Il giorno 31 mar 2021, alle ore 16:43, Stefano Zampini <stefano.zampini@gmail.com> ha scritto:Are you trying to parallelize a 3 equations system? Or you just use your SIR code to experiment with TS?On Mar 31, 2021, at 5:18 PM, Matthew Knepley <knepley@gmail.com> wrote:On Wed, Mar 31, 2021 at 10:15 AM Francesco Brarda <brardafrancesco@gmail.com> wrote: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.My guess is that you do VecGetArray() and index the array using global indices rather than local indices, becausethere memory corruption with a Vec array.Thanks,Mattsteps 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@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@mcs.anl.gov----------
application called MPI_Abort(MPI_COMM_SELF, 256001) - process 0Il giorno 31 mar 2021, alle ore 12:06, Matthew Knepley <knepley@gmail.com> ha scritto:
On Wed, Mar 31, 2021 at 3:54 AM Francesco Brarda <brardafrancesco@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/--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