December 2024 - petsc-users - mailman3.cels.anl.gov

local/global DMPlex Vec output
by Matteo Semplice 30 Jan '25

30 Jan '25

Dear petsc-users, I am having issues with output of parallel data attached to a DMPlex (or maybe more fundamental ones about DMPlex...). So I currently 1. create a DMPlex (DMPlexCreateGmshFromFile or DMPlexCreateBoxMesh) 2. partition it 3. and create a section for my data layout with DMPlexCreateSection(ctx.dmMesh, NULL, numComp, numDof, numBC, NULL, NULL, NULL, NULL, &sUavg) 4. DMSetLocalSection(ctx.dmMesh, sUavg) 5. create solLoc and solGlob vectors with DMCreateGlobalVector and DMCreateLocalVector 6. solve .... 7. VecView(ctx.solGlob, vtkViewer) on a .vtu file but when I load data in ParaView I get more cells than expected and it is as if the cells in the halo are put twice in output. (I could create a MWE if the above is not clear) I guess that the culprit is point (4), but if I replace it with DMSetGlobalSection then I cannot create the local vector at point (5). How should I handle this properly? In my code I need to create both local and global vectors, to perform at least GlobalToLocal and to save the global data. (On a side note, I tried also HDF5 but then it complains about the DM not having a DS...; really, any working solution that allows data to be explored with Paraview is fine) Thanks for any advice! Matteo Semplice

3 7

"-ts_exact_final_time matchstep" leads to DIVERGED_STEP_REJECTED
by Blondel, Sophie 08 Jan '25

08 Jan '25

Hi, I am trying to understand a strange behavior I'm encountering: when running my application with "-ts_exact_final_time stepover" everything goes well, but when I switch to "matchstep" I get DIVERGED_STEP_REJECTED before the first time step is finished. I tried increasing the maximum number of rejections and it just takes longer to diverge, and if I set the value to "unlimited" it is basically an infinite loop. Is there a way to check why is the step rejected? Could the "matchstep" option change tolerances somewhere that would cause that behavior? Let me know if I should provide more information. Best, Sophie Blondel

3 16

PETSC configuration on linux with intel MKL
by Bruno Ramon Batista Fernande 31 Dec '24

31 Dec '24

Hi, I am trying to use the oneAPI MKL 2025 into my PETSC configuration on Linux. However, I get the following error as I enter the names of the mkl libraries: ********************************************************************************************* ERROR in COMMAND LINE ARGUMENT to ./configure --------------------------------------------------------------------------------------------- The option /opt/intel/oneapi/mkl/2025.0/lib/intel64/libmkl_lapack95_lp64.a,/opt/intel/oneapi/mkl/2025.0/lib/intel64/libmkl_gf_lp64.a, should probably be /opt/intel/oneapi/mkl/2025.0/lib/intel64/libmkl-lapack95-lp64.a,/opt/intel/oneapi/mkl/2025.0/lib/intel64/libmkl-gf-lp64.a, ********************************************************************************************* As you can see, the configure suggest to use libraries with hyphen in their names but the original libraries have underscores in it. Any way to bypass this issue without creating links or creating copies of files? Best regards, Bruno

3 8

PETSc using problem
by hj2000＠mail.ustc.edu.cn 27 Dec '24

27 Dec '24

Dear Developer: I am a PETSc user and I have the following error when calculating 1 million grids using PETSc in my windows computer. It came up after calculating it for a while, and before it could calculate many time steps.I wanted to know what caused it. The following is the error message: [1]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [1]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ [1]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!… for trouble shooting. [1]PETSC ERROR: Petsc Release Version 3.18.6, unknown [1]PETSC ERROR: Unknown Name on a arch-mswin-c-opt named DESKTOP-B75P775 by Administrator Wed Dec 25 15:56:22 2024 [1]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-cxx="win32fe cl" --with-fc=0 --with-debugging=0 --with-shared-libraries=0 --with-x=0 --with-quad-precision=0 --with-blaslapack-include=/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/latest/include --with-blaslapack-lib="-L/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/latest/lib/intel64 -L/cygdrive/c/PROGRA~2/Intel/oneAPI/compiler/latest/windows/compiler/lib/intel64_win mkl_core.lib mkl_intel_thread.lib mkl_intel_lp64.lib libiomp5md.lib" --with-mpi-include=/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/include --with-mpi-lib="-L/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/lib/release impi.lib" --with-mpiexec=/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/bin/mpiexec --with-metis-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-metis/install/include --with-metis-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-metis/install/lib metis.lib" --with-parmetis-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-parmetis/install/include --with-parmetis-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-parmetis/install/lib parmetis.lib" --with-hdf5-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-hdf5/install/include --with-hdf5-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-hdf5/install/lib libhdf5.lib" --ignore-cygwin-link [5]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [5]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ [5]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!… for trouble shooting. [5]PETSC ERROR: Petsc Release Version 3.18.6, unknown [5]PETSC ERROR: Unknown Name on a arch-mswin-c-opt named DESKTOP-B75P775 by Administrator Wed Dec 25 15:56:22 2024 [5]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-cxx="win32fe cl" --with-fc=0 --with-debugging=0 --with-shared-libraries=0 --with-x=0 --with-quad-precision=0 --with-blaslapack-include=/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/latest/include --with-blaslapack-lib="-L/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/latest/lib/intel64 -L/cygdrive/c/PROGRA~2/Intel/oneAPI/compiler/latest/windows/compiler/lib/intel64_win mkl_core.lib mkl_intel_thread.lib mkl_intel_lp64.lib libiomp5md.lib" --with-mpi-include=/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/include --with-mpi-lib="-L/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/lib/release impi.lib" --with-mpiexec=/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/bin/mpiexec --with-metis-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-metis/install/include --with-metis-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-metis/install/lib metis.lib" --with-parmetis-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-parmetis/install/include --with-parmetis-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-parmetis/install/lib parmetis.lib" --with-hdf5-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-hdf5/install/include --with-hdf5-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-hdf5/install/lib libhdf5.lib" --ignore-cygwin-link [4]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [4]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ [4]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!… for trouble shooting. [4]PETSC ERROR: Petsc Release Version 3.18.6, unknown [4]PETSC ERROR: Unknown Name on a arch-mswin-c-opt named DESKTOP-B75P775 by Administrator Wed Dec 25 15:56:22 2024 [4]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-cxx="win32fe cl" --with-fc=0 --with-debugging=0 --with-shared-libraries=0 --with-x=0 --with-quad-precision=0 --with-blaslapack-include=/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/latest/include --with-blaslapack-lib="-L/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/latest/lib/intel64 -L/cygdrive/c/PROGRA~2/Intel/oneAPI/compiler/latest/windows/compiler/lib/intel64_win mkl_core.lib mkl_intel_thread.lib mkl_intel_lp64.lib libiomp5md.lib" --with-mpi-include=/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/include --with-mpi-lib="-L/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/lib/release impi.lib" --with-mpiexec=/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/bin/mpiexec --with-metis-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-metis/install/include --with-metis-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-metis/install/lib metis.lib" --with-parmetis-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-parmetis/install/include --with-parmetis-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-parmetis/install/lib parmetis.lib" --with-hdf5-include=/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-hdf5/install/include --with-hdf5-lib="-L/cygdrive/d/PETSc/petsc-v3.18.6-pkgconfig//packages/pkg-hdf5/install/lib libhdf5.lib" --ignore-cygwin-link [1]PETSC ERROR: #1 PetscMallocAlign() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\sys\memory\mal.c:68 [1]PETSC ERROR: #2 PetscMallocA() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\sys\memory\mal.c:410 [1]PETSC ERROR: #3 MatSeqAIJSetPreallocation_SeqAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\seq\aij.c:4008 [1]PETSC ERROR: #4 MatCreateSubMatrix_SeqAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\seq\aij.c:2588 [1]PETSC ERROR: #5 MatCreateSubMatrix_MPIAIJ_SameRowColDist() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\mpi\mpiaij.c:3283 [1]PETSC ERROR: #6 MatCreateSubMatrix_MPIAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\mpi\mpiaij.c:3390 [1]PETSC ERROR: #7 MatCreateSubMatrix() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\interface\matrix.c:8382 [1]PETSC ERROR: #8 SNESSolve_VINEWTONRSLS() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\snes\impls\vi\rs\virs.c:392 [1]PETSC ERROR: [5]PETSC ERROR: #1 PetscMallocAlign() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\sys\memory\mal.c:68 [5]PETSC ERROR: #2 PetscMallocA() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\sys\memory\mal.c:410 [5]PETSC ERROR: #3 MatSeqAIJSetPreallocation_SeqAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\seq\aij.c:4008 [5]PETSC ERROR: #4 MatCreateSubMatrix_SeqAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\seq\aij.c:2588 [5]PETSC ERROR: #5 MatCreateSubMatrix_MPIAIJ_SameRowColDist() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\mpi\mpiaij.c:3283 [5]PETSC ERROR: #6 MatCreateSubMatrix_MPIAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\mpi\mpiaij.c:3390 [5]PETSC ERROR: #7 MatCreateSubMatrix() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\interface\matrix.c:8382 [5]PETSC ERROR: #8 SNESSolve_VINEWTONRSLS() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\snes\impls\vi\rs\virs.c:392 [5]PETSC ERROR: [4]PETSC ERROR: #1 PetscMallocAlign() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\sys\memory\mal.c:68 [4]PETSC ERROR: #2 PetscMallocA() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\sys\memory\mal.c:410 [4]PETSC ERROR: #3 MatSeqAIJSetPreallocation_SeqAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\seq\aij.c:4008 [4]PETSC ERROR: #4 MatCreateSubMatrix_SeqAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\seq\aij.c:2588 [4]PETSC ERROR: #5 MatCreateSubMatrix_MPIAIJ_SameRowColDist() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\mpi\mpiaij.c:3283 [4]PETSC ERROR: #6 MatCreateSubMatrix_MPIAIJ() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\impls\aij\mpi\mpiaij.c:3390 #9 SNESSolve() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\snes\interface\snes.c:4692 [4]PETSC ERROR: #7 MatCreateSubMatrix() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\mat\interface\matrix.c:8382 [4]PETSC ERROR: #8 SNESSolve_VINEWTONRSLS() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\snes\impls\vi\rs\virs.c:392 [4]PETSC ERROR: #9 SNESSolve() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\snes\interface\snes.c:4692 #9 SNESSolve() at D:\PETSc\petsc-v3.18.6-pkgconfig\src\snes\interface\snes.c:4692

3 2

Advice on setting Dirichlet bcs in DMPlex
by Aldo Bonfiglioli 19 Dec '24

19 Dec '24

Dear all, I am using TS to solve the PDE u_t + c * u_c = eps * u_xx in 1D i.e. smthg. similar to https://urldefense.us/v3/__https://petsc.org/release/src/ts/tutorials/ex4.c… except that I am using DMPlex, instead of a structured grid. Since the problem is linear, I tried smthg. like: > PetscCall(RHSMatrixHeat(ts,0.0,u,A,A,&appctx)); > PetscCall(TSSetRHSFunction(ts,NULL,TSComputeRHSFunctionLinear,&appctx)); > > PetscCall(TSSetRHSJacobian(ts,A,A,TSComputeRHSJacobianConstant,&appctx)); > My problem is that the A matrix (as well as the global vector) is missing the rows/cols corresponding to the endpoints where Dirichlet boundary conditions are prescribed; > A global vector is missing both the shared dofs which are not owned by > this process, as well as /constrained/ dofs. These constraints > represent essential (Dirichlet) boundary conditions. They are dofs > that have a given fixed value, so they are present in local vectors > for assembly purposes, but absent from global vectors since they are > never solved for during algebraic solves. therefore, A*u = f(u) except in the two vertices adjacent to the endpoints, i.e. first and last entries of the global vector. The code is attached; when the flag -use_jacobian is set, f(u) is computed as A*u, if it is not set, f(u) is computed in FormRHSFunction. The latter approach works, the former does not. Regards, Aldo -- Dr. Aldo Bonfiglioli Associate professor of Fluid Machines Scuola di Ingegneria Universita' della Basilicata V.le dell'Ateneo lucano, 10 85100 Potenza ITALY tel:+39.0971.205203 fax:+39.0971.205215 web:https://urldefense.us/v3/__http://docenti.unibas.it/site/home/docente.html?m=002423__;!!G_uCfscf7eWS!eeErx_FNg50N1eRlD9eyfoEp8I0llTQmVFpPWoz5_LQhL8K6uOId5zbgle0ghE71NJmon8T_vwwfN3LnEbf4cTUXtlkWzhmq6Yg$

2 1

SLEPC/PETSC for large scale FEM generalised eigenvalue problem
by LUCA SCALIA 19 Dec '24

19 Dec '24

Dear group, I am using libraries PETSC and SLEPC for a Finite Element code written in c++ that I am developing, oriented to the solution of generalised eigenvalue problems for large structural systems featuring up to 10^5 -10^6 degrees of freedom. I manage to successfully run the code for a generalised eigenvalue problem of structures with around 10^4 degrees of freedom in a reasonable amount of time but the problem arises in the case of systems with a number of degrees of freedom from 10^5 or above. The current test case I'm trying has 120.000 degrees of freedom. The EPS solver gets slower and slower as the iterations pass. After a rough estimate, I would say it may take no less than 5-6 hours with 20 MPI processes ( allowing an unlimited number of iterations) I need to compute the first 10 to 30 (nev) modes of the structure (EPS_SMALLEST_MAGNITUDE). I'm using the default KRYLOVSCHUR iterative solver. The problem is generalised Hermitian I tried to play a little bit with different settings and options of the library, e.g.: 1) ncv parameter. different values of ncv, between 10*nev and 40*nev 2) different solvers for the ksp object ( GMRES and CG ), and tolerance as well preconditioner (PCJACOBI and PCBJACOBI) 3) Normalisation of matrices A and B with the respective Frobenius or Infinite norms. ... but I wasn't able to solve the problem. I kindly ask for advice on which strategies I should resort to in order to improve the speed of SLEPC for such large numbers of degrees of freedom, since I'm quite new to the solution of the generalised eigenvalue problem. I also attach two files with the stiffness and mass matrix of one element to show the magnitude of the entries of the two matrices Best regards, Luca

3 3

PCMG with shell restrictions
by Matteo Semplice 12 Dec '24

12 Dec '24

Dear petsc-users, I am trying with a student to modify the MG example 65 to use mat-shells instead of assembled matrices. Our use case is for a method that will use custom shell operators and shell interpolation/restrictions. To start we have modified ex65 and tried to replace the standard restriction/interpolation with a shell matrix that performs the same operations on the DMDA grids. I attach our modifications to ex65. The problem is that the code sometimes completes execution and sometimes errors out like $ ./ex65shell -ksp_monitor -pc_type mg -da_refine 2 -ksp_rtol 1e-1 >> Created DMshell 0x55bbc83c91a0 (0x55bbc8390a80) Calling KSPSolve from main computeRHS on grid 513 computeMatrix on grid 513 Inside Coarsen >> Created DMshell 0x55bbc84c5270 (0x55bbc84b2ff0) Inside Coarsen >> Created DMshell 0x55bbc84e0a30 (0x55bbc84bdb60) >> Create interpolation from 0x55bbc84c5270(0x55bbc84b2ff0) to 0x55bbc83c91a0(0x55bbc8390a80) [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Invalid pointer [0]PETSC ERROR: Invalid Pointer to PetscObject: Argument 'obj' (parameter # 1) [0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!… for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.22.0, unknown [0]PETSC ERROR: ./ex65shell with 1 MPI process(es) and PETSC_ARCH on signalkuppe by matteo Tue Dec 10 12:55:12 2024 [0]PETSC ERROR: Configure options: --prefix=/home/matteo/software/petscsaved/3.22-opt/ PETSC_DIR=/home/matteo/software/petsc --PETSC_ARCH=dbg --with-debugging=1 --with-st rict-petscerrorcode --download-hdf5 --download-ml --with-metis --with-parmetis --with-gmsh --with-triangle --with-zlib --with-p4est-dir=~/software/p4est/local/ [0]PETSC ERROR: #1 PetscObjectReference() at /home/matteo/software/petsc/src/sys/objects/inherit.c:620 [0]PETSC ERROR: #2 PCMGSetRScale() at /home/matteo/software/petsc/src/ksp/pc/impls/mg/mgfunc.c:394 [0]PETSC ERROR: #3 PCSetUp_MG() at /home/matteo/software/petsc/src/ksp/pc/impls/mg/mg.c:998 [0]PETSC ERROR: #4 PCSetUp() at /home/matteo/software/petsc/src/ksp/pc/interface/precon.c:1071 [0]PETSC ERROR: #5 KSPSetUp() at /home/matteo/software/petsc/src/ksp/ksp/interface/itfunc.c:415 [0]PETSC ERROR: #6 KSPSolve_Private() at /home/matteo/software/petsc/src/ksp/ksp/interface/itfunc.c:826 [0]PETSC ERROR: #7 KSPSolve() at /home/matteo/software/petsc/src/ksp/ksp/interface/itfunc.c:1075 [0]PETSC ERROR: #8 main() at ../src/ex65shell.c:79 [0]PETSC ERROR: PETSc Option Table entries: [0]PETSC ERROR: -da_refine 2 (source: command line) [0]PETSC ERROR: -ksp_monitor (source: command line) [0]PETSC ERROR: -ksp_rtol 1e-1 (source: command line) [0]PETSC ERROR: -pc_type mg (source: command line) [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- In all cases valgrind complains like $ valgrind ./ex65shell -ksp_monitor -pc_type mg -da_refine 2 -ksp_rtol 1e-1 -int_view ascii::ascii_info ==2130767== Memcheck, a memory error detector ==2130767== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al. ==2130767== Using Valgrind-3.19.0 and LibVEX; rerun with -h for copyright info ==2130767== Command: ./ex65shell -ksp_monitor -pc_type mg -da_refine 2 -ksp_rtol 1e-1 -int_view ascii::ascii_info ==2130767== hwloc x86 backend cannot work under Valgrind, disabling. May be reenabled by dumping CPUIDs with hwloc-gather-cpuid and reloading them under Valgrind with HWLOC_CPUID_PATH. >> Created DMshell 0xfbf50f0 (0xfb49480) Calling KSPSolve from main computeRHS on grid 513 computeMatrix on grid 513 Inside Coarsen >> Created DMshell 0xff404a0 (0xff062d0) Inside Coarsen >> Created DMshell 0xff78ca0 (0xff4a530) >> Create interpolation from 0xff404a0(0xff062d0) to 0xfbf50f0(0xfb49480) Mat Object: 1 MPI process type: shell rows=513, cols=257 ==2130767== Conditional jump or move depends on uninitialised value(s) ==2130767== at 0x83FDAAE: PCSetUp_MG (mg.c:998) ==2130767== by 0x8620C04: PCSetUp (precon.c:1071) ==2130767== by 0x7DA78D5: KSPSetUp (itfunc.c:415) ==2130767== by 0x7DB2093: KSPSolve_Private (itfunc.c:826) ==2130767== by 0x7DB7A53: KSPSolve (itfunc.c:1075) ==2130767== by 0x10D2F7: main (ex65shell.c:79) ==2130767== ==2130767== Conditional jump or move depends on uninitialised value(s) ==2130767== at 0x5794061: VecDestroy (vector.c:570) ==2130767== by 0x83FDC36: PCSetUp_MG (mg.c:999) ==2130767== by 0x8620C04: PCSetUp (precon.c:1071) ==2130767== by 0x7DA78D5: KSPSetUp (itfunc.c:415) ==2130767== by 0x7DB2093: KSPSolve_Private (itfunc.c:826) ==2130767== by 0x7DB7A53: KSPSolve (itfunc.c:1075) ==2130767== by 0x10D2F7: main (ex65shell.c:79) ==2130767== We are clearly doing something wrong since PCSetUp_MG (mg.c:998) is an area of code where I wouldn't expect we would enter. Can you advise on the proper way to achieve our goal? Best regards Matteo

3 5

Issue with SNES with petsc4py 3.22
by Blauth, Sebastian 10 Dec '24

10 Dec '24

Hi everyone, I am having trouble with using SNES from petsc4py in PETSc 3.22. The problem is similar to https://gitlab.com/petsc/petsc/-/issues/1611 and related to the readonly access of x. Particularly, in my application, based on FEniCS, I want to solve a nonlinear PDE. Therefore, in my callbacks, I want to set the vector of DoFs of my FEniCS function to x with a line like self.u.vector().vec().setArray(x) However, this now raises the error [0] Vector 'Vec_0x84000003_0' (argument #1) was locked for read-only access in unknown_function() at unknown file:0 (line numbers only accurate to function begin) I believe that this is a consequence of https://gitlab.com/petsc/petsc/-/merge_requests/7567#22c226fc29b6fc9dc5781b0 aff4dcc70ac6c3489, but I did not find any information on how to remove the lock from the vector or how I can set use x to update the vector of my function. Using xx = x.getArray(readonly=True) as described in https://gitlab.com/petsc/petsc/-/issues/1611 does not work either, as calling self.u.vector().vec().setArray(xx) then fails with the same error message. Does anyone have an idea how to fix this? Thanks a lot in advance, Sebastian -- Dr. Sebastian Blauth Fraunhofer-Institut für Techno- und Wirtschaftsmathematik ITWM Abteilung Transportvorgänge Fraunhofer-Platz 1, 67663 Kaiserslautern Telefon: +49 631 31600-4968 <mailto:[email protected]> sebastian.blauth(a)itwm.fraunhofer.de <https://www.itwm.fraunhofer.de> https://www.itwm.fraunhofer.de

2 2

Parallel computing in SNES
by David Jiawei LUO LIANG 10 Dec '24

10 Dec '24

Hello PETSc, I want to substitute the existing nonlinear solver codes with SNES. The existing code is Parallel computing. My FormFunction and FormJacobian is attached in file Res_Jac.cpp. The global tangent matrix assembly and residual function assembly are both implemented by invoking user pointers. The following is the message, we can find that SNES just iterate once. I think the problem is input solution Vec y doesn't link to Residual Vec f, because my update is stored in the user variables. If I use  const PetscScalar *yy; VecGetArrayRead(y, &yy);  the value of yy is not identical to Vec y, because there are multi thread. So, my problem is how to assembly residual and tangent in parallel environment? David Jiawei LUO LIANG 南方科技大学/学生/研究生/2024 广东省深圳市南山区学苑大道1088号  

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Question about ordering of the gradient in DS
by Gong Yujie 09 Dec '24

09 Dec '24

Dear PETSc group, I would like to inquire about the storage of the gradient in function PetscDSSetResidual: PetscErrorCode PetscDSSetResidual(PetscDS ds, PetscInt f, void (*f0)(PetscInt dim, PetscInt Nf, PetscInt NfAux, const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]), void (*f1)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[])) Assume u = (u1, u2, u3)^T, the gradient of u is [cid:68b0e2f6-2465-4550-8ae1-4631bfe74163] In PetscDSSetResidual, it is stored in an array. Is it ordered as (u1x,u2x, u3x, u1y, u2y, u3y, u1z, u2z,u3z)? Thanks in advance! Best Regards, Yujie

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