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 [email protected] 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 [email protected] application called MPI_Abort(MPI_COMM_SELF, 256001) - process 0 > Il giorno 31 mar 2021, alle ore 12:06, Matthew Knepley <[email protected]> ha > scritto: > > On Wed, Mar 31, 2021 at 3:54 AM Francesco Brarda <[email protected]> > 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/
