[petsc-users] Parallel TS for ODE

Wed Mar 31 09:15:43 CDT 2021

Thank you for your advices. 
I wrote what seems to me a very basic code, but I got this error when I run it with more than 1 processor:
Clearly the result 299. is wrong but I do not understand what am doing wrong. With 1 processor it works fine.

steps 150, ftime 15.
Vec Object: 2 MPI processes
  type: mpi
Process [0]
16.5613
2.91405
Process [1]
299.
[0]PETSC ERROR: PetscTrFreeDefault() called from VecDestroy_MPI() line 21 in /home/fbrarda/petsc/src/vec/vec/impls/mpi/pdvec.c
[0]PETSC ERROR: Block [id=0(16)] at address 0x15812a0 is corrupted (probably write past end of array)
[0]PETSC ERROR: Block allocated in VecCreate_MPI_Private() line 514 in /home/fbrarda/petsc/src/vec/vec/impls/mpi/pbvec.c
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Memory corruption: https://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind
[0]PETSC ERROR: Corrupted memory
[0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.14.4, unknown 
[0]PETSC ERROR: ./par_sir_model on a arch-debug named srvulx13 by fbrarda Wed Mar 31 16:05:22 2021
[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-openblas-dir=/opt/packages/openblas/0.2.13-gcc --download-mpich PETSC_ARCH=arch-debug
[0]PETSC ERROR: #1 PetscTrFreeDefault() line 310 in /home/fbrarda/petsc/src/sys/memory/mtr.c
[0]PETSC ERROR: #2 VecDestroy_MPI() line 21 in /home/fbrarda/petsc/src/vec/vec/impls/mpi/pdvec.c
[0]PETSC ERROR: #3 VecDestroy() line 396 in /home/fbrarda/petsc/src/vec/vec/interface/vector.c
[0]PETSC ERROR: #4 SNESLineSearchReset() line 284 in /home/fbrarda/petsc/src/snes/linesearch/interface/linesearch.c
[0]PETSC ERROR: #5 SNESReset() line 3229 in /home/fbrarda/petsc/src/snes/interface/snes.c
[0]PETSC ERROR: #6 TSReset() line 2800 in /home/fbrarda/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #7 TSDestroy() line 2856 in /home/fbrarda/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #8 main() line 256 in par_sir_model.c
[0]PETSC ERROR: No PETSc Option Table entries
[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
application called MPI_Abort(MPI_COMM_SELF, 256001) - process 0
[1]PETSC ERROR: PetscTrFreeDefault() called from VecDestroy_MPI() line 21 in /home/fbrarda/petsc/src/vec/vec/impls/mpi/pdvec.c
[1]PETSC ERROR: Block [id=0(16)] at address 0xbd9520 is corrupted (probably write past end of array)
[1]PETSC ERROR: Block allocated in VecCreate_MPI_Private() line 514 in /home/fbrarda/petsc/src/vec/vec/impls/mpi/pbvec.c
[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[1]PETSC ERROR: Memory corruption: https://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind
[1]PETSC ERROR: Corrupted memory
[1]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.14.4, unknown 
[1]PETSC ERROR: ./par_sir_model on a arch-debug named srvulx13 by fbrarda Wed Mar 31 16:05:22 2021
[1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-openblas-dir=/opt/packages/openblas/0.2.13-gcc --download-mpich PETSC_ARCH=arch-debug
[1]PETSC ERROR: #1 PetscTrFreeDefault() line 310 in /home/fbrarda/petsc/src/sys/memory/mtr.c
[1]PETSC ERROR: #2 VecDestroy_MPI() line 21 in /home/fbrarda/petsc/src/vec/vec/impls/mpi/pdvec.c
[1]PETSC ERROR: #3 VecDestroy() line 396 in /home/fbrarda/petsc/src/vec/vec/interface/vector.c
[1]PETSC ERROR: #4 TSReset() line 2806 in /home/fbrarda/petsc/src/ts/interface/ts.c
[1]PETSC ERROR: #5 TSDestroy() line 2856 in /home/fbrarda/petsc/src/ts/interface/ts.c
[1]PETSC ERROR: #6 main() line 256 in par_sir_model.c
[1]PETSC ERROR: No PETSc Option Table entries
[1]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
application called MPI_Abort(MPI_COMM_SELF, 256001) - process 0

> Il giorno 31 mar 2021, alle ore 12:06, Matthew Knepley <knepley at gmail.com> ha scritto:
> 
> On Wed, Mar 31, 2021 at 3:54 AM Francesco Brarda <brardafrancesco at gmail.com> wrote:
> Hi everyone!
> 
> I am trying to solve a system of 3 ODEs (a basic SIR model) with TS. Sequentially works pretty well, but I need to switch it into a parallel version. 
> I started working with TS not very long time ago, there are few questions I’d like to share with you and if you have any advices I’d be happy to hear.
> First of all, do I need to use a DM object even if the model is only time dependent? All the examples I found were using that object for the other variable when solving PDEs.
> 
> You do not need one. We use it in examples because it makes it easy to create the data.
>  
> When I preallocate the space for the Jacobian matrix, is it better to decide the local or global space?
> 
> Since you are producing all the Jacobian values, it is whatever is easier in your code I think.
> 
>   THanks,
> 
>     Matt
>  
> Best,
> Francesco
> 
> 
> -- 
> 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/

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