Separate output parameter and dynamic parameters #11
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dweindl
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Feb 17, 2025
Due to LLNL/sundials#82, we can get exceptions from `CVodeSolver::getSens`, escaping `FinalStateStorer::~FinalStateStorer`, that will result in crashes. This is fixed here. The issue is semi-producible with [Boehm_JProteomeRes2014](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/tree/15b4f78aff1121870537ad3e1a6b902cb8f73930/Benchmark-Models/Boehm_JProteomeRes2014): Progamm output: ``` 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3482: Internal t = 0 and h = 0 are such that t + h = t on the next step. The solver will continue anyway. (99) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVodeGetDky:BAD_T] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3783: Illegal value for t.t = 2.5 is not between tcur - hu = 0 and tcur = 0. (-25) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVodeGetDky:BAD_T] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3783: Illegal value for t.t = 5 is not between tcur - hu = 0 and tcur = 0. (-25) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:ILL_INPUT] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3328: Trouble interpolating at tout = 5. tout too far back in direction of integration (-22) 2025-02-17 14:44:33.988 - amici.swig_wrappers - ERROR - [model1_data1][FORWARD_FAILURE] AMICI forward simulation failed at t = 5: AMICI failed to integrate the forward problem terminate called after throwing an instance of 'amici::CvodeException' what(): CVODE routine CVodeGetSens failed with error code -25. Thread 1 "python" received signal SIGABRT, Aborted. ``` Stacktrace: ``` AMICI-dev#10 0x00007ffff70811f1 in _Unwind_RaiseException (exc=0x6d5ff10) at ../../../src/libgcc/unwind.inc:136 AMICI-dev#11 0x00007ffff48bb384 in __cxxabiv1::__cxa_throw (obj=<optimized out>, tinfo=0x7fff5c6d6aa8 <typeinfo for amici::CvodeException>, dest=0x7fff5c5476c4 <amici::CvodeException::~CvodeException()>) at ../../../../src/libstdc++-v3/libsupc++/eh_throw.cc:93 AMICI-dev#12 0x00007fff5c5bdb64 in amici::CVodeSolver::getSens (this=0x6d130d0) at python/sdist/amici/src/solver_cvodes.cpp:663 AMICI-dev#13 0x00007fffbc5709e8 in amici::Solver::getStateSensitivity (this=0x6d130d0, t=2.5) at python/sdist/amici/src/solver.cpp:1340 AMICI-dev#14 0x00007fffbc570750 in amici::Solver::writeSolution (this=0x6d130d0, t=0x6d26db0, x=..., dx=..., sx=..., xQ=...) at python/sdist/amici/src/solver.cpp:1303 AMICI-dev#15 0x00007fffbc5d376d in amici::ForwardProblem::getSimulationState (this=0x6d26c90) at python/sdist/amici/src/forwardproblem.cpp:421 AMICI-dev#16 0x00007fffbc5d45df in amici::FinalStateStorer::~FinalStateStorer (this=0x7fffffffb308, __in_chrg=<optimized out>) at include/amici/forwardproblem.h:450 AMICI-dev#17 0x00007fffbc5d2285 in amici::ForwardProblem::workForwardProblem (this=0x6d26c90) at python/sdist/amici/src/forwardproblem.cpp:203 AMICI-dev#18 0x00007fffbc54fbf9 in amici::runAmiciSimulation (solver=..., edata=0x5078010, model=..., rethrow=false) at python/sdist/amici/src/amici.cpp:108 ```
dweindl
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Feb 18, 2025
Due to LLNL/sundials#82, we can get exceptions from `CVodeSolver::getSens`, escaping `FinalStateStorer::~FinalStateStorer`, that will result in crashes. This is fixed here. The issue is semi-producible with [Boehm_JProteomeRes2014](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/tree/15b4f78aff1121870537ad3e1a6b902cb8f73930/Benchmark-Models/Boehm_JProteomeRes2014) with forward sensitivities: Program output: ``` 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3482: Internal t = 0 and h = 0 are such that t + h = t on the next step. The solver will continue anyway. (99) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVodeGetDky:BAD_T] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3783: Illegal value for t.t = 2.5 is not between tcur - hu = 0 and tcur = 0. (-25) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVodeGetDky:BAD_T] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3783: Illegal value for t.t = 5 is not between tcur - hu = 0 and tcur = 0. (-25) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:ILL_INPUT] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3328: Trouble interpolating at tout = 5. tout too far back in direction of integration (-22) 2025-02-17 14:44:33.988 - amici.swig_wrappers - ERROR - [model1_data1][FORWARD_FAILURE] AMICI forward simulation failed at t = 5: AMICI failed to integrate the forward problem terminate called after throwing an instance of 'amici::CvodeException' what(): CVODE routine CVodeGetSens failed with error code -25. Thread 1 "python" received signal SIGABRT, Aborted. ``` Stack trace: ``` #10 0x00007ffff70811f1 in _Unwind_RaiseException (exc=0x6d5ff10) at ../../../src/libgcc/unwind.inc:136 #11 0x00007ffff48bb384 in __cxxabiv1::__cxa_throw (obj=<optimized out>, tinfo=0x7fff5c6d6aa8 <typeinfo for amici::CvodeException>, dest=0x7fff5c5476c4 <amici::CvodeException::~CvodeException()>) at ../../../../src/libstdc++-v3/libsupc++/eh_throw.cc:93 #12 0x00007fff5c5bdb64 in amici::CVodeSolver::getSens (this=0x6d130d0) at python/sdist/amici/src/solver_cvodes.cpp:663 #13 0x00007fffbc5709e8 in amici::Solver::getStateSensitivity (this=0x6d130d0, t=2.5) at python/sdist/amici/src/solver.cpp:1340 #14 0x00007fffbc570750 in amici::Solver::writeSolution (this=0x6d130d0, t=0x6d26db0, x=..., dx=..., sx=..., xQ=...) at python/sdist/amici/src/solver.cpp:1303 #15 0x00007fffbc5d376d in amici::ForwardProblem::getSimulationState (this=0x6d26c90) at python/sdist/amici/src/forwardproblem.cpp:421 #16 0x00007fffbc5d45df in amici::FinalStateStorer::~FinalStateStorer (this=0x7fffffffb308, __in_chrg=<optimized out>) at include/amici/forwardproblem.h:450 #17 0x00007fffbc5d2285 in amici::ForwardProblem::workForwardProblem (this=0x6d26c90) at python/sdist/amici/src/forwardproblem.cpp:203 #18 0x00007fffbc54fbf9 in amici::runAmiciSimulation (solver=..., edata=0x5078010, model=..., rethrow=false) at python/sdist/amici/src/amici.cpp:108 ```
dweindl
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Feb 18, 2025
…dev#2647) Due to LLNL/sundials#82, we can get exceptions from `CVodeSolver::getSens`, escaping `FinalStateStorer::~FinalStateStorer`, that will result in crashes. This is fixed here. The issue is semi-producible with [Boehm_JProteomeRes2014](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/tree/15b4f78aff1121870537ad3e1a6b902cb8f73930/Benchmark-Models/Boehm_JProteomeRes2014) with forward sensitivities: Program output: ``` 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3482: Internal t = 0 and h = 0 are such that t + h = t on the next step. The solver will continue anyway. (99) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVodeGetDky:BAD_T] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3783: Illegal value for t.t = 2.5 is not between tcur - hu = 0 and tcur = 0. (-25) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVodeGetDky:BAD_T] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3783: Illegal value for t.t = 5 is not between tcur - hu = 0 and tcur = 0. (-25) 2025-02-17 14:44:33.988 - amici.swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:ILL_INPUT] python/sdist/amici/ThirdParty/sundials/src/cvodes/cvodes.c:3328: Trouble interpolating at tout = 5. tout too far back in direction of integration (-22) 2025-02-17 14:44:33.988 - amici.swig_wrappers - ERROR - [model1_data1][FORWARD_FAILURE] AMICI forward simulation failed at t = 5: AMICI failed to integrate the forward problem terminate called after throwing an instance of 'amici::CvodeException' what(): CVODE routine CVodeGetSens failed with error code -25. Thread 1 "python" received signal SIGABRT, Aborted. ``` Stack trace: ``` AMICI-dev#10 0x00007ffff70811f1 in _Unwind_RaiseException (exc=0x6d5ff10) at ../../../src/libgcc/unwind.inc:136 AMICI-dev#11 0x00007ffff48bb384 in __cxxabiv1::__cxa_throw (obj=<optimized out>, tinfo=0x7fff5c6d6aa8 <typeinfo for amici::CvodeException>, dest=0x7fff5c5476c4 <amici::CvodeException::~CvodeException()>) at ../../../../src/libstdc++-v3/libsupc++/eh_throw.cc:93 AMICI-dev#12 0x00007fff5c5bdb64 in amici::CVodeSolver::getSens (this=0x6d130d0) at python/sdist/amici/src/solver_cvodes.cpp:663 AMICI-dev#13 0x00007fffbc5709e8 in amici::Solver::getStateSensitivity (this=0x6d130d0, t=2.5) at python/sdist/amici/src/solver.cpp:1340 AMICI-dev#14 0x00007fffbc570750 in amici::Solver::writeSolution (this=0x6d130d0, t=0x6d26db0, x=..., dx=..., sx=..., xQ=...) at python/sdist/amici/src/solver.cpp:1303 AMICI-dev#15 0x00007fffbc5d376d in amici::ForwardProblem::getSimulationState (this=0x6d26c90) at python/sdist/amici/src/forwardproblem.cpp:421 AMICI-dev#16 0x00007fffbc5d45df in amici::FinalStateStorer::~FinalStateStorer (this=0x7fffffffb308, __in_chrg=<optimized out>) at include/amici/forwardproblem.h:450 AMICI-dev#17 0x00007fffbc5d2285 in amici::ForwardProblem::workForwardProblem (this=0x6d26c90) at python/sdist/amici/src/forwardproblem.cpp:203 AMICI-dev#18 0x00007fffbc54fbf9 in amici::runAmiciSimulation (solver=..., edata=0x5078010, model=..., rethrow=false) at python/sdist/amici/src/amici.cpp:108 ```
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Currently, sensitivities are computed for all model parameters and not only for those that have nonzero state sensitivities. This does not matter too much for small systems but can become problematic for larger systems.
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