November 2015 - petsc-users - mailman3.cels.anl.gov

Nodes coordinates in distributed dmplex
by Alejandro D Otero 16 Jul '22

16 Jul '22

Hi, sorry if this is an obvious question, but I cannot figure out how to recover finite element nodes coordinates once I have distributed a mesh stored as a dmplex. I am using petsc4py as interface to petsc rutines. I first created a dmplex using: dm.createFromCellList() In a sequential run I got the coordinates with: Coords = dm.getCoordinates() which gave a sequential vector with the coordinates of the mesh nodes. When I distribute the mesh with: dm.distribute() each mpi process has it own dm but the indexing of the vector resulting from getCoordinates() or getCoordinatesLocal() seems not consistent with the local numbering of the cells and nodes. Which is the correct way of doing this in PETSc philosophy? Thanks in advance, Alejandro

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MatGetDiagonal
by Nachiket Gokhale 09 Dec '19

09 Dec '19

Any chance of making this work in serial? http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetDiago… Not a show stopper, I am trying to get the diagonal of some small projected, dense matrices (which come from large sparse matrices). I am running in serial because 1) Since my projected matrices are small, and 2) PETSc does not do certain matrix multiplications involving a dense matrix in parallel, -Nachiket

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monitoring the convergence of fieldsplit 0 and 1
by Klaij, Christiaan 15 May '18

15 May '18

A question when using PCFieldSplit: for each linear iteration of the system, how many iterations for fielsplit 0 and 1? One way to find out is to run with -ksp_monitor, -fieldsplit_0_ksp_monitor and -fieldsplit_0_ksp_monitor. This gives the complete convergence history. Another way, suggested by Matt, is to use -ksp_monitor, -fieldsplit_0_ksp_converged_reason and -fieldsplit_1_ksp_converged_reason. This gives only the totals for fieldsplit 0 and 1 (but without saying for which one). Both ways require to somehow process the output, which is a bit inconvenient. Could KSPGetResidualHistory perhaps return (some) information on the subsystems' convergence for processing inside the code? Chris dr. ir. Christiaan Klaij CFD Researcher Research & Development E mailto:[email protected] T +31 317 49 33 44 MARIN 2, Haagsteeg, P.O. Box 28, 6700 AA Wageningen, The Netherlands T +31 317 49 39 11, F +31 317 49 32 45, I www.marin.nl

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How to use class function in SNESSetFunction
by behzad baghapour 20 Mar '17

20 Mar '17

Dear developers, In my code, the function "residual" used in SNESSetFunction() for calculating Nonlinear function is a member of a class called "solver". When compiling with Petsc, I received the error: error: argument of type ‘PetscErrorCode (solver::)(_p_SNES*, _p_Vec*, _p_Vec*, void*)’ does not match ‘PetscErrorCode (*)(_p_SNES*, _p_Vec*, _p_Vec*, void*)’ How can I access that class member function is SNESSetFunction()? I need to keep my code structure as before. Thanks, BB.

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Column #j is wrong in parallel from message "Inserting a new nonzero (i, j) into matrix"
by Eric Chamberland 21 Oct '16

21 Oct '16

Hi, while looking for where in the world do I insert the (135,9) entry in my matrix, I have discovered that the column # shown is wrong in parallel! I am using PETsc 3.5.3. The full error message is: [0]PETSC ERROR: MatSetValues_MPIAIJ() line 564 in /home/mefpp_ericc/petsc-3.5.3/src/mat/impls/aij/mpi/mpiaij.c Inserting a new nonzero (135, 9) into matrix This line code is a call to a #defined macro: MatSetValues_SeqAIJ_B_Private(row,col,value,addv); where the "col" parameter is not equal to "in[j]"!!! in gdb, printing "in[j]" gave me: print in[j] $6 = 537 while "col" is: print col $7 = 9 So, I expected to have a message telling me that (135,537) and not (135,9) is a new entry matrix!!! Would it be a big work to fix this so that the col # displayed is correct? Thanks! Eric

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On the edge of 2^31 unknowns
by Eric Chamberland 22 Jun '16

22 Jun '16

Hi, we just tried this morning to solve a 1.7 billion dofs problem (on 1060 processors task) . Unfortunately, petsc-3.5.3 didn't succeed within a MatMatMult product with the following backtrace: [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 4126371840 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 18446744070461249536 [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, Jan, 31, 2015 [0]PETSC ERROR: /rap/jsf-051-aa/ericc/GIREF/bin/probGD.opt on a linux-gnu-intel named r101-n31 by [0]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-intel CFLAGS="-O3 -xHost -mkl -fPIC -m64 -n [0]PETSC ERROR: #1 PetscMallocAlign() line 46 in /software6/src/petsc-3.5.3/src/sys/memory/mal.c [0]PETSC ERROR: #2 PetscLLCondensedCreate_Scalable() line 1327 in /software6/src/petsc-3.5.3/inclu [0]PETSC ERROR: #3 MatMatMultSymbolic_MPIAIJ_MPIAIJ() line 741 in /software6/src/petsc-3.5.3/src/m [0]PETSC ERROR: #4 MatMatMult_MPIAIJ_MPIAIJ() line 33 in /software6/src/petsc-3.5.3/src/mat/impls/ [0]PETSC ERROR: #5 MatMatMult() line 8713 in /software6/src/petsc-3.5.3/src/mat/interface/matrix.c The amount of memory requested is, apparently, an overflow of a PetscInt which is a 32 bit signed int. Bad user I am, I didn't expected that to solve a problem with less than 2^31 unknowns, it could be mandatory to compile petsc with 64bit indices... Is compiling with "--with-64-bit-indices" the only solution to my problem? Is it a known limitation/bug with a "Petsc-32bit-indices"? Thanks, Eric

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block matrix in serial
by Adrian Croucher 24 May '16

24 May '16

hi I have a test code (attached) that sets up a finite volume mesh using DMPlex, with 2 degrees of freedom per cell. I then create a matrix using DMCreateMatrix(), having used DMSetMatType() to set the matrix type to MATBAIJ or MATMPIBAIJ, to take advantage of the block structure. This works OK and gives me the expected matrix structure when I run on > 1 processor, but neither MATBAIJ or MATMPIBAIJ works if I run it in serial: [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Petsc has generated inconsistent data [0]PETSC ERROR: Blocksize of layout 2 must match that of mapping 1 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Development GIT revision: v3.6.1-811-gaf4f2ea GIT Date: 2015-08-18 17:44:25 -0500 [0]PETSC ERROR: ./testmat on a linux-gnu-c-opt named des108 by acro018 Wed Sep 16 13:51:27 2015 [0]PETSC ERROR: Configure options --download-netcdf --download-exodusii --with-hdf5-dir=/usr --download-triangle --download-ptscotch - -download-chaco [0]PETSC ERROR: #1 PetscLayoutSetISLocalToGlobalMapping() line 248 in /home/acro018/software/PETSc/code/src/vec/is/utils/pmap.c [0]PETSC ERROR: #2 MatSetLocalToGlobalMapping() line 1876 in /home/acro018/software/PETSc/code/src/mat/interface/matrix.c [0]PETSC ERROR: #3 DMCreateMatrix_Plex() line 853 in /home/acro018/software/PETSc/code/src/dm/impls/plex/plex.c [0]PETSC ERROR: #4 DMCreateMatrix() line 961 in /home/acro018/software/PETSc/code/src/dm/interface/dm.c -------------------------------------------------------------------------- It only works in serial if I use MATAIJ. Is there a reason why the block matrix types don't appear to work in serial, at least in this case? (I'm running the PETSc 'next' branch.) - Adrian -- Dr Adrian Croucher Senior Research Fellow Department of Engineering Science University of Auckland, New Zealand email: a.croucher(a)auckland.ac.nz tel: +64 (0)9 923 84611

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Allocating memory for off-diagonal matrix blocks when using DMComposite
by Gautam Bisht 28 Apr '16

28 Apr '16

Hi, The comment on line 419 of SNES ex 28.c <http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex28…> says that the approach used in this example is not the best way to allocate off-diagonal blocks. Is there an example that shows a better way off allocating memory for off-diagonal matrix blocks when using DMComposite? Thanks, -Gautam.

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Solving/creating SPD systems
by Justin Chang 11 Dec '15

11 Dec '15

Hi all, Say I have a saddle-point system for the mixed-poisson equation: [I -grad] [u] = [0] [-div 0 ] [p] [-f] The above is symmetric but indefinite. I have heard that one could make the above symmetric and positive definite (SPD). How would I do that? And if that's the case, would this allow me to use CG instead of GMRES? Thanks, Justin

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Output newton step
by Alex Lindsay 01 Dec '15

01 Dec '15

Is there an option for outputting the Newton step after my linear solve? Alex

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