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Fix crashes due to uncaught exceptions in ~FinalStateStorer (#2647)
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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
```
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dweindl authored Feb 18, 2025
1 parent 8366b87 commit 2c117a5
Showing 1 changed file with 30 additions and 12 deletions.
42 changes: 30 additions & 12 deletions include/amici/forwardproblem.h
Original file line number Diff line number Diff line change
Expand Up @@ -441,19 +441,37 @@ class FinalStateStorer : public ContextManager {
/**
* @brief destructor, stores simulation state
*/
~FinalStateStorer() {
~FinalStateStorer() noexcept(false) {
if (fwd_) {
fwd_->final_state_ = fwd_->getSimulationState();
// if there is an associated output timepoint, also store it in
// timepoint_states if it's not present there.
// this may happen if there is an error just at
// (or indistinguishably before) an output timepoint
auto final_time = fwd_->getFinalTime();
auto const timepoints = fwd_->model->getTimepoints();
if (!fwd_->timepoint_states_.count(final_time)
&& std::find(timepoints.cbegin(), timepoints.cend(), final_time)
!= timepoints.cend()) {
fwd_->timepoint_states_[final_time] = fwd_->final_state_;
try {
// This may throw in `CVodeSolver::getSens`
// due to https://github.com/LLNL/sundials/issues/82.
// Therefore, this dtor must be `noexcept(false)` to avoid
// programm termination.
fwd_->final_state_ = fwd_->getSimulationState();
// if there is an associated output timepoint, also store it in
// timepoint_states if it's not present there.
// this may happen if there is an error just at
// (or indistinguishably before) an output timepoint
auto final_time = fwd_->getFinalTime();
auto const timepoints = fwd_->model->getTimepoints();
if (!fwd_->timepoint_states_.count(final_time)
&& std::find(timepoints.cbegin(), timepoints.cend(), final_time)
!= timepoints.cend()) {
fwd_->timepoint_states_[final_time] = fwd_->final_state_;
}
} catch (std::exception const&) {
// We must not throw in case we are already in the stack
// unwinding phase due to some other active exception, otherwise
// this will also lead to termination.
//
// In case there is another active exception,
// `fwd_->{final_state_,timepoint_states_}` won't be set,
// and we assume that they are either not accessed anymore, or
// that there is appropriate error handling in place.
if(!std::uncaught_exceptions()) {
throw;
}
}
}
}
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