[petsc-users] A number of questions about DMDA with SNES and Quasi-Newton methods

Sun Oct 8 04:57:46 CDT 2017

  There is apparently confusing in understanding the ordering. Is this all on one process that you get funny results? Are you using MatSetValuesStencil() to provide the matrix (it is generally easier than providing it yourself). In parallel MatView() always maps the rows and columns to the natural ordering before printing, if you use a matrix created from the DMDA. If you create the matrix yourself it has a different MatView in parallel that is in in thePETSc ordering.\

   Barry

> On Oct 8, 2017, at 8:05 AM, zakaryah . <zakaryah at gmail.com> wrote:
> 
> I'm more confused than ever.  I don't understand the output of -snes_type test -snes_test_display.
> 
> For the user-defined state of the vector (where I'd like to test the Jacobian), the finite difference Jacobian at row 0 evaluates as:
> 
> row 0: (0, 10768.6)  (1, 2715.33)  (2, -1422.41)  (3, -6121.71)  (4, 287.797)  (5, 744.695)  (9, -1454.66)  (10, 6.08793)  (11, 148.172)  (12, 13.1089)  (13, -36.5783)  (14, -9.99399)  (27, -3423.49)  (28, -2175.34)  (29, 548.662)  (30, 145.753)  (31, 17.6603)  (32, -15.1079)  (36, 76.8575)  (37, 16.325)  (38, 4.83918)
> 
> But the hand-coded Jacobian at row 0 evaluates as:
> 
> row 0: (0, 10768.6)  (1, 2715.33)  (2, -1422.41)  (3, -6121.71)  (4, 287.797)  (5, 744.695)  (33, -1454.66)  (34, 6.08792)  (35, 148.172)  (36, 13.1089)  (37, -36.5783)  (38, -9.99399)  (231, -3423.49)  (232, -2175.34)  (233, 548.662)  (234, 145.753)  (235, 17.6603)  (236, -15.1079)  (264, 76.8575)  (265, 16.325)  (266, 4.83917)  (267, 0.)  (268, 0.)  (269, 0.)
> and the difference between the Jacobians at row 0 evaluates as:
> 
> row 0: (0, 0.000189908)  (1, 7.17315e-05)  (2, 9.31778e-05)  (3, 0.000514947)  (4, 0.000178659)  (5, 0.000178217)  (9, -2.25457e-05)  (10, -6.34278e-06)  (11, -5.93241e-07)  (12, 9.48544e-06)  (13, 4.79709e-06)  (14, 2.40016e-06)  (27, -0.000335696)  (28, -0.000106734)  (29, -0.000106653)  (30, 2.73119e-06)  (31, -7.93382e-07)  (32, 1.24048e-07)  (36, -4.0302e-06)  (37, 3.67494e-06)  (38, -2.70115e-06)  (39, 0.)  (40, 0.)  (41, 0.)
> 
> The difference between the column numbering between the finite difference and the hand-coded Jacobians looks like a serious problem to me, but I'm probably missing something.
> 
> I am trying to use a 3D DMDA with 3 dof, a box stencil of width 1, and for this test problem the grid dimensions are 11x7x6.  For a grid point x,y,z, and dof c, is the index calculated as c + 3*x + 3*11*y + 3*11*7*z?  If so, then the column numbers of the hand-coded Jacobian match those of the 27 point stencil I have in mind.  However, I am then at a loss to explain the column numbers in the finite difference Jacobian.
> 
> 
> 
> 
> On Sat, Oct 7, 2017 at 1:49 PM, zakaryah . <zakaryah at gmail.com> wrote:
> OK - I ran with -snes_monitor -snes_converged_reason -snes_linesearch_monitor -ksp_monitor -ksp_monitor_true_residual -ksp_converged_reason -pc_type svd -pc_svd_monitor -snes_type newtonls -snes_compare_explicit
> 
> and here is the full error message, output immediately after 
> 
> Finite difference Jacobian
> Mat Object: 24 MPI processes
>   type: mpiaij
> 
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> 
> [0]PETSC ERROR: Invalid argument
> 
> [0]PETSC ERROR: Matrix not generated from a DMDA
> 
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> 
> [0]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017 
> 
> [0]PETSC ERROR: ./CalculateOpticalFlow on a arch-linux2-c-opt named node046.hpc.rockefeller.internal by zfrentz Sat Oct  7 13:44:44 2017
> 
> [0]PETSC ERROR: Configure options --prefix=/ru-auth/local/home/zfrentz/PETSc-3.7.6 --download-fblaslapack -with-debugging=0
> 
> [0]PETSC ERROR: #1 MatView_MPI_DA() line 551 in /rugpfs/fs0/home/zfrentz/PETSc/build/petsc-3.7.6/src/dm/impls/da/fdda.c
> 
> [0]PETSC ERROR: #2 MatView() line 901 in /rugpfs/fs0/home/zfrentz/PETSc/build/petsc-3.7.6/src/mat/interface/matrix.c
> 
> [0]PETSC ERROR: #3 SNESComputeJacobian() line 2371 in /rugpfs/fs0/home/zfrentz/PETSc/build/petsc-3.7.6/src/snes/interface/snes.c
> 
> [0]PETSC ERROR: #4 SNESSolve_NEWTONLS() line 228 in /rugpfs/fs0/home/zfrentz/PETSc/build/petsc-3.7.6/src/snes/impls/ls/ls.c
> 
> [0]PETSC ERROR: #5 SNESSolve() line 4005 in /rugpfs/fs0/home/zfrentz/PETSc/build/petsc-3.7.6/src/snes/interface/snes.c
> 
> [0]PETSC ERROR: #6 solveWarp3D() line 659 in /ru-auth/local/home/zfrentz/Code/OpticalFlow/working/October6_2017/mshs.c
> 
> 
> On Tue, Oct 3, 2017 at 5:37 PM, Jed Brown <jed at jedbrown.org> wrote:
> Always always always send the whole error message.
> 
> "zakaryah ." <zakaryah at gmail.com> writes:
> 
> > I tried -snes_compare_explicit, and got the following error:
> >
> > [0]PETSC ERROR: Invalid argument
> >
> > [0]PETSC ERROR: Matrix not generated from a DMDA
> >
> > What am I doing wrong?
> >
> > On Tue, Oct 3, 2017 at 10:08 AM, Jed Brown <jed at jedbrown.org> wrote:
> >
> >> Barry Smith <bsmith at mcs.anl.gov> writes:
> >>
> >> >> On Oct 3, 2017, at 5:54 AM, zakaryah . <zakaryah at gmail.com> wrote:
> >> >>
> >> >> I'm still working on this.  I've made some progress, and it looks like
> >> the issue is with the KSP, at least for now.  The Jacobian may be
> >> ill-conditioned.  Is it possible to use -snes_test_display during an
> >> intermediate step of the analysis?  I would like to inspect the Jacobian
> >> after several solves have already completed,
> >> >
> >> >    No, our currently code for testing Jacobians is poor quality and
> >> poorly organized. Needs a major refactoring to do things properly. Sorry
> >>
> >> You can use -snes_compare_explicit or -snes_compare_coloring to output
> >> differences on each Newton step.
> >>
> 
> 