[petsc-users] Memory leak when combining PETSc-based vectors and boost::odeint
Matthew Knepley
knepley at gmail.com
Fri Apr 1 06:19:05 CDT 2022
On Fri, Apr 1, 2022 at 6:50 AM Roland Richter <roland.richter at ntnu.no>
wrote:
> I re-run my code with a debug version of PETSc, resulting in
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Corrupt argument: https://petsc.org/release/faq/#valgrind
> [0]PETSC ERROR: Object already free: Parameter # 1
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.17.0-8-gf6d6129e50 GIT
> Date: 2022-03-31 18:10:33 +0000
> [0]PETSC ERROR: #1 VecGetSize() at
> /home/roland/Downloads/git-files/petsc/src/vec/vec/interface/vector.c:670
> 0 64
> [0]PETSC ERROR: #2 VecDestroy() at
> /home/roland/Downloads/git-files/petsc/src/vec/vec/interface/vector.c:375
> 0 64
> [0]PETSC ERROR: #3 VecGetArray() at
> /home/roland/Downloads/git-files/petsc/src/vec/vec/interface/rvector.c:1780
>
> I do not understand why it tries to access the vector, even though it has
> been set to PETSC_NULL in the previous free-call.
>
> What code is setting that pointer to NULL?
Thanks,
Matt
> Regards,
>
> Roland
> Am 31.03.22 um 15:50 schrieb Matthew Knepley:
>
> On Thu, Mar 31, 2022 at 9:47 AM Roland Richter <roland.richter at ntnu.no>
> wrote:
>
>> The backtrace is
>>
>> #0 0x00007fffeec4ba97 in VecGetSize_Seq () from
>> /opt/petsc/lib/libpetsc.so.3.016
>> #1 0x00007fffeec78f5a in VecGetSize () from
>> /opt/petsc/lib/libpetsc.so.3.016
>> #2 0x0000000000410b73 in test_ts_arma_with_pure_petsc_preconfigured_clean(unsigned
>> long, unsigned long, arma::Col<std::complex<doubl
>> e> > const&, arma::Col<std::complex<double> >&, double, double, double)
>> [clone .constprop.0] ()
>> #3 0x0000000000414384 in test_RK4_solvers_clean(unsigned long, unsigned
>> long, unsigned long, bool) [clone .constprop.0] ()
>> #4 0x0000000000405c6c in main ()
>>
> It looks like you are passing an invalid vector. If you compiled in debug
> mode, it would tell you. I would run
> in debug until my code was running like I expect, then switch to
> optimized. You can do that by using two
> different PETSC_ARCH configures, and switch at runtime with that variable.
>
> Thanks,
>
> Matt
>
>> Regards,
>> Roland Richter
>>
>> Am 31.03.22 um 15:35 schrieb Matthew Knepley:
>>
>> On Thu, Mar 31, 2022 at 9:01 AM Roland Richter <roland.richter at ntnu.no>
>> wrote:
>>
>>> Hei,
>>>
>>> Thanks for the idea! I added a simple std::cout for both constructor and
>>> destructor, and found out that my destructor is called multiple times,
>>> while the constructor is called only once. This could explain the error
>>> (double free), but I do not know why segfault is thrown even though I
>>> explicitly check if the vector has been used. Are there explanations for
>>> that?
>>>
>> Run with -start_in_debugger and get the stack trace when it faults. Right
>> now, I have no idea where it is faulting.
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> Regards,
>>>
>>> Roland Richter
>>> Am 31.03.22 um 12:14 schrieb Matthew Knepley:
>>>
>>> On Thu, Mar 31, 2022 at 5:58 AM Roland Richter <roland.richter at ntnu.no>
>>> wrote:
>>>
>>>> Hei,
>>>>
>>>> For a project I wanted to combine boost::odeint for timestepping and
>>>> PETSc-based vectors and matrices for calculating the right hand side. As
>>>> comparison for both timing and correctness I set up an armadillo-based
>>>> right hand side (with the main-function being in *main.cpp*, and the
>>>> test code in *test_timestepping_clean.cpp*)
>>>>
>>>> In theory, the code works fine, but I have some issues with cleaning up
>>>> afterwards in my struct *Petsc_RHS_state_clean*. My initial intention
>>>> was to set up all involved matrices and vectors within the constructor, and
>>>> free the memory in the destructor. To avoid freeing vectors I have not used
>>>> I initially set them to *PETSC_NULL*, and check if this value has been
>>>> changed before calling *VecDestroy().*
>>>>
>>> You do not need to check. Destroy() functions already check for NULL.
>>>
>>>> However, when doing that I get the following error:
>>>>
>>>> [0]PETSC ERROR:
>>>> ------------------------------------------------------------------------
>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>>>> probably memory access out of range
>>>> [0]PETSC ERROR: Try option -start_in_debugger or
>>>> -on_error_attach_debugger
>>>> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind
>>>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>>>> OS X to find memory corruption errors
>>>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>>>> and run
>>>> [0]PETSC ERROR: to get more information on the crash.
>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> --------------------------------------------------------------
>>>>
>>>> If I comment out that code in ~Petsc_RHS_state_clean(), the program
>>>> runs, but will use ~17 GByte of RAM during runtime. As the memory is not
>>>> used immediately in full, but rather increases during running, I assume a
>>>> memory leak somewhere. Where does it come from, and how can I avoid it?
>>>>
>>> It must be that your constructor is called multiple times without
>>> calling your destructor. I cannot understand this code in order
>>> to see where that happens, but you should just be able to run in the
>>> debugger and put a break point at the creation and
>>> destruction calls.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>> Thanks!
>>>>
>>>> Regards,
>>>>
>>>> Roland Richter
>>>>
>>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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