MCMC sampling diagnostics¶
In this notebook, we illustrate how to assess the quality of your MCMC samples, e.g. convergence and auto-correlation, in pyPESTO.
The pipeline¶
First, we load the model and data to generate the MCMC samples from. In this example we show a toy example of a conversion reaction, loaded as a PEtab problem.
[1]:
import pypesto
import pypesto.petab
import pypesto.optimize as optimize
import pypesto.sample as sample
import pypesto.visualize as visualize
import petab
import numpy as np
import logging
import matplotlib.pyplot as plt
# log diagnostics
logger = logging.getLogger("pypesto.sample.diagnostics")
logger.setLevel(logging.INFO)
logger.addHandler(logging.StreamHandler())
# 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()
2020-12-03 12:50:36.856 - amici.petab_import - INFO - Importing model ...
2020-12-03 12:50:36.858 - 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'.
2020-12-03 12:50:36.859 - amici.petab_import - INFO - Species: 2
2020-12-03 12:50:36.860 - amici.petab_import - INFO - Global parameters: 2
2020-12-03 12:50:36.860 - amici.petab_import - INFO - Reactions: 2
2020-12-03 12:50:36.945 - amici.petab_import - INFO - Observables: 1
2020-12-03 12:50:36.946 - amici.petab_import - INFO - Sigmas: 1
2020-12-03 12:50:36.949 - amici.petab_import - DEBUG - Adding output parameters to model: OrderedDict()
2020-12-03 12:50:36.950 - amici.petab_import - DEBUG - Condition table: (1, 0)
2020-12-03 12:50:36.950 - amici.petab_import - DEBUG - Fixed parameters are []
2020-12-03 12:50:36.951 - amici.petab_import - INFO - Overall fixed parameters: 0
2020-12-03 12:50:36.952 - amici.petab_import - INFO - Variable parameters: 2
2020-12-03 12:50:36.993 - amici.sbml_import - INFO - Finished gathering local SBML symbols ++ (5.09E-03s)
2020-12-03 12:50:37.013 - amici.sbml_import - INFO - Finished processing SBML parameters ++ (1.77E-04s)
2020-12-03 12:50:37.030 - amici.sbml_import - INFO - Finished processing SBML compartments ++ (3.28E-04s)
2020-12-03 12:50:37.069 - amici.sbml_import - INFO - Finished processing SBML species initials +++ (2.99E-04s)
2020-12-03 12:50:37.084 - amici.sbml_import - INFO - Finished processing SBML rate rules +++ (5.46E-05s)
2020-12-03 12:50:37.085 - amici.sbml_import - INFO - Finished processing SBML species ++ (3.27E-02s)
2020-12-03 12:50:37.109 - amici.sbml_import - INFO - Finished processing SBML reactions ++ (1.59E-03s)
2020-12-03 12:50:37.128 - amici.sbml_import - INFO - Finished processing SBML rules ++ (2.23E-04s)
2020-12-03 12:50:37.144 - amici.sbml_import - INFO - Finished processing SBML initial assignments++ (1.81E-04s)
2020-12-03 12:50:37.163 - amici.sbml_import - INFO - Finished processing SBML species references ++ (2.54E-04s)
2020-12-03 12:50:37.164 - amici.sbml_import - INFO - Finished importing SBML + (1.94E-01s)
2020-12-03 12:50:37.231 - amici.sbml_import - INFO - Finished processing SBML observables + (4.97E-02s)
2020-12-03 12:50:37.260 - amici.ode_export - INFO - Finished running smart_multiply ++ (1.42E-03s)
2020-12-03 12:50:37.262 - amici.ode_export - INFO - Finished importing SbmlImporter + (1.44E-02s)
2020-12-03 12:50:37.331 - amici.ode_export - INFO - Finished simplifying Jy ++++ (1.25E-02s)
2020-12-03 12:50:37.332 - amici.ode_export - INFO - Finished computing Jy +++ (2.55E-02s)
2020-12-03 12:50:37.352 - amici.ode_export - INFO - Finished writing Jy.cpp ++ (5.79E-02s)
2020-12-03 12:50:37.399 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (8.60E-03s)
2020-12-03 12:50:37.419 - amici.ode_export - INFO - Finished simplifying dJydsigmay ++++ (3.61E-03s)
2020-12-03 12:50:37.419 - amici.ode_export - INFO - Finished computing dJydsigmay +++ (3.86E-02s)
2020-12-03 12:50:37.422 - amici.ode_export - INFO - Finished writing dJydsigmay.cpp ++ (5.75E-02s)
2020-12-03 12:50:37.476 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (3.61E-03s)
2020-12-03 12:50:37.504 - amici.ode_export - INFO - Finished simplifying dJydy ++++ (6.75E-03s)
2020-12-03 12:50:37.505 - amici.ode_export - INFO - Finished computing dJydy +++ (4.53E-02s)
2020-12-03 12:50:37.514 - amici.ode_export - INFO - Finished writing dJydy.cpp ++ (6.92E-02s)
2020-12-03 12:50:37.571 - amici.ode_export - INFO - Finished simplifying w +++++ (1.76E-03s)
2020-12-03 12:50:37.572 - amici.ode_export - INFO - Finished computing w ++++ (1.82E-02s)
2020-12-03 12:50:37.588 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (2.96E-03s)
2020-12-03 12:50:37.601 - amici.ode_export - INFO - Finished simplifying dwdp ++++ (1.85E-03s)
2020-12-03 12:50:37.602 - amici.ode_export - INFO - Finished computing dwdp +++ (6.13E-02s)
2020-12-03 12:50:37.606 - amici.ode_export - INFO - Finished writing dwdp.cpp ++ (7.85E-02s)
2020-12-03 12:50:37.643 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (2.91E-03s)
2020-12-03 12:50:37.657 - amici.ode_export - INFO - Finished simplifying dwdx ++++ (8.44E-04s)
2020-12-03 12:50:37.658 - amici.ode_export - INFO - Finished computing dwdx +++ (2.82E-02s)
2020-12-03 12:50:37.663 - amici.ode_export - INFO - Finished writing dwdx.cpp ++ (4.43E-02s)
2020-12-03 12:50:37.706 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (1.71E-04s)
2020-12-03 12:50:37.719 - amici.ode_export - INFO - Finished simplifying dwdw ++++ (6.41E-05s)
2020-12-03 12:50:37.720 - amici.ode_export - INFO - Finished computing dwdw +++ (3.39E-02s)
2020-12-03 12:50:37.722 - amici.ode_export - INFO - Finished writing dwdw.cpp ++ (4.66E-02s)
2020-12-03 12:50:37.763 - amici.ode_export - INFO - Finished simplifying xdot ++++ (2.00E-03s)
2020-12-03 12:50:37.764 - amici.ode_export - INFO - Finished computing xdot +++ (1.40E-02s)
2020-12-03 12:50:37.770 - amici.ode_export - INFO - Finished writing dxdotdw.cpp ++ (3.24E-02s)
2020-12-03 12:50:37.810 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (1.09E-03s)
2020-12-03 12:50:37.829 - amici.ode_export - INFO - Finished simplifying dxdotdx_explicit ++++ (9.47E-05s)
2020-12-03 12:50:37.830 - amici.ode_export - INFO - Finished computing dxdotdx_explicit +++ (3.03E-02s)
2020-12-03 12:50:37.832 - amici.ode_export - INFO - Finished writing dxdotdx_explicit.cpp ++ (4.87E-02s)
2020-12-03 12:50:37.877 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (1.30E-04s)
2020-12-03 12:50:37.892 - amici.ode_export - INFO - Finished simplifying dxdotdp_explicit ++++ (7.49E-05s)
2020-12-03 12:50:37.893 - amici.ode_export - INFO - Finished computing dxdotdp_explicit +++ (3.15E-02s)
2020-12-03 12:50:37.895 - amici.ode_export - INFO - Finished writing dxdotdp_explicit.cpp ++ (4.88E-02s)
2020-12-03 12:50:37.966 - amici.ode_export - INFO - Finished simplifying y ++++++ (7.81E-05s)
2020-12-03 12:50:37.967 - amici.ode_export - INFO - Finished computing y +++++ (1.24E-02s)
2020-12-03 12:50:37.983 - amici.ode_export - INFO - Finished running smart_jacobian +++++ (3.66E-04s)
2020-12-03 12:50:37.995 - amici.ode_export - INFO - Finished simplifying dydx +++++ (7.21E-05s)
2020-12-03 12:50:37.996 - amici.ode_export - INFO - Finished computing dydx ++++ (5.35E-02s)
2020-12-03 12:50:38.029 - amici.ode_export - INFO - Finished running smart_jacobian +++++ (9.50E-05s)
2020-12-03 12:50:38.046 - amici.ode_export - INFO - Finished simplifying dydw +++++ (9.55E-05s)
2020-12-03 12:50:38.047 - amici.ode_export - INFO - Finished computing dydw ++++ (3.35E-02s)
2020-12-03 12:50:38.064 - amici.ode_export - INFO - Finished simplifying dydx ++++ (7.66E-05s)
2020-12-03 12:50:38.064 - amici.ode_export - INFO - Finished computing dydx +++ (1.37E-01s)
2020-12-03 12:50:38.066 - amici.ode_export - INFO - Finished writing dydx.cpp ++ (1.49E-01s)
2020-12-03 12:50:38.128 - amici.ode_export - INFO - Finished running smart_jacobian +++++ (9.25E-05s)
2020-12-03 12:50:38.151 - amici.ode_export - INFO - Finished simplifying dydp +++++ (8.81E-05s)
2020-12-03 12:50:38.152 - amici.ode_export - INFO - Finished computing dydp ++++ (3.52E-02s)
2020-12-03 12:50:38.165 - amici.ode_export - INFO - Finished simplifying dydp ++++ (5.76E-05s)
2020-12-03 12:50:38.165 - amici.ode_export - INFO - Finished computing dydp +++ (6.53E-02s)
2020-12-03 12:50:38.167 - amici.ode_export - INFO - Finished writing dydp.cpp ++ (7.73E-02s)
2020-12-03 12:50:38.224 - amici.ode_export - INFO - Finished simplifying sigmay +++++ (7.37E-05s)
2020-12-03 12:50:38.225 - amici.ode_export - INFO - Finished computing sigmay ++++ (1.93E-02s)
2020-12-03 12:50:38.244 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (2.34E-04s)
2020-12-03 12:50:38.259 - amici.ode_export - INFO - Finished simplifying dsigmaydp ++++ (1.03E-04s)
2020-12-03 12:50:38.259 - amici.ode_export - INFO - Finished computing dsigmaydp +++ (6.65E-02s)
2020-12-03 12:50:38.261 - amici.ode_export - INFO - Finished writing dsigmaydp.cpp ++ (7.81E-02s)
2020-12-03 12:50:38.277 - amici.ode_export - INFO - Finished writing sigmay.cpp ++ (7.10E-04s)
2020-12-03 12:50:38.297 - amici.ode_export - INFO - Finished writing w.cpp ++ (1.72E-03s)
2020-12-03 12:50:38.346 - amici.ode_export - INFO - Finished simplifying x0 ++++ (7.39E-05s)
2020-12-03 12:50:38.347 - amici.ode_export - INFO - Finished computing x0 +++ (2.06E-02s)
2020-12-03 12:50:38.349 - amici.ode_export - INFO - Finished writing x0.cpp ++ (4.04E-02s)
2020-12-03 12:50:38.396 - amici.ode_export - INFO - Finished simplifying x0_fixedParameters ++++ (4.06E-05s)
2020-12-03 12:50:38.397 - amici.ode_export - INFO - Finished computing x0_fixedParameters +++ (1.22E-02s)
2020-12-03 12:50:38.398 - amici.ode_export - INFO - Finished writing x0_fixedParameters.cpp ++ (2.86E-02s)
2020-12-03 12:50:38.443 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (2.03E-04s)
2020-12-03 12:50:38.463 - amici.ode_export - INFO - Finished simplifying sx0 ++++ (7.03E-05s)
2020-12-03 12:50:38.464 - amici.ode_export - INFO - Finished computing sx0 +++ (3.13E-02s)
2020-12-03 12:50:38.466 - amici.ode_export - INFO - Finished writing sx0.cpp ++ (4.81E-02s)
2020-12-03 12:50:38.511 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (5.74E-05s)
2020-12-03 12:50:38.524 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (4.22E-05s)
2020-12-03 12:50:38.536 - amici.ode_export - INFO - Finished simplifying sx0_fixedParameters ++++ (6.61E-05s)
2020-12-03 12:50:38.537 - amici.ode_export - INFO - Finished computing sx0_fixedParameters +++ (4.65E-02s)
2020-12-03 12:50:38.543 - amici.ode_export - INFO - Finished writing sx0_fixedParameters.cpp ++ (6.36E-02s)
2020-12-03 12:50:38.564 - amici.ode_export - INFO - Finished writing xdot.cpp ++ (2.97E-03s)
2020-12-03 12:50:38.577 - amici.ode_export - INFO - Finished writing y.cpp ++ (4.90E-04s)
2020-12-03 12:50:38.622 - amici.ode_export - INFO - Finished simplifying x_rdata ++++ (6.08E-05s)
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2020-12-03 12:50:38.624 - amici.ode_export - INFO - Finished writing x_rdata.cpp ++ (2.95E-02s)
2020-12-03 12:50:38.661 - amici.ode_export - INFO - Finished simplifying total_cl ++++ (3.71E-05s)
2020-12-03 12:50:38.662 - amici.ode_export - INFO - Finished computing total_cl +++ (8.79E-03s)
2020-12-03 12:50:38.663 - amici.ode_export - INFO - Finished writing total_cl.cpp ++ (2.47E-02s)
2020-12-03 12:50:38.698 - amici.ode_export - INFO - Finished simplifying x_solver ++++ (8.49E-05s)
2020-12-03 12:50:38.699 - amici.ode_export - INFO - Finished computing x_solver +++ (9.70E-03s)
2020-12-03 12:50:38.701 - amici.ode_export - INFO - Finished writing x_solver.cpp ++ (2.21E-02s)
2020-12-03 12:50:38.706 - amici.ode_export - INFO - Finished generating cpp code + (1.43E+00s)
2020-12-03 12:51:02.545 - amici.ode_export - INFO - Finished compiling cpp code + (2.38E+01s)
2020-12-03 12:51:02.548 - amici.petab_import - INFO - Finished Importing PEtab model (2.57E+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-0.11.8-py3.8-linux-x86_64.egg/amici/swig -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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-0.11.8-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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_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_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_dwdw_rowvals.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/local/lib/python3.8/dist-packages/amici-0.11.8-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
Create the sampler object, in this case we will use adaptive parallel tempering with 3 temperatures.
[2]:
sampler = sample.AdaptiveParallelTemperingSampler(
internal_sampler=sample.AdaptiveMetropolisSampler(),
n_chains=3)
First, we will initiate the MCMC chain at a “random” point in parameter space, e.g. \(\theta_{start} = [3, -4]\)
[3]:
result = sample.sample(problem, n_samples=10000, sampler=sampler, x0=np.array([3,-4]))
elapsed_time = result.sample_result.time
print(f'Elapsed time: {round(elapsed_time,2)}')
100%|██████████| 10000/10000 [00:56<00:00, 176.13it/s]
Elapsed time: 69.56
[4]:
ax = visualize.sampling_parameters_trace(result, use_problem_bounds=False, size=(12,5))
Burn in index not found in the results, the full chain will be shown.
You may want to use, e.g., 'pypesto.sample.geweke_test'.
By visualizing the chains, we can see a warm up phase occurring until convergence of the chain is reached. This is commonly known as “burn in” phase and should be discarded. An automatic way to evaluate and find the index of the chain in which the warm up is finished can be done by using the Geweke test.
[5]:
sample.geweke_test(result=result)
ax = visualize.sampling_parameters_trace(result, use_problem_bounds=False, size=(12,5))
Geweke burn-in index: 500
[6]:
ax = visualize.sampling_parameters_trace(result, use_problem_bounds=False, full_trace=True, size=(12,5))
Calculate the effective sample size per computation time. We save the results in a variable as we will compare them later.
[7]:
sample.effective_sample_size(result=result)
ess = result.sample_result.effective_sample_size
print(f'Effective sample size per computation time: {round(ess/elapsed_time,2)}')
Estimated chain autocorrelation: 7.285355458658169
Estimated effective sample size: 1146.7220745576444
Effective sample size per computation time: 16.48
Commonly, as a first step, optimization is performed, in order to find good parameter point estimates.¶
[8]:
res = optimize.minimize(problem, n_starts=10)
Parameters obtained from history and optimizer do not match: [-0.2541754 -0.60835856], [-0.25416791 -0.60834117]
By passing the result object to the function, the previously found global optimum is used as starting point for the MCMC sampling.
[9]:
res = sample.sample(problem, n_samples=10000, sampler=sampler, result=res)
elapsed_time = res.sample_result.time
print('Elapsed time: '+str(round(elapsed_time,2)))
100%|██████████| 10000/10000 [00:58<00:00, 171.62it/s]
Elapsed time: 71.8
When the sampling is finished, we can analyse our results. 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:
[10]:
ax = visualize.sampling_parameters_trace(res, use_problem_bounds=False, size=(12,5))
Burn in index not found in the results, the full chain will be shown.
You may want to use, e.g., 'pypesto.sample.geweke_test'.
By visual inspection one can see that the chain is already converged from the start. This is already showing the benefit of initiating the chain at the optimal parameter vector. However, this may not be always the case.
[11]:
sample.geweke_test(result=res)
ax = visualize.sampling_parameters_trace(res, use_problem_bounds=False, size=(12,5))
Geweke burn-in index: 0
[12]:
sample.effective_sample_size(result=res)
ess = res.sample_result.effective_sample_size
print(f'Effective sample size per computation time: {round(ess/elapsed_time,2)}')
Estimated chain autocorrelation: 7.6331400037456
Estimated effective sample size: 1158.4429298796192
Effective sample size per computation time: 16.13