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@dweindl
dweindl committed Nov 22, 2023
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21 changes: 10 additions & 11 deletions documentation/ExampleJax.ipynb
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"output_type": "stream",
"text": [
"Cloning into 'tmp/benchmark-models'...\n",
"remote: Enumerating objects: 336, done.\u001b[K\n",
"remote: Counting objects: 100% (336/336), done.\u001b[K\n",
"remote: Compressing objects: 100% (285/285), done.\u001b[K\n",
"remote: Total 336 (delta 88), reused 216 (delta 39), pack-reused 0\u001b[K\n",
"remote: Enumerating objects: 336, done.\u001B[K\n",
"remote: Counting objects: 100% (336/336), done.\u001B[K\n",
"remote: Compressing objects: 100% (285/285), done.\u001B[K\n",
"remote: Total 336 (delta 88), reused 216 (delta 39), pack-reused 0\u001B[K\n",
"Receiving objects: 100% (336/336), 2.11 MiB | 7.48 MiB/s, done.\n",
"Resolving deltas: 100% (88/88), done.\n"
]
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"clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -I/Users/fabian/Documents/projects/AMICI/documentation/amici_models/Boehm_JProteomeRes2014 -I/Users/fabian/Documents/projects/AMICI/python/sdist/amici/include -I/Users/fabian/Documents/projects/AMICI/python/sdist/amici/ThirdParty/gsl -I/Users/fabian/Documents/projects/AMICI/python/sdist/amici/ThirdParty/sundials/include -I/Users/fabian/Documents/projects/AMICI/python/sdist/amici/ThirdParty/SuiteSparse/include -I/opt/homebrew/Cellar/hdf5/1.12.2_2/include -I/Users/fabian/Documents/projects/AMICI/build/venv/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c swig/Boehm_JProteomeRes2014_wrap.cpp -o build/temp.macosx-13-arm64-cpython-310/swig/Boehm_JProteomeRes2014_wrap.o -std=c++14\n",
"clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -I/Users/fabian/Documents/projects/AMICI/documentation/amici_models/Boehm_JProteomeRes2014 -I/Users/fabian/Documents/projects/AMICI/python/sdist/amici/include -I/Users/fabian/Documents/projects/AMICI/python/sdist/amici/ThirdParty/gsl -I/Users/fabian/Documents/projects/AMICI/python/sdist/amici/ThirdParty/sundials/include -I/Users/fabian/Documents/projects/AMICI/python/sdist/amici/ThirdParty/SuiteSparse/include -I/opt/homebrew/Cellar/hdf5/1.12.2_2/include -I/Users/fabian/Documents/projects/AMICI/build/venv/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c wrapfunctions.cpp -o build/temp.macosx-13-arm64-cpython-310/wrapfunctions.o -std=c++14\n",
"clang++ -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_Jy.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dJydsigma.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dJydy.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dJydy_colptrs.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dJydy_rowvals.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dsigmaydp.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdp.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdp_colptrs.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdp_rowvals.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdw.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdw_colptrs.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdw_rowvals.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdx.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdx_colptrs.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dwdx_rowvals.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dxdotdw.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dxdotdw_colptrs.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dxdotdw_rowvals.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_dydx.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_sigmay.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_sx0_fixedParameters.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_w.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_x0.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_x0_fixedParameters.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_x_rdata.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_x_solver.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_xdot.o build/temp.macosx-13-arm64-cpython-310/Boehm_JProteomeRes2014_y.o build/temp.macosx-13-arm64-cpython-310/swig/Boehm_JProteomeRes2014_wrap.o build/temp.macosx-13-arm64-cpython-310/wrapfunctions.o -L/opt/homebrew/Cellar/hdf5/1.12.2_2/lib -L/Users/fabian/Documents/projects/AMICI/python/sdist/amici/libs -lamici -lsundials -lsuitesparse -lcblas -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 -o /Users/fabian/Documents/projects/AMICI/documentation/amici_models/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014/_Boehm_JProteomeRes2014.cpython-310-darwin.so\n",
"ld: warning: -undefined dynamic_lookup may not work with chained fixups\n",
"\n"
"ld: warning: -undefined dynamic_lookup may not work with chained fixups\n"
]
},
{
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}
],
"source": [
"from amici.petab_import import import_petab_problem\n",
"from amici.petab.petab_import import import_petab_problem\n",
"\n",
"amici_model = import_petab_problem(petab_problem, force_compile=True)"
]
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"id": "e2ef051a",
"metadata": {},
"source": [
"For full jax support, we would have to implement a new [primitive](https://jax.readthedocs.io/en/latest/notebooks/How_JAX_primitives_work.html), which would require quite a bit of engineering, and in the end wouldn't add much benefit since AMICI can't run on GPUs. Instead will interface AMICI using the experimental jax module [`host_callback`](https://jax.readthedocs.io/en/latest/jax.experimental.host_callback.html). "
"For full jax support, we would have to implement a new [primitive](https://jax.readthedocs.io/en/latest/notebooks/How_JAX_primitives_work.html), which would require quite a bit of engineering, and in the end wouldn't add much benefit since AMICI can't run on GPUs. Instead, we will interface AMICI using the experimental jax module [`host_callback`](https://jax.readthedocs.io/en/latest/jax.experimental.host_callback.html). "
]
},
{
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"metadata": {},
"outputs": [],
"source": [
"from amici.petab_objective import simulate_petab\n",
"from amici.petab.simulations import simulate_petab\n",
"import amici\n",
"\n",
"amici_solver = amici_model.getSolver()\n",
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"id": "98e819bd",
"metadata": {},
"source": [
"Now we can finally define the JAX function that runs amici simulation using the host callback. We add a `custom_jvp` decorater so that we can define a custom jacobian vector product function in the next step. More details about custom jacobian vector product functions can be found in the [JAX documentation](https://jax.readthedocs.io/en/latest/notebooks/Custom_derivative_rules_for_Python_code.html)"
"Now we can finally define the JAX function that runs amici simulation using the host callback. We add a `custom_jvp` decorator so that we can define a custom jacobian vector product function in the next step. More details about custom jacobian vector product functions can be found in the [JAX documentation](https://jax.readthedocs.io/en/latest/notebooks/Custom_derivative_rules_for_Python_code.html)"
]
},
{
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"metadata": {},
"source": [
"We see quite some differences in the gradient calculation. The primary reason is that running JAX in default configuration will use float32 precision for the parameters that are passed to AMICI, which uses float64, and the derivative of the parameter transformation \n",
"As AMICI simulations that run on the CPU are the most expensive operation, there is barely any tradeoff for using float32 vs float64 in JAX. Therefore we configure JAX to use float64 instead and rerun simulations."
"As AMICI simulations that run on the CPU are the most expensive operation, there is barely any tradeoff for using float32 vs float64 in JAX. Therefore, we configure JAX to use float64 instead and rerun simulations."
]
},
{
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4 changes: 2 additions & 2 deletions documentation/GettingStarted.ipynb
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"metadata": {},
"source": [
"## Model Compilation\n",
"Before simulations can be run, the model must be imported and compiled. In this process, AMICI performs all symbolic manipulations that later enable scalable simulations and efficient sensitivity computation. The first step towards model compilation is the creation of an [SbmlImporter](https://amici.readthedocs.io/en/latest/generated/amici.sbml_import.SbmlImporter.html) instance, which requires an SBML Document that specifies the model using the [Systems Biology Markup Language (SBML)](http://sbml.org/Main_Page). \n",
"Before simulations can be run, the model must be imported and compiled. In this process, AMICI performs all symbolic manipulations that later enable scalable simulations and efficient sensitivity computation. The first step towards model compilation is the creation of an [SbmlImporter](https://amici.readthedocs.io/en/latest/generated/amici.sbml_import.SbmlImporter.html) instance, which requires an SBML Document that specifies the model using the [Systems Biology Markup Language (SBML)](https://sbml.org/). \n",
"\n",
"For the purpose of this tutorial, we will use `model_steadystate_scaled.xml`, which is contained in the same directory as this notebook."
]
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"cell_type": "markdown",
"metadata": {},
"source": [
"Model simulations can be executed using the [amici.runAmiciSimulations](https://amici.readthedocs.io/en/latest/generated/amici.html#amici.runAmiciSimulation) routine. By default the model does not not contain any timepoints for which the model is to be simulated. Here we define a simulation timecourse with two timepoints at `0` and `1` and then run the simulation."
"Model simulations can be executed using the [amici.runAmiciSimulations](https://amici.readthedocs.io/en/latest/generated/amici.html#amici.runAmiciSimulation) routine. By default, the model does not contain any timepoints for which the model is to be simulated. Here we define a simulation timecourse with two timepoints at `0` and `1` and then run the simulation."
]
},
{
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1 change: 1 addition & 0 deletions documentation/python_modules.rst
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amici.petab.pysb_import
amici.petab.sbml_import
amici.petab.simulations
amici.petab.simulator
amici.petab_import
amici.petab_import_pysb
amici.petab_objective
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