[petsc-users] CVODE N_Vector PETSc interface gives a memory corruption error

[Matthew Knepley]

On Wed, Nov 18, 2020 at 11:11 PM Praharsh Suryadevara via petsc-users <
petsc-users at mcs.anl.gov> wrote:

> Hi All,
> I asked this on StackOverflow but I realized it's better off asked here,
>
> I'm trying to use the CVODE_PETSc interface, and I've been getting
> memory corruption errors I couldn't understand, so I tried to make a
> minimal reproducible example for one below. Running this,
>

There is a bug in CVODE's PETSc interface:

==16192== Invalid write of size 8
==16192==    at 0x4E4553C: N_VNewEmpty_Petsc (in
/home/praharsh/.local/lib/libsundials_nvecpetsc.so.5.5.0)
==16192==    by 0x4E45630: N_VMake_Petsc (in
/home/praharsh/.local/lib/libsundials_nvecpetsc.so.5.5.0)
==16192==    by 0x108AF8: main (in
/home/praharsh/.local/examples/cvode/petsc/cv_petsc_ex7)
==16192==  Address 0xfaf8708 is 0 bytes after a block of size 392 alloc'd
==16192==    at 0x4C2FB0F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==16192==    by 0x4044922: ??? (in
/var/empty/local/lib/libsundials_cvode.so.5.3.0)
==16192==    by 0x84000001: ???
==16192==    by 0x4E4532E: N_VNewEmpty_Petsc (in
/home/praharsh/.local/lib/libsundials_nvecpetsc.so.5.5.0)
==16192==    by 0x4E45630: N_VMake_Petsc (in
/home/praharsh/.local/lib/libsundials_nvecpetsc.so.5.5.0)
==16192==    by 0x108AF8: main (in
/home/praharsh/.local/examples/cvode/petsc/cv_petsc_ex7)

An alternative is to use CVODE through PETSc, meaning you would configure
using --download-sundials, and
then use the CVODE solvers from Sundials.

  Thanks,

    Matt


> int main(int argc,char **argv)
>
> {
>     N_Vector           nvecx;
>     PetscErrorCode       ierr;
>     Vec                  x;
>     int nr_dof = 3;
>     PetscInitializeNoArguments();
>     VecCreateSeq(PETSC_COMM_SELF, nr_dof, &x);
>     VecZeroEntries(x);
>     VecAssemblyBegin(x);
>     VecAssemblyEnd(x);
>     nvecx = N_VMake_Petsc(x);
>     if (check_retval((void *)nvecx, "N_VMake_Petsc", 0)) return 1;
>     N_VDestroy(nvecx);
>     ierr = VecDestroy(&x);CHKERRQ(ierr);
>     printf("Corruption is happening below\n");
>     ierr = PetscFinalize();
>     printf("PETSC FINALIZE\n");
>     return ierr;
> }
>
> gives me
>
> Corruption is happening below
> double free or corruption (out)
> [1]    14133 abort (core dumped)  ./cv_petsc_ex7
>
> I've also attached the output of valgrind --leak-check=full
> ./my_program_executable &> valgrind_output.log
> I'm not particularly sure why PetscFinalize is causing memory
> corruption here. I'm using Sundials 5.5.0 and Petsc 3.14.0. I don't
> really understand CVODE or PETSc internals or manual memory management
> well since I'm new to all of them. Any help pinpointing the issue
> would be appreciated.
>
> Thank you!
> Praharsh
>


-- 
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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