On Mon, Feb 6, 2023 at 4:45 PM Karthikeyan Chockalingam - STFC UKRI via petsc-users <petsc-users@mcs.anl.gov> wrote:
> No problem. I don’t completely follow. > > > > (Q1) I have used MATMPIAJI but not sure what is MatZero* (star) and what > it does? And its relevance to my problem. > Barry means MatZeroRows(), MatZeroRowsColumns(), etc. > (Q2) Since I am creating a MATMPIAJI system– what would be the best way to > insert 0.0 in to ALL diagonals (both active and inactive rows) to begin > with? > I would just write a loop to SetValues on (i,i). > (Q3) If I have to insert 0.0 only into diagonals of “inactive” rows after > I have put values into the matrix would be an effort. Unless there is a > straight forward to do it in PETSc. > You can just do it for all rows. > (Q4) For my problem do I need to use PCREDISTIBUTE or any linear solve > would eliminate those rows? > Only REDISTRIBUTE will eliminate zero rows. Thanks, Matt > > > Best, > > Karthik. > > > > *From: *Barry Smith <bsm...@petsc.dev> > *Date: *Monday, 6 February 2023 at 20:18 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> > *Subject: *Re: [petsc-users] Eliminating rows and columns which are zeros > > > > Sorry, I had a mistake in my thinking, PCREDISTRIBUTE supports > completely empty rows but MatZero* does not. > > > > When you put values into the matrix you will need to insert a 0.0 on the > diagonal of each "inactive" row; all of this will be eliminated during the > linear solve process. It would be a major project to change the MatZero* > functions to handle empty rows. > > > > Barry > > > > > > On Feb 4, 2023, at 12:06 PM, Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalin...@stfc.ac.uk> wrote: > > > > Thank you very much for offering to debug. > > > > I built PETSc along with AMReX, so I tried to extract the PETSc code alone > which would reproduce the same error on the smallest sized problem possible. > > > > I have attached three files: > > > > petsc_amrex_error_redistribute.txt – The error message from amrex/petsc > interface, but THE linear system solves and converges to a solution. > > > > problem.c – A simple stand-alone petsc code, which produces almost the > same error message. > > > > petsc_ error_redistribute.txt – The error message from problem.c but > strangely it does NOT solve – I am not sure why? > > > > Please use problem.c to debug the issue. > > > > Kind regards, > > Karthik. > > > > > > *From: *Barry Smith <bsm...@petsc.dev> > *Date: *Saturday, 4 February 2023 at 00:22 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> > *Subject: *Re: [petsc-users] Eliminating rows and columns which are zeros > > > > If you can help me reproduce the problem with a simple code I can debug > the problem and fix it. > > > > Barry > > > > > > > On Feb 3, 2023, at 6:42 PM, Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalin...@stfc.ac.uk> wrote: > > > > I updated the main branch to the below commit but the same problem > persists. > > > > *[0]PETSC ERROR: Petsc Development GIT revision: > v3.18.4-529-g995ec06f92 GIT Date: 2023-02-03 18:41:48 +0000* > > > > > > *From: *Barry Smith <bsm...@petsc.dev> > *Date: *Friday, 3 February 2023 at 18:51 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> > *Subject: *Re: [petsc-users] Eliminating rows and columns which are zeros > > > > 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.chockalin...@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 <bsm...@petsc.dev> > *Date: *Friday, 3 February 2023 at 17:41 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *petsc-users@mcs.anl.gov <petsc-users@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.chockalin...@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 <bsm...@petsc.dev> > *Date: *Tuesday, 10 January 2023 at 18:50 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *petsc-users@mcs.anl.gov <petsc-users@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.chockalin...@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 <bsm...@petsc.dev> > *Date: *Tuesday, 10 January 2023 at 16:04 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *petsc-users@mcs.anl.gov <petsc-users@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@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. > > This email and any attachments are intended solely for the use of the > named recipients. If you are not the intended recipient you must not use, > disclose, copy or distribute this email or any of its attachments and > should notify the sender immediately and delete this email from your > system. UK Research and Innovation (UKRI) has taken every reasonable > precaution to minimise risk of this email or any attachments containing > viruses or malware but the recipient should carry out its own virus and > malware checks before opening the attachments. UKRI does not accept any > liability for any losses or damages which the recipient may sustain due to > presence of any viruses. > > > > <petsc_redistribute.txt> > > > > > <petsc_error_redistribute.txt><petsc_amrex_error_redistribute.txt><problem.c> > > > -- 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/ <http://www.cse.buffalo.edu/~knepley/>