June 2021 - 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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Question about PCFieldSplit
by Jorti, Zakariae 31 Jan '22

31 Jan '22

Hello, I have a DMStag grid with one dof on each edge and face center. I want to use a PCFieldSplit preconditioner on a Jacobian matrix that I assume is already split but I am not sure how to determine the fields. In the DMStag examples (ex2.c and ex3.c), the function PCFieldSplitSetDetectSaddlePoint is used to determine those fields based on zero diagonal entries. In my case, I have a Jacobian matrix that does not have zero diagonal entries. Can I use that PCFieldSplitSetDetectSaddlePoint in this case? If not, how should I do? Should I do like this example (https://www.mcs.anl.gov/petsc/petsc-master/src/ksp/ksp/tutorials/ex43.c.html) const PetscInt Bfields[1] = {0},Efields[1] = {1}; KSPGetPC(ksp,&pc); PCFieldSplitSetBlockSize(pc,2); PCFieldSplitSetFields(pc,"B",1,Bfields,Bfields); PCFieldSplitSetFields(pc,"E",1,Efields,Efields); where my B unknowns are defined on face centers and E unknowns are defined on edge centers? One last thing, I do not know which field comes first. Is it the one defined for face dofs or edge dofs. Thank you. Best regards, Zakariae

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PETSC installation on Cray
by Enrico 13 Sep '21

13 Sep '21

Hi, I'm having some problems installing PETSC with Cray compiler. I use this configuration: ./configure --with-cc=cc --with-cxx=CC --with-fc=0 --with-debugging=1 --with-shared-libraries=1 COPTFLAGS=-O0 CXXOPTFLAGS=-O0 and when I do make all I get the following error because of cmathcalls.h: CC-1043 craycc: ERROR File = /usr/include/bits/cmathcalls.h, Line = 55 _Complex can only be used with floating-point types. __MATHCALL (cacos, (_Mdouble_complex_ __z)); ^ Am I doing something wrong? Regards, Enrico Degregori

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SLEPc: HDF5 support for SVD/EPSValuesView?
by Peder Jørgensgaard Olesen 21 Jul '21

21 Jul '21

Hello In SLEPc one may write singular vectors to an HDF5 file using SVDVectorsView(), but a similar option doesn't seem to work for singular values using SVDValuesView(). The values are viewed correctly using other viewers, but nothing is seemingly produced when using an HDF5 viewer. Looking at the source code seems to confirm this, and suggests that there is a similar situation with EPS. Is this correct, and if so, might there be plans to include such functionality in future releases? Med venlig hilsen / Best Regards Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby

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Scatter parallel Vec to sequential Vec on non-zeroth process
by Peder Jørgensgaard Olesen 04 Jul '21

04 Jul '21

Hello I have a parallel vector, and I'd like to copy its data to a sequential vector located on a given process that is not necessarily the 0th process, so using VecScatterCreateToZero wouldn't do here. How might one approach this? Med venlig hilsen / Best Regards Peder Jørgensgaard Olesen PhD Student, Turbulence Research Lab Dept. of Mechanical Engineering Technical University of Denmark Koppels Allé Bygning 403, Rum 105 DK-2800 Kgs. Lyngby

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Boundary ghost cell types in PETSc 3.15
by Adrian Croucher 30 Jun '21

30 Jun '21

hi I've been testing building my code with PETSc 3.15 and have hit a weird problem. If I create a DMPlex and add boundary ghost cells using DMPlexConstructGhostCells(), I expect the boundary ghost cells to have cell type DM_POLYTOPE_FV_GHOST, if I check the cell types using DMPlexGetCellTypeLabel() and DMLabelGetValue(). That is true if I build using PETSc 3.14. But with 3.15 it appears the boundary ghost cells are ending up with cell type DM_POLYTOPE_INTERIOR_GHOST. These types are defined in include/petscdmtypes.h and currently DM_POLYTOPE_FV_GHOST = 11 and DM_POLYTOPE_INTERIOR_GHOST = 12. I've attached a minimal example program in Fortran. It creates a box mesh and adds boundary ghost cells, then counts how many have type DM_POLYTOPE_FV_GHOST. With PETSc 3.14 it is 24, the same as the number of ghost cells. With PETSc 3.15 it is zero, and the boundary ghost cells all have type 12. Any clues? Regards, 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 4611

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Any workarounds for TAO in a complex scalar type code?
by Lucas Banting 24 Jun '21

24 Jun '21

Hi, I have a complex valued optimization code that requires non-linear least squares curve fitting at each iteration. I wanted to use Tao to do the non-linear least squares problem, but just discovered that Tao can only be used with real scalar types. Is there any workarounds? I was wondering if maybe I could somehow use two different Petsc installations at once, or is there any other ways to hack tao into working? Thanks, Lucas

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Getting nodal coordinates from a FEM computation
by Abisheik Panneerselvam 24 Jun '21

24 Jun '21

Hello, Good Morning. My name is Abisheik Panneerselvam and I am presently working in Max-Planck Düsseldorf. I am working on a FE software development project. The FE computation code is already written in Fortran (using Petsc for solving) few years ago. I am currently working on post-processing the results of the computation (nodal displacements, integration point displacements etc.). I am facing problems in getting the coordinates of vertices. I tried the following call SNESGetDM(mechanical_snes,dm_local,ierr); CHKERRQ(ierr) !Gets the local DM from the SNES solve call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr) !Gets the local vector from the DM This functions successfully gets the coordinates of all the nodes. This works fine for linear elements as there are only nodes on cell vertices. But for higher order elements, the local vector (x_local) contains additional nodal points (I think its called ghost points in Petsc) on the edges. In this case how do I get the coordinates of only the cell vertices? I tried the below code for getting the vertex coordinates but its giving random values. call DMPlexGetDepthStratum(dm_local, 0, vStart, vEnd,ierr); CHKERRQ(ierr) !Get the vertices call VecGetArrayF90(x_local, node_coords_local,ierr) v_count=1 do v=vStart, vEnd-1 call DMPlexGetPointLocal(dm_local, v, x, y, ierr); CHKERRQ(ierr) !Get the position of the vertice in the local DM d_count=1 do d=x,y-1 node_coords(d_count,v_count)=node_coords_local(d) d_count=d_count+1 end do v_count = v_count+1 end do It will be really helpful if you could advise me on this. Best regards Abisheik ------------------------------------------------- Max-Planck-Institut für Eisenforschung GmbH Max-Planck-Straße 1 D-40237 Düsseldorf Handelsregister B 2533 Amtsgericht Düsseldorf Geschäftsführung Prof. Dr. Gerhard Dehm Prof. Dr. Jörg Neugebauer Prof. Dr. Dierk Raabe Dr. Kai de Weldige Ust.-Id.-Nr.: DE 11 93 58 514 Steuernummer: 105 5891 1000 Please consider that invitations and e-mails of our institute are only valid if they end with …(a)mpie.de. If you are not sure of the validity please contact rco(a)mpie.de Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails aus unserem Haus nur mit der Endung …(a)mpie.de gültig sind. In Zweifelsfällen wenden Sie sich bitte an rco(a)mpie.de -------------------------------------------------

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Tracking a NaN in FVM gradient computation
by Ellen M. Price 20 Jun '21

20 Jun '21

Hi there PETSc, I am working my way through ex11.c and have encountered a problem. On the first pass through mesh adaption, the gradient computation in PETSc triggers a NaN, even though none of the input data are NaN. To reproduce: PETSc v3.15 with latest MPICH, no external libraries, debugging on Compile ex11.c using GCC 9.3 on Ubuntu 20.04 Run as: ./ex11 -ufv_use_amr -fp_trap Running under GDB shows that the offending line is: src/dm/impls/plex/plexfvm.c:111 This originates from the call to DMPlexReconstructGradientsFVM. I only noticed this because I was trying to resolve a discontinuity in my own initial condition for a Sod shock tube problem, but then I found that it occurs in the example without any modification, too. Is this somehow intended? If not, what steps can one take to make sure the gradients are actual numeric values? It doesn't make sense to me that they would be undefined on the first step when nothing else is NaN. Or is it that AMR in ex11 doesn't quite work yet? Thanks, Ellen Price

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New PETSc website, documentation and 3.15.1 patch release
by Satish Balay 18 Jun '21

18 Jun '21

Dear PETSc users, We are migrating PETSc website and docs to a new location. https://petsc.org/release/ Let us know via petsc-users or petsc-maint if you encounter any issues. For now, the old website https://www.mcs.anl.gov/petsc/ will be accessible - but the content is frozen. The patch release petsc-3.15.1 is also available for download. https://petsc.org/release/download/ Satish

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