08:50:23.407 - amici.ode_export - INFO - Finished writing xdot.cpp                    ++ (2.42E-03s)
2021-03-15 08:50:23.412 - amici.ode_export - INFO - Finished writing y.cpp                       ++ (5.83E-04s)
2021-03-15 08:50:23.425 - amici.ode_export - INFO - Finished simplifying x_rdata               ++++ (6.01E-05s)
2021-03-15 08:50:23.425 - amici.ode_export - INFO - Finished computing x_rdata                  +++ (4.55E-03s)
2021-03-15 08:50:23.427 - amici.ode_export - INFO - Finished writing x_rdata.cpp                 ++ (9.85E-03s)
2021-03-15 08:50:23.442 - amici.ode_export - INFO - Finished simplifying total_cl              ++++ (3.69E-05s)
2021-03-15 08:50:23.442 - amici.ode_export - INFO - Finished computing total_cl                 +++ (4.29E-03s)
2021-03-15 08:50:23.443 - amici.ode_export - INFO - Finished writing total_cl.cpp                ++ (9.21E-03s)
2021-03-15 08:50:23.459 - amici.ode_export - INFO - Finished simplifying x_solver              ++++ (7.44E-05s)
2021-03-15 08:50:23.460 - amici.ode_export - INFO - Finished computing x_solver                 +++ (5.19E-03s)
2021-03-15 08:50:23.462 - amici.ode_export - INFO - Finished writing x_solver.cpp                ++ (1.14E-02s)
2021-03-15 08:50:23.472 - amici.ode_export - INFO - Finished generating cpp code                  + (6.78E-01s)
2021-03-15 08:50:55.810 - amici.ode_export - INFO - Finished compiling cpp code                   + (3.23E+01s)
2021-03-15 08:50:55.813 - amici.petab_import - INFO - Finished Importing PEtab model                (3.32E+01s)
running build_ext
Changed extra_compile_args for unix to ['-fopenmp', '-std=c++14']
building 'conversion_reaction_0._conversion_reaction_0' extension
Testing SWIG executable swig4.0... FAILED.
Testing SWIG executable swig3.0... SUCCEEDED.
swigging swig/conversion_reaction_0.i to swig/conversion_reaction_0_wrap.cpp
swig3.0 -python -c++ -modern -outdir conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/swig -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -o swig/conversion_reaction_0_wrap.cpp swig/conversion_reaction_0.i
creating build
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/swig
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c swig/conversion_reaction_0_wrap.cpp -o build/temp.linux-x86_64-3.8/swig/conversion_reaction_0_wrap.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_Jy.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_Jy.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_deltasx.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_deltasx.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdp_explicit_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdw.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdp_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_w.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_w.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dydx.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dydx.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_stau.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_stau.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_x0.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_x0.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_total_cl.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_total_cl.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdw_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dJydsigmay.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydsigmay.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdx_explicit.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dydp.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dydp.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_sigmay.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_sigmay.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dJydy_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdx_explicit_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_xdot.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_xdot.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdx.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdp.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdw.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_y.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_y.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_x_solver.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_x_solver.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dJydy_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_sx0.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_sx0.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dsigmaydp.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dsigmaydp.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c wrapfunctions.cpp -o build/temp.linux-x86_64-3.8/wrapfunctions.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdx_explicit_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdw_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_x_rdata.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_x_rdata.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdp_explicit.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_sx0_fixedParameters.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_sx0_fixedParameters.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdp_explicit_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdx_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdp_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_x0_fixedParameters.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_x0_fixedParameters.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdw_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dJydy.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdx_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_root.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_root.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdw_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/swig/conversion_reaction_0_wrap.o build/temp.linux-x86_64-3.8/conversion_reaction_0_Jy.o build/temp.linux-x86_64-3.8/conversion_reaction_0_deltasx.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_w.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dydx.o build/temp.linux-x86_64-3.8/conversion_reaction_0_stau.o build/temp.linux-x86_64-3.8/conversion_reaction_0_x0.o build/temp.linux-x86_64-3.8/conversion_reaction_0_total_cl.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydsigmay.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dydp.o build/temp.linux-x86_64-3.8/conversion_reaction_0_sigmay.o build/temp.linux-x86_64-3.8/conversion_reaction_0.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_xdot.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw.o build/temp.linux-x86_64-3.8/conversion_reaction_0_y.o build/temp.linux-x86_64-3.8/conversion_reaction_0_x_solver.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_sx0.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dsigmaydp.o build/temp.linux-x86_64-3.8/wrapfunctions.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_x_rdata.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit.o build/temp.linux-x86_64-3.8/conversion_reaction_0_sx0_fixedParameters.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_x0_fixedParameters.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_root.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw_rowvals.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/libs -lamici -lsundials -lsuitesparse -lcblas -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 -o /home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0/conversion_reaction_0/_conversion_reaction_0.cpython-38-x86_64-linux-gnu.so -fopenmp

Commonly, as a first step, optimization is performed, in order to find good parameter point estimates.

[2]:
%%time
result = optimize.minimize(problem, n_starts=10)
Parameters obtained from history and optimizer do not match: [ -0.91617976 -10.39367452], [ -0.9161923  -10.39367204]
CPU times: user 2.21 s, sys: 406 ms, total: 2.62 s
Wall time: 2.06 s
[3]:
ax = visualize.waterfall(result, size=(4,4))
../_images/example_sampler_study_7_0.png

Next, we perform sampling. Here, we employ a pypesto.sample.AdaptiveParallelTemperingSampler sampler, which runs Markov Chain Monte Carlo (MCMC) chains on different temperatures. For each chain, we employ a pypesto.sample.AdaptiveMetropolisSampler. For more on the samplers see below or the API documentation.

[4]:
sampler = sample.AdaptiveParallelTemperingSampler(
    internal_sampler=sample.AdaptiveMetropolisSampler(),
    n_chains=3)

For the actual sampling, we call the pypesto.sample.sample function. By passing the result object to the function, the previously found global optimum is used as starting point for the MCMC sampling.

[5]:
%%time
result = sample.sample(problem, n_samples=10000, sampler=sampler, result=result)
100%|██████████| 10000/10000 [00:55<00:00, 179.06it/s]
CPU times: user 1min, sys: 9.35 s, total: 1min 9s
Wall time: 55.9 s

When the sampling is finished, we can analyse our results. A first thing to do is to analyze the sampling burn-in:

[6]:
sample.geweke_test(result)
[6]:
0

pyPESTO provides functions to analyse both the sampling process as well as the obtained sampling result. Visualizing the traces e.g. allows to detect burn-in phases, or fine-tune hyperparameters. First, the parameter trajectories can be visualized:

[7]:
sample.geweke_test(result)
ax = visualize.sampling_parameter_traces(result, use_problem_bounds=False)
../_images/example_sampler_study_15_0.png

Next, also the log posterior trace can be visualized:

[8]:
ax = visualize.sampling_fval_traces(result)
../_images/example_sampler_study_17_0.png

To visualize the result, there are various options. The scatter plot shows histograms of 1-dim parameter marginals and scatter plots of 2-dimensional parameter combinations:

[9]:
ax = visualize.sampling_scatter(result, size=[13,6])
../_images/example_sampler_study_19_0.png

sampling_1d_marginals allows to plot e.g. kernel density estimates or histograms (internally using seaborn):

[10]:
for i_chain in range(len(result.sample_result.betas)):
    visualize.sampling_1d_marginals(
        result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
../_images/example_sampler_study_21_0.png
../_images/example_sampler_study_21_1.png
../_images/example_sampler_study_21_2.png

That’s it for the moment on using the sampling pipeline.

1-dim test problem

To compare and test the various implemented samplers, we first study a 1-dimensional test problem of a gaussian mixture density, together with a flat prior.

[1]:
import numpy as np
from scipy.stats import multivariate_normal
import seaborn as sns
import pypesto
import pypesto.sample as sample
import pypesto.visualize as visualize

def density(x):
    return 0.3*multivariate_normal.pdf(x, mean=-1.5, cov=0.1) + \
        0.7*multivariate_normal.pdf(x, mean=2.5, cov=0.2)

def nllh(x):
    return - np.log(density(x))

objective = pypesto.Objective(fun=nllh)
problem = pypesto.Problem(
    objective=objective, lb=-4, ub=5, x_names=['x'])

The likelihood has two separate modes:

[2]:
xs = np.linspace(-4, 5, 100)
ys = [density(x) for x in xs]

ax = sns.lineplot(xs, ys, color='C1')
../_images/example_sampler_study_27_0.png

Metropolis sampler

For this problem, let us try out the simplest sampler, the pypesto.sample.MetropolisSampler.

[13]:
%%time
sampler = sample.MetropolisSampler({'std': 0.5})
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:03<00:00, 2774.43it/s]
CPU times: user 3.65 s, sys: 194 ms, total: 3.84 s
Wall time: 3.62 s

[14]:
sample.geweke_test(result)
ax = visualize.sampling_1d_marginals(result)
ax[0][0].plot(xs, ys)
[14]:
[<matplotlib.lines.Line2D at 0x7f8466613f40>]
../_images/example_sampler_study_31_1.png

The obtained posterior does not accurately represent the distribution, often only capturing one mode. This is because it is hard for the Markov chain to jump between the distribution’s two modes. This can be fixed by choosing a higher proposal variation std:

[15]:
%%time
sampler = sample.MetropolisSampler({'std': 1})
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:03<00:00, 2849.08it/s]
CPU times: user 3.55 s, sys: 190 ms, total: 3.74 s
Wall time: 3.52 s

[16]:
sample.geweke_test(result)
ax = visualize.sampling_1d_marginals(result)
ax[0][0].plot(xs, ys)
[16]:
[<matplotlib.lines.Line2D at 0x7f844fffcdf0>]
../_images/example_sampler_study_34_1.png

In general, MCMC have difficulties exploring multimodel landscapes. One way to overcome this is to used parallel tempering. There, various chains are run, lifting the densities to different temperatures. At high temperatures, proposed steps are more likely to get accepted and thus jumps between modes more likely.

Parallel tempering sampler

In pyPESTO, the most basic parallel tempering algorithm is the pypesto.sample.ParallelTemperingSampler. It takes an internal_sampler parameter, to specify what sampler to use for performing sampling the different chains. Further, we can directly specify what inverse temperatures betas to use. When not specifying the betas explicitly but just the number of chains n_chains, an established near-exponential decay scheme is used.

[17]:
%%time
sampler = sample.ParallelTemperingSampler(
    internal_sampler=sample.MetropolisSampler(),
    betas=[1, 1e-1, 1e-2])
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:11<00:00, 863.05it/s]
CPU times: user 11.8 s, sys: 621 ms, total: 12.4 s
Wall time: 11.6 s

[18]:
sample.geweke_test(result)
for i_chain in range(len(result.sample_result.betas)):
    visualize.sampling_1d_marginals(
        result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
../_images/example_sampler_study_39_0.png
../_images/example_sampler_study_39_1.png
../_images/example_sampler_study_39_2.png

Of interest is here finally the first chain at index i_chain=0, which approximates the posterior well.

Adaptive Metropolis sampler

The problem of having to specify the proposal step variation manually can be overcome by using the pypesto.sample.AdaptiveMetropolisSampler, which iteratively adjusts the proposal steps to the function landscape.

[19]:
%%time
sampler = sample.AdaptiveMetropolisSampler()
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:04<00:00, 2337.47it/s]
CPU times: user 4.35 s, sys: 55.4 ms, total: 4.41 s
Wall time: 4.3 s

[20]:
sample.geweke_test(result)
ax = visualize.sampling_1d_marginals(result)
../_images/example_sampler_study_44_0.png

Adaptive parallel tempering sampler

The pypesto.sample.AdaptiveParallelTemperingSampler iteratively adjusts the temperatures to obtain good swapping rates between chains.

[21]:
%%time
sampler = sample.AdaptiveParallelTemperingSampler(
    internal_sampler=sample.AdaptiveMetropolisSampler(), n_chains=3)
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:13<00:00, 752.49it/s]
CPU times: user 13.3 s, sys: 91 ms, total: 13.4 s
Wall time: 13.3 s

[22]:
sample.geweke_test(result)
for i_chain in range(len(result.sample_result.betas)):
    visualize.sampling_1d_marginals(
        result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
../_images/example_sampler_study_48_0.png
../_images/example_sampler_study_48_1.png
../_images/example_sampler_study_48_2.png
[23]:
result.sample_result.betas
[23]:
array([1.0000000e+00, 2.1503801e-01, 2.0000000e-05])

Pymc3 sampler

[24]:
%%time
sampler = sample.Pymc3Sampler()
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
Auto-assigning NUTS sampler...
Initializing NUTS using jitter+adapt_diag...
Initializing NUTS failed. Falling back to elementwise auto-assignment.
Sequential sampling (1 chains in 1 job)
Slice: [x]
Sampling chain 0, 0 divergences: 100%|██████████| 10500/10500 [00:25<00:00, 407.36it/s]
Only one chain was sampled, this makes it impossible to run some convergence checks
CPU times: user 29.2 s, sys: 860 ms, total: 30.1 s
Wall time: 30.8 s
[25]:
sample.geweke_test(result)
for i_chain in range(len(result.sample_result.betas)):
    visualize.sampling_1d_marginals(
        result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
../_images/example_sampler_study_52_0.png

If not specified, pymc3 chooses an adequate sampler automatically.

Emcee sampler

[4]:
%%time
sampler = sample.EmceeSampler(nwalkers=10, run_args={'progress': True})
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:35<00:00, 278.38it/s]
CPU times: user 35.8 s, sys: 344 ms, total: 36.2 s
Wall time: 35.9 s

[5]:
sample.geweke_test(result)
for i_chain in range(len(result.sample_result.betas)):
    visualize.sampling_1d_marginals(
        result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
../_images/example_sampler_study_56_0.png

2-dim test problem: Rosenbrock banana

The adaptive parallel tempering sampler with chains running adaptive Metropolis samplers is also able to sample from more challenging posterior distributions. To illustrates this shortly, we use the Rosenbrock function.

[26]:
import scipy.optimize as so
import pypesto

# first type of objective
objective = pypesto.Objective(fun=so.rosen)

dim_full = 4
lb = -5 * np.ones((dim_full, 1))
ub = 5 * np.ones((dim_full, 1))

problem = pypesto.Problem(objective=objective, lb=lb, ub=ub)
[27]:
%%time
sampler = sample.AdaptiveParallelTemperingSampler(
    internal_sampler=sample.AdaptiveMetropolisSampler(), n_chains=10)
result =sample.sample(problem, 1e4, sampler, x0=np.zeros(dim_full))
100%|██████████| 10000/10000 [00:35<00:00, 279.44it/s]
CPU times: user 35.6 s, sys: 47.5 ms, total: 35.7 s
Wall time: 35.9 s

[28]:
sample.geweke_test(result)
ax = visualize.sampling_scatter(result)
ax = visualize.sampling_1d_marginals(result)
../_images/example_sampler_study_61_0.png
../_images/example_sampler_study_61_1.png