July 2021 - petsc-users - mailman3.cels.anl.gov

How to combine different element types into a single DMPlex?
by Eric Chamberland 01 Aug '24

01 Aug '24

Hi, while playing with DMPlexBuildFromCellListParallel, I noticed we have to specify "numCorners" which is a fixed value, then gives a fixed number of nodes for a series of elements. How can I then add, for example, triangles and quadrangles into a DMPlex? Thanks, Eric -- Eric Chamberland, ing., M. Ing Professionnel de recherche GIREF/Université Laval (418) 656-2131 poste 41 22 42

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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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Is it possible to keep track of original elements # after a call to DMPlexDistribute ?
by Eric Chamberland 11 Nov '21

11 Nov '21

Hi, I want to use DMPlexDistribute from PETSc for computing overlapping and play with the different partitioners supported. However, after calling DMPlexDistribute, I noticed the elements are renumbered and then the original number is lost. What would be the best way to keep track of the element renumbering? a) Adding an optional parameter to let the user retrieve a vector or "IS" giving the old number? b) Adding a DMLabel (seems a wrong good solution) c) Other idea? Of course, I don't want to loose performances with the need of this "mapping"... Thanks, Eric -- Eric Chamberland, ing., M. Ing Professionnel de recherche GIREF/Université Laval (418) 656-2131 poste 41 22 42

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SLEPc: smallest eigenvalues
by Varun Hiremath 05 Oct '21

05 Oct '21

Hi All, I am trying to compute the smallest eigenvalues of a generalized system A*x= lambda*B*x. I don't explicitly know the matrix A (so I am using a shell matrix with a custom matmult function) however, the matrix B is explicitly known so I compute inv(B)*A within the shell matrix and solve inv(B)*A*x = lambda*x. To compute the smallest eigenvalues it is recommended to solve the inverted system, but since matrix A is not explicitly known I can't invert the system. Moreover, the size of the system can be really big, and with the default Krylov solver, it is extremely slow. So is there a better way for me to compute the smallest eigenvalues of this system? Thanks, Varun

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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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DMPlex box mesh periodicity bug (?)
by Thibault Bridel-Bertomeu 02 Aug '21

02 Aug '21

Dear all, I have noticed what I think is a bug with a 3D DMPlex box mesh with periodic boundaries. When I project a function onto it, it behaves as if the last row of cells in X and in Y direction do not have the right coordinates. I attach to this email a minimal example that reproduces the bug (files mwe_periodic_3d.F90, wrapper_petsc.c, wrapper_petsc.h90, makefile), as well as the output of this code (initmesh.vtu for an output of the DM, solution.vtu for an output of the data projected onto the mesh). There is also a screenshot of what's going on. If one considers the function I project onto the mesh, what should normally happen is that there is a "hole" is the density field around the x=0, y=0 region, the rest being equal to one. I hope it is just a mishandling from my end !! Thank you in advance for your help, Cheers, Thibault

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Is PetscSFBcast deterministic (just checking, I assume it is)
by Mark Adams 30 Jul '21

30 Jul '21

GAMG is not deterministic and I'm trying to figure out why. Thanks, Mark

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is PETSc's random deterministic?
by Mark Adams 28 Jul '21

28 Jul '21

Also, when I google function the Argonne web pages are not found (MIT seems to have mirrored this and that works). Thanks, Mark

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DMPlex doubt
by Miguel Angel Tapia 26 Jul '21

26 Jul '21

Hello. I am a master's student in Mexico. I am currently working on a project in which we are implementing DMPlex in a code for electromagnetic modeling. Right now I am working on understanding the tool in C. But I'm stuck on something and that's why my next doubt: I am trying to get the coordinates of the nodes of a mesh in DMPlex. I already understood how the DAG is structured, how to obtain the nodes that make up some point. But the ordering of the nodes changes in DMPlex. So I need to know the coordinates of each node to compare them with my initial mesh and confirm that the same nodes form the same point in the software I am using as well as in the DMPlex DAG. It would be great if you could guide me a bit on how to do this or indicate which DMPlex examples would be good to review or which examples solve something similar to my situation. Thank you in advance. Regards.

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