Re: [petsc-users] Inquiry about reading an exodus II file from coreform Cubit

On Sep 21, 2024, at 9:54 AM, neil liu wrote: Caution: External email.  Thanks a lot, David. That works. Then I tried another example from Cubit. The script is defined as follows, reset brick x 1 mesh vol 1 block 1 volume 1 sideset 1 surface 1 block 2 surface 1 #sides of the

Re: [petsc-users] DMPlex and Gmsh

Hi, I think that you need to use the magical keyword “-dm_plex_gmsh_mark_vertices” for that Blaise On Nov 8, 2023, at 1:13 PM, Sharan Roongta wrote: Caution: External email.  Dear Petsc team,   I want to load a .msh file generated using

Re: [petsc-users] Face Set not appearing when loading GMSH mesh to DMPlex

Can you send me the geo or msh file, or instruction on how to build your example? I am not familiar with the gmsh API Blaise On Sep 20, 2023, at 8:16 AM, Anna Dalklint via petsc-users wrote: Caution: External email.  Hello, I am trying to lo

Re: [petsc-users] PETSc with Xcode 15

FWIW, CLT 15.0 also seems to include changes to the linker, with incompatible options etc… I was able to rebuild mpich and petsc but I get many linker warnings and have not fully tested my build Before CLT 15.0 update SiMini:mef90-dmplex (dmplex)$ ld -v @(#)PROGRAM:ld  PROJECT:ld

[petsc-users] MatSetSizes: C vs python

Hi, Does anybody understand why MatSetSizes seem to behave differently in C and python? I would expect the attached examples to be strictly equivalent but the python version fails in parallel. It may be that the python interface is different, but I don’t see any mention of this in the

Re: [petsc-users] Composing different Field Components into single Vector (or data array)

ames Wright Graduate Research Assistant, PhD University of Colorado Boulder Cell: (864) 498 8869  Email: ja...@jameswright.xyz Website: jameswright.xyz On Mon, Apr 17, 2023 at 12:42 PM Blaise Bourdin <bour...@mcmaster.ca> wrote: Hi, If you have created y

Re: [petsc-users] Composing different Field Components into single Vector (or data array)

Hi, If you have created your vectors using sections, all you need is to call DMCreateSuperDM. See src/dm/impls/plex/tests/ex26.c:300 for an example. Blaise On Apr 17, 2023, at 1:30 PM, James Wright wrote: Hello, I currently have two DMPlex objects, both `DMClone`

Re: [petsc-users] GAMG failure

On Mar 27, 2023, at 9:11 PM, Mark Adams wrote: Yes, the eigen estimates are converging slowly. BTW, have you tried hypre? It is a good solver (lots lots more woman years) These eigen estimates are conceptually simple, but they can lead to problems like this (hypre and an eig

Re: [petsc-users] GAMG failure

On Mar 24, 2023, at 3:21 PM, Mark Adams wrote: * Do you set:     PetscCall(MatSetOption(Amat, MAT_SPD, PETSC_TRUE));     PetscCall(MatSetOption(Amat, MAT_SPD_ETERNAL, PETSC_TRUE)); Yes Do that to get CG Eigen estimates. Outrigh

[petsc-users] GAMG failure

Hi, I am having issue with GAMG for some very ill-conditioned 2D linearized elasticity problems (sharp variation of elastic moduli with thin regions of nearly incompressible material). I use snes_type newtonls, linesearch_type cp, and pc_type gamg without any further options. pc_type Jacobi co

Re: [petsc-users] dmplex overlap questions

On Feb 16, 2023, at 10:54 AM, Lawrence Mitchell wrote: Hi Blaise, On Thu, 16 Feb 2023 at 15:17, Blaise Bourdin wrote: Hi, I am trying to implement a non-local finite elements reconstruction operator in parallel. Given a dmplex distributed with an overlap, is there a

[petsc-users] dmplex overlap questions

Hi, I am trying to implement a non-local finite elements reconstruction operator in parallel. Given a dmplex distributed with an overlap, is there a way to figure out which cells are in the overlap and which are not? Alternatively, suppose that I distribute the same DM with and without an over

Re: [petsc-users] PETSc Fortran 64-bit

On Feb 1, 2023, at 3:50 PM, Satish Balay via petsc-users wrote: call DMPlexGetDepthStratum(dm, 0, vst, vend, ierr);CHKERRA(ierr)  gives an error regarding the datatype of ierr. The error basically leads: Error: Type mismatch in argument ‘b’ at (1); passed INTEGER(4) to INTE

Re: [petsc-users] PETSc Fortran 64-bit

I use the following I all my fortran codes (inspired by a post from Michael Metcalf on comp.lang.fortran many many moons ago): PetscReal,Parameter :: PReal = 1.0 Integer,Parameter,Public :: Kr = Selected_Real_Kind(Precision(PReal)) PetscInt,Parameter :: PInt = 1 Integer,Para

Re: [petsc-users] about repeat of expensive functions using VecScatterCreateToAll

bottommost slice of the array and update it as I move up. Every slice needs the updated values below that slice.   Vysakh   From: Blaise Bourdin <bour...@mcmaster.ca>  Sent: Tuesday, January 17, 2023 4:47 PM To: Venugopal, Vysakh (venugovh) <venug...@mail.uc.edu> Cc: Barr

Re: [petsc-users] about repeat of expensive functions using VecScatterCreateToAll

What type of filter are you implementing? Convolution filters are expensive to parallelize since you need an overlap of the size of the support of the filter, but it may still not be worst than doing it sequentially (typically the filter size is only one or 2 element diameters). Or you may b

Re: [petsc-users] coordinate degrees of freedom for 2nd-order gmsh mesh

Out of curiosity, what is the rationale for _reading_ high order gmsh meshes? Is it so that one can write data back in native gmsh format?  Regards, Blaise On Jan 12, 2023, at 7:13 PM, Matthew Knepley wrote: On Thu, Jan 12, 2023 at 1:33 PM Jed Brown w

[petsc-users] GAMG and linearized elasticity

Hi, I am getting close to finish porting a code from petsc 3.3 / sieve to main / dmplex, but am now encountering difficulties I am reasonably sure that the Jacobian and residual are correct. The codes handle boundary conditions differently (MatZeroRowCols vs dmplex constraints) so it

Re: [petsc-users] Union of sequential vecs

Hi, If you use an IS to store your ints, you can also do ISAllGather followed by ISSortRemoveDups Blaise On Dec 9, 2022, at 4:14 PM, Barry Smith wrote:   Ok, so you want the unique list of integers sorted from all the seq vectors on ever MPI rank?

[petsc-users] Postdoctoral openings at McMaster University

should reach out to me by email (bour...@mcmaster.ca <mailto:bour...@mcmaster.ca>) and attach a vitae and list of publications. Feel free to forward this posting. Blaise Bourdin — Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1) Professor, Departm

Re: [petsc-users] Reference element in DMPlexComputeCellGeometryAffineFEM

, 2022 at 3:46 PM Blaise Bourdin <bour...@mcmaster.ca> wrote: I am not sure I am buying this… If the tet was inverted, detJ would be negative, but it is always 1/8, as expected. The attached mesh is a perfectly valid tet generated by Cubit, with orientation matching the exodus documen

Re: [petsc-users] Reference element in DMPlexComputeCellGeometryAffineFEM

Bourdin <bour...@mcmaster.ca> wrote: On Nov 9, 2022, at 10:04 AM, Matthew Knepley <knep...@gmail.com> wrote: On Tue, Nov 8, 2022 at 9:14 PM Blaise Bourdin <bour...@mcmaster.ca> wrote: Hi, What reference simplex is DMPlexComputeCellGeometryAffineFEM using

Re: [petsc-users] Reference element in DMPlexComputeCellGeometryAffineFEM

On Nov 9, 2022, at 10:04 AM, Matthew Knepley wrote: On Tue, Nov 8, 2022 at 9:14 PM Blaise Bourdin <bour...@mcmaster.ca> wrote: Hi, What reference simplex is DMPlexComputeCellGeometryAffineFEM using in 2 and 3D? I am used to computing my shape functions on th

[petsc-users] Reference element in DMPlexComputeCellGeometryAffineFEM

Hi, What reference simplex is DMPlexComputeCellGeometryAffineFEM using in 2 and 3D? I am used to computing my shape functions on the unit simplex (vertices at the origin and each e_i), but it does not look to be the reference simplex in this function: In 3D, for the unit simplex with vertices a

Re: [petsc-users] Dof ordering in DMPlexVecGet/Set/RestoreClosure

Thanks. I had figured out the ordering by stratum but was dreading reconstructing the ordering on test and hexes… Blaise On Nov 7, 2022, at 12:14 PM, Matthew Knepley wrote: On Mon, Nov 7, 2022 at 10:51 AM Blaise Bourdin <bour...@mcmaster.ca> wrote: Hi, H

[petsc-users] Dof ordering in DMPlexVecGet/Set/RestoreClosure

Hi, How are degree of freedom ordered in calls to DMPlexVec[Set/Get/Restore]Closure? Given a FE mesh and a section for P2-Lagrange elements (i.e. 1 dof per vertex and edge), I was naively assuming that the “local” vector would contain dof at vertices then edges (in this order), since it matches

Re: [petsc-users] Problem about optimized version

e not touched the code since a bit after Chukwudi graduated and you must have had to do a few changes to compile it with petsc 3.17. WOuld you mind contributing your changes back to the main repository? A pull request would be greatly appreciated. Regards, Blaise Bourdin On Aug 31, 2022,

Re: [petsc-users] DMPlex: a Mapping Array between Natural and Distributed Cell Index

Alexis noticed a problem with the natural SF when constraints are defined. He has a MR coming.  @Alexis: Could it be that what Bora sees is exactly what you fixed? Blaise On Jul 18, 2022, at 8:35 PM, Bora Jeong wrote: Thank you for the reply.  I am act

[petsc-users] List of points with dof>0 in a PetscSection

Hi, Given a PetscSection, is there an easy way to get a list of point at which the number of dof is >0? For instance, when projecting over a FE space, I’d rather do a loop over such points than do a loop over all points in a DM, get the number of dof, and test if it is >0. Regards, Blaise --

Re: [petsc-users] problems with petsc4py on M1 mac when configuring PETSc

Veronika, There is something screwy going on with some hombrew gcc installs. Not sure why.  In many case, creating a symbolic link libgcc_s.dylib -> libgcc_s.1.1.dylib in /opt/homebrew/opt/gcc/lib/gcc/11 fixes this Regards, Blaise On Apr 8, 2022, at 5:41 AM, Veronika Ulanova <19veronik...@

Re: [petsc-users] Message length unit in log_view

Thanks, Blaise On Feb 25, 2022, at 10:30 AM, Junchao Zhang <junchao.zh...@gmail.com> wrote: On Fri, Feb 25, 2022 at 9:20 AM Blaise Bourdin <bour...@mcmaster.ca> wrote: Hi, What is the unit for messages length in PetscLogView? MPI Messages:         3.500e+00     1.000

[petsc-users] Message length unit in log_view

Hi, What is the unit for messages length in PetscLogView? MPI Messages: 3.500e+00 1.000 3.500e+00 7.000e+00 MPI Message Lengths: 9.200e+01 1.000 2.629e+01 1.840e+02 MPI Reductions: 4.000e+01 1.000 Are these bytes, words, KB? Regards, Blaise -- Professor, Depart

Re: [petsc-users] Output data using ExodusIIViewer

David, Here is a modified example. Exodus needs some additional work prior to saving fields. See the attached modified example. Blaise On Dec 1, 2021, at 1:54 PM, Blaise Bourdin <bour...@mcmaster.ca> wrote: OK, let me have a look. Blaise On

Re: [petsc-users] Output data using ExodusIIViewer

to make it work. ​ ​David ​​ On Nov 30 2021, at 11:39 AM, Blaise Bourdin <bour...@mcmaster.ca> wrote: It looks like your DM cannot be saved in exodus format as such. The exodus format requires that all cells be part of a single block (defined by ‘Cell Set’ labels), and that the cell sets

Re: [petsc-users] Output data using ExodusIIViewer

It looks like your DM cannot be saved in exodus format as such. The exodus format requires that all cells be part of a single block (defined by ‘Cell Set’ labels), and that the cell sets consists of sequentially numbered cells. Can you see if that is enough? If not, I will go through your ex

Re: [petsc-users] [petsc-announce] Question regarding updating PETSc Fortran examples to embrace post F77 constructs

FINALLY! Let's get rid of fortran77 free form in examples. I can't think of any reason to self inflict such a suffering. Are there ANY compiler around that people use and would not be able to process free form examples?I can see a point in keeping compatibility with fortran77 in petsc. It woul

[petsc-users] LineSearch question

: > > Blaise, > >We are confused. Can you run both the bt and l2 with all those options and > send ALL the output from each of the two runs. > > Thanks > >Barry > > > On Aug 14, 2012, at 6:24 PM, Blaise Bourdin wrote: > >> Hi, >&g

[petsc-users] LineSearch question

nge to give access to others if necessary. Blaise > > Barry > > > > On Aug 14, 2012, at 5:53 PM, Blaise Bourdin wrote: > >> HI, >> >> I am trying to understand if the following behavior is normal / expected: >> >> I am solving a quasi-s

[petsc-users] LineSearch question

HI, I am trying to understand if the following behavior is normal / expected: I am solving a quasi-static evolution where at each time step, SNESSolve is called. My validation problem is a _static_ problem with 2 time steps (i.e. 2 successive calls to SNESSolve with the same operator, jacobian,

[petsc-users] pc_gamg_type geo broken in 3.3?

and get a line number? > > Mark > > On Jul 24, 2012, at 10:59 PM, Blaise Bourdin wrote: > >> Hi, >> >> is pc_gamg_type geo broken in petsc-3.3? I get the following when I make >> runex54 in src/ksp/ksp/examples/tutorials: >> >> iMac:tutori

[petsc-users] pc_gamg_type geo broken in 3.3?

Hi, is pc_gamg_type geo broken in petsc-3.3? I get the following when I make runex54 in src/ksp/ksp/examples/tutorials: iMac:tutorials blaise$ make runex54 1,28c1,128 < 0 KSP Residual norm 132.598 < 1 KSP Residual norm 39.159 < 2 KSP Residual norm 15.7856 < 3 KSP Residual norm 8.9132

[petsc-users] block size

search for an older thread on this list possible fixes are to either delete / not create the .info files or to assign different prefix to each vec B On Jul 18, 2012, at 12:39 PM, Anton Popov wrote: > "Comment out one of vectors, your code works fine." > I wouldn't say "fine" because I need to s

[petsc-users] [petsc-dev] second patch for DMDAVecGetArrayF90

Rectification: clone petsc-3.3, not petsc-dev, of course... B > There is something fishy in your tree or your build: the patch that Satish > sent addressed this issue, but it clearly has not been applied to your tree. > The patch I had originally sent contained an error. For instance, > F90ARRA

[petsc-users] [petsc-dev] second patch for DMDAVecGetArrayF90

On Jul 11, 2012, at 3:44 PM, TAY wee-beng wrote: > On 11/7/2012 8:10 PM, Satish Balay wrote: >> On Wed, 11 Jul 2012, TAY wee-beng wrote: >> >>> I just tried on a different system and the same error occurs. The 1st >>> command >>> : >>> / >>> / >>> >>> /patch -Np1 -R < DMDAVecRestoreArrayF90-2.p

[petsc-users] [petsc-dev] Getting 2d array with updated ghost values from DM global vector

On Jul 6, 2012, at 6:02 PM, TAY wee-beng wrote: > On 3/7/2012 1:23 PM, Satish Balay wrote: >> On Tue, 3 Jul 2012, Barry Smith wrote: >> >>> On Jul 3, 2012, at 3:08 AM, Blaise Bourdin wrote: >>> >>>> On Jul 3, 2012, at 4:10 AM, Barry Smith wro

[petsc-users] [petsc-dev] Getting 2d array with updated ghost values from DM global vector

oid**)&fa PETSC_F90_2PTR_PARAM(ptrd));if (*__ierr) return; *__ierr = F90Array1dDestroy(ptr,PETSC_SCALAR PETSC_F90_2PTR_PARAM(ptrd));if (*__ierr) return; *__ierr = VecRestoreArray(*x,&fa); Why aren't the calls to F90Array1dAccess and F90Array1dDestroy necessary in the context of DMDAVecGetArrayF9

[petsc-users] [petsc-dev] Getting 2d array with updated ghost values from DM global vector

etArrayF90? Blaise > > Thanks > > Barry > > On Jul 2, 2012, at 10:10 AM, Blaise Bourdin wrote: > >> Hi, >> >> There appears to be a bug in DMDAVecRestoreArrayF90. It is probably only >> triggered when the intel compilers. gfortran and intel

[petsc-users] Getting 2d array with updated ghost values from DM global vector

Hi, There appears to be a bug in DMDAVecRestoreArrayF90. It is probably only triggered when the intel compilers. gfortran and intel seem to have very different internal implementations of fortran90 allocatable arrays. Developers, can you check if the attached patch makes sense? It will not fix

[petsc-users] VecValid

Hi, As a side note: this is actually a problem I have met in one of the TS examples. When using fortran datatypes, the statements "A=0" and "if (A .eq. 0)" are not valid. They would require overloading the assignment and comparison operators. Can anybody see an alternative? Blaise > > VecVa

[petsc-users] ex52_integrateElement.cu

On Mar 27, 2012, at 1:23 PM, Matthew Knepley wrote: > On Tue, Mar 27, 2012 at 12:58 PM, David Fuentes > wrote: > Hi, > > I had a question about the status of example 52. > > http://petsc.cs.iit.edu/petsc/petsc-dev/file/a8e2f2c19319/src/snes/examples/tutorials/ex52.c > http://petsc.cs.iit.edu

[petsc-users] Binary VTK viewer

; mailing list with talk between Blaise Bourdin and Matt Knepley of adding > support for output of binary vtk files. Was this ever done? > > Thanks for your help, > Max -- Department of Mathematics and Center for Computation & Technology Louisiana State University, Baton Rouge, L

[petsc-users] ISAllGather withoutduplicates

On Feb 17, 2012, at 2:45 PM, Matthew Knepley wrote: > On Fri, Feb 17, 2012 at 2:39 PM, Blaise Bourdin wrote: >> The way I do it right now is >> ierr = ISGetTotalIndices(csIS,&labels);CHKERRQ(ierr); >> ierr = ISGetSize(csIS,&num_cs_global);CHKERRQ(ierr); >>

[petsc-users] ISAllGather withoutduplicates

> The way I do it right now is > ierr = ISGetTotalIndices(csIS,&labels);CHKERRQ(ierr); > ierr = ISGetSize(csIS,&num_cs_global);CHKERRQ(ierr); > > I would violate PETSc semantics here since you are going to destroy csIS > anyway: > > PetscSortRemoveDupsInt(&num_cs_global, labels); That's wha

[petsc-users] ISAllGather withoutduplicates

Hi, Is there an easy way to gather all values of an IS across all processes in a communicator while removing duplicates? Basically, I want to go from [0] Number of indices in set 2 [0] 0 1 [0] 1 2 [1] Number of indices in set 2 [1] 0 2 [1] 1 3 to [0] Number of indices in set 3 [0] 0 1 [0] 1 2

[petsc-users] SNESVI convergence spped

Hi, Ata and I are working together on this. The problem he describes is 1/2 of the iteration of our variational fracture code. In our application, E is position dependant, and typically becomes very large along very thin bands with width of the order of epsilon in the domain. Essentially, we e

[petsc-users] query about PETSc usage in Fortran applications

Lois, I use petsc through the fortran interface for my variational fracture mechanics code. (unstructured finite elements, 2d-3d). petsc has been instrumental in getting a parallel version. Sieve really helped me getting to large problems (largest to date being a 24M elements, 2,400 cores simul

[petsc-users] Questions about TS

On Oct 19, 2011, at 4:13 PM, Sean Farley wrote: > Is it right to think of the division between ODE, DAE and IMEX in the > documentation as Fully Explicit vs. Fully implicit vs. Semi-implicit? > > Mostly, yes. Indeed, we made 'shortcuts' such as "if the user provides no > IFunction, then treat

[petsc-users] Questions about TS

On Oct 19, 2011, at 4:16 PM, Jed Brown wrote: > On Wed, Oct 19, 2011 at 16:08, Blaise Bourdin wrote: > I get it now... My confusion was due to being used to derived all scheme on > the pde, then discretizing, whereas the documentation assumes that the > equation is already di

[petsc-users] Questions about TS

documentation as Fully Explicit vs. Fully implicit vs. Semi-implicit? Blaise On Oct 19, 2011, at 12:55 PM, Jed Brown wrote: > On Wed, Oct 19, 2011 at 12:32, Blaise Bourdin wrote: > Hi, > > > > On Wed, Oct 19, 2011 at 10:54, Blaise Bourdin > > wrote: > > Hi, &g

[petsc-users] Questions about TS

Hi, > On Wed, Oct 19, 2011 at 10:54, Blaise Bourdin wrote: > Hi, > > I am trying to use TS to solve a simple transient problem in an unstructured > finite element f90 code. > > 1. Section 6.1.1 of the manual refers to a TSSetMatrices function that can be > use

[petsc-users] Questions about TS

Hi, I am trying to use TS to solve a simple transient problem in an unstructured finite element f90 code. 1. Section 6.1.1 of the manual refers to a TSSetMatrices function that can be used to set the RHS and LHS matrices, but I can;t find it. Is this section outdated? 2. Since we are using uns

[petsc-users] hdf5 directive

PETSC_HAVE_HDF5 On Jul 26, 2011, at 5:25 PM, Ataollah Mesgarnejad wrote: > Dear all, > > Is there a preprocessor directive to check if PETSc has been compiled with > hdf5 or not ? (something like PETSC_HAS_HDF5?!!) > > Best, > Ata -- Department of Mathematics and Center for Computation & Tech

[petsc-users] PETSc recommended visualization packages

Hi, Let me add to Barry's frustration. I have spent most the last week trying to render animations of reasonably large computations (about 25M 3d unstructured elements divided in up to 25,000 exodusII files). - Paraview is simple to get started with in the GUI. In theory, it is scriptable in p

[petsc-users] tecplot viewer

Hi, Has anybody in this list ever written a tecplot viewer for DA based data? I have been fighting with tecplot hdf5 reader and it seems like it is not capable of reading vector valued fields. Blaise -- Department of Mathematics and Center for Computation & Technology Louisiana State Universi

[petsc-users] Storing an array in a PetscBag

Hi, Is there an easy way to use PetscBag to manage arrays of user data? optimally, I would like to something like typedef struct { PetscInt n; PetscReal *values; } MyParameters; MyParameters *params and be able to register "values" in the bag so that I can specify its values as

[petsc-users] [petsc4py] PETSc.Viewer().createHDF5 wipes out existing files

Hi, Hopefully this does not get double posted. I sent the original email from the wrong account to the wrong list? I am trying to do HDF5 IO in petsc4py. I noticed that when I create a viewer using PETSc.Viewer().createHDF5(inputfile,comm= PETSc.COMM_WORLD) the file "outputfile" is wiped out

[petsc-users] VTKViewer with petsc4py

> On 30 July 2010 23:50, Blaise Bourdin wrote: >> Great! that works. >> >> Now my problem is with DASetUniformCoordinates or DASetCoordinates. Do they >> exist in petsc4py? I can't see them when I do a dir(da). >> > > No, they are not available.

[petsc-users] VTKViewer with petsc4py

Great! that works. Now my problem is with DASetUniformCoordinates or DASetCoordinates. Do they exist in petsc4py? I can't see them when I do a dir(da). Thanks, Blaise On Jul 30, 2010, at 9:10 PM, Lisandro Dalcin wrote: > On 30 July 2010 21:13, Blaise Bourdin wrote: >>

[petsc-users] VTKViewer with petsc4py

Hi, Is PetscViewerSetFormat implemented in petsc4py (I am using petsc-3.1-p3 and petsc4py-1.1)? I am trying to save a DA and Vec in vtk format, but can't figure out the python equivalent to PetscViewerSetFormat(VTKViewer,PETSC_VIEWER_ASCII_VTK). My C code would be ierr = PetscViewerCreate(P