[petsc-users] Allocation errors

Wed May 27 13:16:17 CDT 2015

Thank you, Matthew.
Mat A is the only matrix I am working on in this function.
If I remove the  following lines from the code,  it will run smoothly.
// Allocate A
  ierr = MatCreate(PETSC_COMM_WORLD,&A); CHKERRQ(ierr);
  ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,4*ngen,4*ngen); CHKERRQ(ierr);
  ierr = MatSetFromOptions(A); CHKERRQ(ierr);
 ierr = MatSetUp(A); CHKERRQ(ierr);

From: Matthew Knepley [mailto:knepley at gmail.com]
Sent: Wednesday, May 27, 2015 10:56 AM
To: Li, Xinya
Cc: petsc-users at mcs.anl.gov
Subject: Re: [petsc-users] Allocation errors

On Wed, May 27, 2015 at 12:39 PM, Li, Xinya <Xinya.Li at pnnl.gov<mailto:Xinya.Li at pnnl.gov>> wrote:

The error messages were still the same.

In original code, I called  MatAssemblyBegin and  MatAssemblyEnd after I use MatSetValues to evaluate A.

That error message is given when a matrix you give PETSc is not assembled. If the message persists, you have
called MatAssemblyBegin/End() on the wrong matrix. Maybe it would be easier for you to use the debugger to
track down which matrix you need to assemble.

   Matt

From: Matthew Knepley [mailto:knepley at gmail.com<mailto:knepley at gmail.com>]
Sent: Wednesday, May 27, 2015 10:04 AM
To: Li, Xinya
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] Allocation errors

On Wed, May 27, 2015 at 11:58 AM, Li, Xinya <Xinya.Li at pnnl.gov<mailto:Xinya.Li at pnnl.gov>> wrote:
Dear Sir/Madam,

I am trying to assembling a large sparse complex matrix for parallel computing. I need to pre-allocate for this sparse matrix A.

This is what I included in the code
***************************************************************************************************
// Allocate A
  ierr = MatCreate(PETSC_COMM_WORLD,&A); CHKERRQ(ierr);
  ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,4*ngen,4*ngen); CHKERRQ(ierr);
  ierr = MatSetFromOptions(A); CHKERRQ(ierr);
 ierr = MatSetUp(A); CHKERRQ(ierr);

  ierr = MatGetOwnershipRange(A, &xstart, &xend); CHKERRQ(ierr);
  if (iteration > 0) {
    ierr = MatRetrieveValues(A); CHKERRQ(ierr);
  }

Call MatAssemblyBeginEnd().

  Thanks,

    Matt

***************************************************************************************************

This is the error message
***************************************************************************************************
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: Not for unassembled matrix
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.5.3, unknown
[0]PETSC ERROR: ./dynSim on a arch-complex named olympus.local by lixi729 Wed May 27 09:46:05 2015
[0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --with-scalar-type=complex --with-clanguage=C++ --with-fortran-kernels=generic --with-cxx-dialect=C++11 --download-fblaslapack --download-mpich --download-superlu_dist --download-mumps --download-scalapack --download-parmetis --download-metis --download-elemental
[0]PETSC ERROR: #1 MatGetOrdering() line 189 in /people/lixi729/petsc/src/mat/order/sorder.c
[0]PETSC ERROR: #2 PCSetUp_ILU() line 196 in /people/lixi729/petsc/src/ksp/pc/impls/factor/ilu/ilu.c
[0]PETSC ERROR: #3 PCSetUp() line 902 in /people/lixi729/petsc/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: #4 KSPSetUp() line 306 in /people/lixi729/petsc/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #5 KSPSolve() line 418 in /people/lixi729/petsc/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #6 SNESSolve_NEWTONLS() line 232 in /people/lixi729/petsc/src/snes/impls/ls/ls.c
[0]PETSC ERROR: #7 SNESSolve() line 3743 in /people/lixi729/petsc/src/snes/interface/snes.c
[0]PETSC ERROR: #8 TSStep_Theta() line 194 in /people/lixi729/petsc/src/ts/impls/implicit/theta/theta.c
[0]PETSC ERROR: #9 TSStep() line 2629 in /people/lixi729/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #10 TSSolve() line 2748 in /people/lixi729/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #11 simu() line 638 in simulation.C
[0]PETSC ERROR: #12 runSimulation() line 99 in dynSim.h
****************************************************************************************************

Thank you very much. I really appreciate your help and time.
Regards
__________________________________________________
Xinya Li
Scientist
EED/Hydrology
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN K9-33
Richland, WA  99352 USA
Tel:  509-372-6248<tel:509-372-6248>
Fax: 509-372-6089<tel:509-372-6089>
Xinya.Li at pnl.gov<mailto:Xinya.Li at pnl.gov>

--
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

--
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
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