[petsc-users] Eliminating rows and columns which are zeros
Barry Smith
bsmith at petsc.dev
Fri Feb 3 12:51:12 CST 2023
If you switch to use the main branch of petsc https://petsc.org/release/install/download/#advanced-obtain-petsc-development-version-with-git you will not have the problem below (previously we required that a row exist before we zeroed it but now we allow the row to initially have no entries and still be zeroed.
Barry
> On Feb 3, 2023, at 1:04 PM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk> wrote:
>
> Thank you. The entire error output was an attachment in my previous email. I am pasting here for your reference.
>
>
>
> [1;31m[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0;39m[0;49m[0]PETSC ERROR: Object is in wrong state
> [0]PETSC ERROR: Matrix is missing diagonal entry in row 0 (65792)
> [0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc!
> [0]PETSC ERROR: Option left: name:-options_left (no value)
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.18.1-127-ga207d08eda GIT Date: 2022-10-30 11:03:25 -0500
> [0]PETSC ERROR: /Users/karthikeyan.chockalingam/AMReX/amrFEM/build/Debug/amrFEM on a named HC20210312 by karthikeyan.chockalingam Fri Feb 3 11:10:01 2023
> [0]PETSC ERROR: Configure options --with-debugging=0 --prefix=/Users/karthikeyan.chockalingam/AMReX/petsc --download-fblaslapack=yes --download-scalapack=yes --download-mumps=yes --with-hypre-dir=/Users/karthikeyan.chockalingam/AMReX/hypre/src/hypre
> [0]PETSC ERROR: #1 MatZeroRowsColumns_SeqAIJ() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/impls/aij/seq/aij.c:2218
> [0]PETSC ERROR: #2 MatZeroRowsColumns() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6085
> [0]PETSC ERROR: #3 MatZeroRowsColumns_MPIAIJ() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/impls/aij/mpi/mpiaij.c:879
> [0]PETSC ERROR: #4 MatZeroRowsColumns() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6085
> [0]PETSC ERROR: #5 MatZeroRowsColumnsIS() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6124
> [0]PETSC ERROR: #6 localAssembly() at /Users/karthikeyan.chockalingam/AMReX/amrFEM/src/FENodalPoisson.cpp:435
> Residual norms for redistribute_ solve.
> 0 KSP preconditioned resid norm 5.182603110407e+00 true resid norm 1.382027496109e+01 ||r(i)||/||b|| 1.000000000000e+00
> 1 KSP preconditioned resid norm 1.862430383976e+00 true resid norm 4.966481023937e+00 ||r(i)||/||b|| 3.593619546588e-01
> 2 KSP preconditioned resid norm 2.132803507689e-01 true resid norm 5.687476020503e-01 ||r(i)||/||b|| 4.115313216645e-02
> 3 KSP preconditioned resid norm 5.499797533437e-02 true resid norm 1.466612675583e-01 ||r(i)||/||b|| 1.061203687852e-02
> 4 KSP preconditioned resid norm 2.829814271435e-02 true resid norm 7.546171390493e-02 ||r(i)||/||b|| 5.460217985345e-03
> 5 KSP preconditioned resid norm 7.431048995318e-03 true resid norm 1.981613065418e-02 ||r(i)||/||b|| 1.433844891652e-03
> 6 KSP preconditioned resid norm 3.182040728972e-03 true resid norm 8.485441943932e-03 ||r(i)||/||b|| 6.139850305312e-04
> 7 KSP preconditioned resid norm 1.030867020459e-03 true resid norm 2.748978721225e-03 ||r(i)||/||b|| 1.989091193167e-04
> 8 KSP preconditioned resid norm 4.469429300003e-04 true resid norm 1.191847813335e-03 ||r(i)||/||b|| 8.623908111021e-05
> 9 KSP preconditioned resid norm 1.237303313796e-04 true resid norm 3.299475503456e-04 ||r(i)||/||b|| 2.387416685085e-05
> 10 KSP preconditioned resid norm 5.822094326756e-05 true resid norm 1.552558487134e-04 ||r(i)||/||b|| 1.123391894522e-05
> 11 KSP preconditioned resid norm 1.735776150969e-05 true resid norm 4.628736402585e-05 ||r(i)||/||b|| 3.349236115503e-06
> Linear redistribute_ solve converged due to CONVERGED_RTOL iterations 11
> KSP Object: (redistribute_) 1 MPI process
> type: cg
> maximum iterations=10000, initial guess is zero
> tolerances: relative=1e-05, absolute=1e-50, divergence=10000.
> left preconditioning
> using PRECONDITIONED norm type for convergence test
> PC Object: (redistribute_) 1 MPI process
> type: jacobi
> type DIAGONAL
> linear system matrix = precond matrix:
> Mat Object: 1 MPI process
> type: mpiaij
> rows=48896, cols=48896
> total: nonzeros=307976, allocated nonzeros=307976
> total number of mallocs used during MatSetValues calls=0
> not using I-node (on process 0) routines
> End of program
> solve time 0.564714744 seconds
> Starting max value is: 0
> Min value of level 0 is: 0
> Interpolated min value is: 741.978761
> Unused ParmParse Variables:
> [TOP]::model.type(nvals = 1) :: [3]
> [TOP]::ref_ratio(nvals = 1) :: [2]
>
> AMReX (22.10-20-g3082028e4287) finalized
> #PETSc Option Table entries:
> -ksp_type preonly
> -options_left
> -pc_type redistribute
> -redistribute_ksp_converged_reason
> -redistribute_ksp_monitor_true_residual
> -redistribute_ksp_type cg
> -redistribute_ksp_view
> -redistribute_pc_type jacobi
> #End of PETSc Option Table entries
> There are no unused options.
> Program ended with exit code: 0
>
>
> Best,
> Karthik.
>
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Date: Friday, 3 February 2023 at 17:41
> To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] Eliminating rows and columns which are zeros
>
>
> We need all the error output for the errors you got below to understand why the errors are happening.
>
>
> On Feb 3, 2023, at 11:41 AM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
>
> Hello Barry,
>
> I would like to better understand pc_type redistribute usage.
>
> I am plan to use pc_type redistribute in the context of adaptive mesh refinement on a structured grid in 2D. My base mesh (level 0) is indexed from 0 to N-1 elements and refined mesh (level 1) is indexed from 0 to 4(N-1) elements. When I construct system matrix A on (level 1); I probably only use 20% of 4(N-1) elements, however the indexes are scattered in the range of 0 to 4(N-1). That leaves 80% of the rows and columns of the system matrix A on (level 1) to be zero. From your earlier response, I believe this would be a use case for petsc_type redistribute.
>
> Indeed the linear solve will be more efficient if you use the redistribute solver.
>
> But I don't understand your plan. With adaptive refinement I would just create the two matrices, one for the initial grid on which you solve the system, this will be a smaller matrix and then create a new larger matrix for the refined grid (and discard the previous matrix).
>
>
>
> Question (1)
>
>
> If N is really large, I would have to allocate memory of size 4(N-1) for the system matrix A on (level 1). How does pc_type redistribute help? Because, I did end up allocating memory for a large system, where most of the rows and columns are zeros. Is most of the allotted memory not wasted? Is this the correct usage?
>
> See above
>
>
>
> Question (2)
>
>
> I tried using pc_type redistribute for a two level system.
> I have attached the output only for (level 1)
> The solution converges to right solution but still petsc outputs some error messages.
>
> [0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc!
> [0]PETSC ERROR: Option left: name:-options_left (no value)
>
> But the there were no unused options
>
> #PETSc Option Table entries:
> -ksp_type preonly
> -options_left
> -pc_type redistribute
> -redistribute_ksp_converged_reason
> -redistribute_ksp_monitor_true_residual
> -redistribute_ksp_type cg
> -redistribute_ksp_view
> -redistribute_pc_type jacobi
> #End of PETSc Option Table entries
> There are no unused options.
> Program ended with exit code: 0
>
> I cannot explain this
>
>
> Question (2)
>
> [0;39m[0;49m[0]PETSC ERROR: Object is in wrong state
> [0]PETSC ERROR: Matrix is missing diagonal entry in row 0 (65792)
>
> What does this error message imply? Given I only use 20% of 4(N-1) indexes, I can imagine most of the diagonal entrees are zero. Is my understanding correct?
>
>
> Question (3)
>
>
> [0]PETSC ERROR: #5 MatZeroRowsColumnsIS() at /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/mat/interface/matrix.c:6124
>
> I am using MatZeroRowsColumnsIS to set the homogenous Dirichelet boundary. I don’t follow why I get this error message as the linear system converges to the right solution.
>
> Thank you for your help.
>
> Kind regards,
> Karthik.
>
>
>
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Date: Tuesday, 10 January 2023 at 18:50
> To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] Eliminating rows and columns which are zeros
>
>
> Yes, after the solve the x will contain correct values for ALL the locations including the (zeroed out rows). You use case is exactly what redistribute it for.
>
> Barry
>
>
>
>
> On Jan 10, 2023, at 11:25 AM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
>
> Thank you Barry. This is great!
>
> I plan to solve using ‘-pc_type redistribute’ after applying the Dirichlet bc using
> MatZeroRowsColumnsIS(A, isout, 1, x, b);
>
> While I retrieve the solution data from x (after the solve) – can I index them using the original ordering (if I may say that)?
>
> Kind regards,
> Karthik.
>
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Date: Tuesday, 10 January 2023 at 16:04
> To: Chockalingam, Karthikeyan (STFC,DL,HC) <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] Eliminating rows and columns which are zeros
>
>
> https://petsc.org/release/docs/manualpages/PC/PCREDISTRIBUTE/#pcredistribute -pc_type redistribute
>
>
> It does everything for you. Note that if the right hand side for any of the "zero" rows is nonzero then the system is inconsistent and the system does not have a solution.
>
> Barry
>
>
>
>
> On Jan 10, 2023, at 10:30 AM, Karthikeyan Chockalingam - STFC UKRI via petsc-users <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>> wrote:
>
> Hello,
>
> I am assembling a MATIJ of size N, where a very large number of rows (and corresponding columns), are zeros. I would like to potentially eliminate them before the solve.
>
> For instance say N=7
>
> 0 0 0 0 0 0 0
> 0 1 -1 0 0 0 0
> 0 -1 2 0 0 0 -1
> 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0
> 0 0 -1 0 0 0 1
>
> I would like to reduce it to a 3x3
>
> 1 -1 0
> -1 2 -1
> 0 -1 1
>
> I do know the size N.
>
> Q1) How do I do it?
> Q2) Is it better to eliminate them as it would save a lot of memory?
> Q3) At the moment, I don’t know which rows (and columns) have the zero entries but with some effort I probably can find them. Should I know which rows (and columns) I am eliminating?
>
> Thank you.
>
> Karthik.
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>
> <petsc_redistribute.txt>
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