October 2022 - petsc-users - mailman3.cels.anl.gov

PETSc Windows Installation
by Mohammad Ali Yaqteen 01 Nov '22

01 Nov '22

Dear Sir, During the Installation of PETSc in windows, I installed Cygwin and the required libraries as mentioned on your website: [cid:[email protected]] However, when I install PETSc using the configure commands present on the petsc website: ./configure --with-cc=gcc --with-cxx=0 --with-fc=0 --download-f2cblaslapack --download-mpich it gives me the following error: [cid:[email protected]] I already installed OpenMPI using Cygwin installer but it still asks me to. When I configure without "-download-mpich" and run "make check" command, it gives me the following errors: [cid:[email protected]] Could you kindly look into this and help me with this? Your prompt response will highly be appreciated. Thank you! Mohammad Ali Researcher, Sejong University

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Combining DMDA and DMStag
by Carl-Johan Thore 01 Nov '22

01 Nov '22

Hi! I'm working on a convection-diffusion heat transfer problem. The temperature is discretized using standard Q1 elements and a DMDA. The flow is modelled using a stabilized Q1-Q0 method for which DMStag seemed like a good choice. The codes for the temperature and flow work fine separately (both in serial and parallel), but when combined and running in parallel, a problem sometimes arises in the assembly of the thermal system matrix. Here's a rough sketch of the combined code: // Create dmda for thermal problem and dmstag for flow problem DMDACreate3d(PETSC_COMM_WORLD, bx, by, bz, DMDA_STENCIL_BOX, nelx+1, nely+1, nelz+1, PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, 1, stencilWidth, 0, 0, 0, &dmthermal); ... // A bit of code to adjust Lx,Ly,Lz so that dmthermal and dmflow are compatible in the sense of having the same // local elements ... DMStagCreate3d(PETSC_COMM_WORLD, bx, by, bz, nelx, nely, nelz, md,nd,pd, 3,0,0,0,DMSTAG_STENCIL_BOX,stencilWidth,Lx,Ly,Lz,&dmflow); PetscInt edofT[8]; // 8-noded element with 1 temp DOF per node DMStagStencil edofF[24]; // 8 nodes with 3 velocity DOFs each // Assemble thermal system matrix K for (PetscInt e=0 ...) // Loop over local elements { // Populate edofF, edofT // Get element velocities in ue from local velocity vector uloc DMStagVecGetValuesStencil(dmflow,uloc,24,edof,ue); ... Ke = Ke_diffusion + Ke_convection(ue) ... MatSetValuesLocal(K, 8, edofT, 8, edofT, Ke, ADD_VALUES); } This always works fine in serial, but depending on the mesh and the number of ranks, we don't always get the correct values in the element velocity vector ue. I suspect this has something to do with the ordering of the elements and/or the DOFs, because the elements in the global velocity vector are always the same but their order may change (judging from the output of VecView at least). Is it possible to ensure compatibility between the dm:s, or find some kind of mapping between them, so that something along the lines of the code above always works? Kind regards, Carl-Johan

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An issue of extraction of factorization matrices in sparse direct solver
by 赵刚 27 Oct '22

27 Oct '22

Dear developers, I have another question. How can I get the L and U matrices and store them in a file when I call SuperLU through PETSc? Thanks. Best Regards, Gang

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basis/basisDer/Jac in FE
by Yann Jobic 27 Oct '22

27 Oct '22

Hello, I'm trying to understand how to use the lowlevel Petsc Finit Element Framework. I've got few questions about it. 1) I'm checking the determinant of the Jacobian transformation from real space to the parametric one. The source code is in : https://petsc.org/main/src/dm/impls/plex/plexgeometry.c.html#DMPlexComputeT… I don't quite understand the 0.5 factor in front of it. Geometrically, it should be the ratio of the area/volume of the reel element over the referenced one. It's not the case here no ? It seems that, for other elements, this factor still applies. What this factor represent ? 2) I only checked triangle elements here. The ordering of the test functions and its derivatives is different it seems, with also the 0.5 factor. Am i mistaken ? I could not find any informations about it in the user-doc. Maybe it's written somewhere else ? Many Thanks, Best regards, Yann

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Questions about matrix permutation
by 晓峰何 27 Oct '22

27 Oct '22

Dear developers, To avoid zero pivot error in IC/ILU preconditioners, I plan to permute matrix before solving the linear system. I referred example ex10(https://petsc.org/main/src/ksp/ksp/tutorials/ex10.c.html) and ex18(https://petsc.org/main/src/ksp/ksp/tutorials/ex18.c.html), and was confused that why vector b is permuted by column permutation index set: // in ex18.c 174: if (permute) { 175: Mat<https://petsc.org/main/docs/manualpages/Mat/Mat/> Aperm; 176: MatGetOrdering<https://petsc.org/main/docs/manualpages/MatOrderings/MatGetOrdering/>(A, ordering, &rowperm, &colperm); 177: MatPermute<https://petsc.org/main/docs/manualpages/Mat/MatPermute/>(A, rowperm, colperm, &Aperm); 178: VecPermute<https://petsc.org/main/docs/manualpages/Vec/VecPermute/>(b, colperm, PETSC_FALSE<https://petsc.org/main/docs/manualpages/Sys/PETSC_FALSE/>); 179: MatDestroy<https://petsc.org/main/docs/manualpages/Mat/MatDestroy/>(&A); 180: A = Aperm; /* Replace original operator with permuted version */ 181: } As far as I understand, vector b should be only affected by permuting rows in matrix A, instead of column permutation. How to understand that permuting vector b with column permutation index set of matrix A? Another question is why MatReorderForNonzeroDiagonal function only works for type MATSEQAIJ? If it works for other matrix types, then this function will meet my requirement. Thanks, Xiaofeng

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petsc-3.18.1 now available
by Satish Balay 26 Oct '22

26 Oct '22

Dear PETSc users, The patch release petsc-3.18.1 is now available for download. https://petsc.org/release/install/download/ Satish

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A question about solving a saddle point system with a direct solver
by Jau-Uei Chen 24 Oct '22

24 Oct '22

To whom it may concern, I am writing to ask about using PETSc with a direct solver to solve a linear system where a single zero-value eigenvalue exists. Currently, I am working on developing a finite-element solver for a linearized incompressible MHD equation. The code is based on an open-source library called MFEM which has its own wrapper for PETSc and is used in my code. From analysis, I already know that the linear system (Ax=b) to be solved is a saddle point system. By using the flags "solver_pc_type svd" and "solver_pc_svd_monitor", I indeed observe it. Here is an example of an output: SVD: condition number 3.271390119581e+18, 1 of 66 singular values are (nearly) zero SVD: smallest singular values: 3.236925932523e-17 3.108788619412e-04 3.840514506502e-04 4.599292003910e-04 4.909419974671e-04 SVD: largest singular values : 4.007319935079e+00 4.027759008411e+00 4.817755760754e+00 4.176127583956e+01 1.058924751347e+02 However, What surprises me is that the numerical solutions are still relatively accurate by comparing to the exact ones (i.e. manufactured solutions) when I perform convergence tests even if I am using a direct solver (i.e. -solver_ksp_type preonly -solver_pc_type lu -solver_pc_factor_mat_solver_type mumps). My question is: Why the direct solver won't break down in this context? I understand that it won't be an issue for iterative solvers such as GMRES [1][2] but not really sure why it won't cause trouble in direct solvers. Any comments or suggestions are greatly appreciated. Best Regards, Jau-Uei Chen Reference: [1] Benzi, Michele, et al. “Numerical Solution of Saddle Point Problems.” Acta Numerica, vol. 14, May 2005, pp. 1–137. DOI.org (Crossref), https://doi.org/10.1017/S0962492904000212. [2] Elman, Howard C., et al. Finite Elements and Fast Iterative Solvers: With Applications in Incompressible Fluid Dynamics. Second edition, Oxford University Press, 2014.

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Clarification on MatMPIBAIJSetPreallocation (d_nnz and o_nnz)
by Edoardo alinovi 24 Oct '22

24 Oct '22

Hello Barry, I am doing some preliminary work to add a coupled solver in my code. I am reading some documentation on MPIBAIJ as the matrix will be composed of blocks of size 3x3 in 2D and 4x4 in 3D for each cell in the domain. I can't quite understand how to set d_nnz and o_nnz. What is their size? Should I provide a number of non-zero entries for each block or should I do it line by line as in MATAIJ? Would you be able to provide me with a silly example? Thank you!

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Calling SuperLU_MT in PETSc
by 赵刚 23 Oct '22

23 Oct '22

Dear PETSc team, I want to call the multithreading sparse direct solver SuperLU_MT in PETSc, Could I download by "--download-superlu-mt"? Or what is a good way to support calling SuperLU_MT interface in PETSc? Thank you. Best Regards, Gang

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Trouble with ISEmbed
by TARDIEU Nicolas 21 Oct '22

21 Oct '22

Dear PETSc Team, I am trying to use IS embeding in parallel. In order to (try to) understand how it works, I have built a simple example, attached to this email. I consider a 20X20 matrix. The dof (u, p, t) in global numbering are the following : u: 0..9 p: 10..14 t: 15..19 I have defined 4 IS to describe the dof u, p, t and the agglomeration of u and p, called up. I first extract the submatrix matrix(up,up), then I would like to extract from it the (u,u) block. The example runs OK in sequential but I do not obtain the (u,u) block on 2 processes. I have a mistake in the build of the sub-IS but I cannot find it for days. Best regards, Nicolas -- Nicolas Tardieu Ing PhD Computational Mechanics EDF - R&D Dpt ERMES PARIS-SACLAY, FRANCE Ce message et toutes les pièces jointes (ci-après le 'Message') sont établis à l'intention exclusive des destinataires et les informations qui y figurent sont strictement confidentielles. Toute utilisation de ce Message non conforme à sa destination, toute diffusion ou toute publication totale ou partielle, est interdite sauf autorisation expresse. Si vous n'êtes pas le destinataire de ce Message, il vous est interdit de le copier, de le faire suivre, de le divulguer ou d'en utiliser tout ou partie. Si vous avez reçu ce Message par erreur, merci de le supprimer de votre système, ainsi que toutes ses copies, et de n'en garder aucune trace sur quelque support que ce soit. Nous vous remercions également d'en avertir immédiatement l'expéditeur par retour du message. Il est impossible de garantir que les communications par messagerie électronique arrivent en temps utile, sont sécurisées ou dénuées de toute erreur ou virus. ____________________________________________________ This message and any attachments (the 'Message') are intended solely for the addressees. The information contained in this Message is confidential. Any use of information contained in this Message not in accord with its purpose, any dissemination or disclosure, either whole or partial, is prohibited except formal approval. If you are not the addressee, you may not copy, forward, disclose or use any part of it. If you have received this message in error, please delete it and all copies from your system and notify the sender immediately by return message. E-mail communication cannot be guaranteed to be timely secure, error or virus-free.

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