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Memory deallocation in case of errors #13

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FFroehlich opened this issue Jul 12, 2016 · 1 comment
Closed

Memory deallocation in case of errors #13

FFroehlich opened this issue Jul 12, 2016 · 1 comment
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@FFroehlich
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The code for memory cleanup is quite messy at the moment. Especially in the case of error I am not too sure that we do not run into memory leaks. Here the structure should definitely be improved (set flags whether certain parts of the memory have been allocated?)
@FFroehlich FFroehlich added the bug label Jul 12, 2016
@dweindl
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dweindl commented Sep 12, 2016

I started initializing all pointers in UserData ... with 0 to be able to test whether memory has been allocated and added respective freeUserData ... functions. Currently only on branch feature_compile_standalone. Will try to merge soon.

@FFroehlich FFroehlich added this to the v0.4.0 adjoint sensitivitis for events milestone Sep 30, 2016
dweindl added a commit to dweindl/AMICI that referenced this issue Feb 17, 2025
@dweindl
Fix crashes due to uncaught exceptions
21e28e2 
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 added a commit that referenced this issue Feb 18, 2025
@dweindl
Fix crashes due to uncaught exceptions in ~FinalStateStorer (#2647)
2c117a5 
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 added a commit to dweindl/AMICI that referenced this issue Feb 18, 2025
@dweindl
Fix crashes due to uncaught exceptions in ~FinalStateStorer (AMICI-…
f087352 
…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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