[petsc-users] Tracking a NaN in FVM gradient computation

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

[petsc-users] Guidance on using Tao for unconstrained minimization

Hello PETSc users! I am using Tao for an unconstrained minimization problem. I have found that CG works better than the other types for this application. After about 85 iterations, I get an error about line search failure. I'm not clear on what this means, or how I could mitigate the problem, and

Re: [petsc-users] Updating TS solution outside PETSc

get the 3d mirror written. > >Others may have alternative advice for Neumann with DMDA, > >Barry > > >> On Dec 5, 2019, at 10:00 AM, Ellen M. Price >> wrote: >> >> Hi PETSc users, >> >> I am working with a code that solves a set of

[petsc-users] Updating TS solution outside PETSc

Hi PETSc users, I am working with a code that solves a set of PDEs on a rectangular domain with Neumann boundary conditions. My understanding of implementing the boundary condition is that I should set the boundary value to be the value that makes the finite difference derivative go to zero (or so

[petsc-users] DMCompositeSetCoupling -- simple example?

Hello again! For my multiphysics problem, I think a DMComposite might make the most sense, since some variables are only defined in 1d (so any 2d information is just wasting memory and CPU), while others have a full 2d distribution. To tell PETSc how the two DMs should be coupled, it looks like I

[petsc-users] Correct way to access a sequential version of a DMDA Vec?

Hi PETSc users! I'm trying to access a DMDA Vec's values after doing a scatter to all processors. I've run into some trouble, however, because the call to DMDAVecGetArray doesn't seem to care that I'm using a sequential vector. The calling sequence that "works" (runs without error *until* I try to

Re: [petsc-users] Changing nonzero structure and Jacobian coloring

several Newton solves) construct a very sparse matrix >> that captures just the very local coupling in the problem. Once particles >> have moved around a bit you would throw away the old matrix and construct a >> new one. For example the matrix might just captures interactions between &

Re: [petsc-users] Changing nonzero structure and Jacobian coloring

> can't imagine how) and the Jacobian changes truly dramatically in structure > then what I suggest may not be appropriate but you'll need to tell us your > problem in that case so we can make suggestions. > >Barry > > > >> On Oct 15, 2019, at 2:56 PM, E

[petsc-users] Changing nonzero structure and Jacobian coloring

Hi PETSc users! I have a problem that I am integrating with TS, and I think an implicit method would let me take larger timesteps. The Jacobian is difficult to compute, but, more importantly, the nonzero structure is changing with time, so even if I use coloring and finite differences to compute t

Re: [petsc-users] Using DMCOMPOSITE with TS

Quick update: I found that changing TS_EXACTFINALTIME_INTERPOLATE to TS_EXACTFINALTIME_MATCHSTEP fixes the problem; is there a reason I can't use the interpolation when using a DMCOMPOSITE? Ellen Price On 2/20/19 1:42 PM, Ellen Price wrote: > Hi fellow PETSc users! > > I am attempting to use a

Re: [petsc-users] Increasing norm with finer mesh

Maybe a stupid suggestion, but sometimes I forget to call the *SetFromOptions function on my object, and then get confused when changing the options has no effect. Just a thought from a fellow grad student. Ellen On 10/16/2018 09:36 PM, Matthew Knepley wrote: > On Tue, Oct 16, 2018 at 9:14 PM We

Re: [petsc-users] DMPLEX project function error

comes closest, looks like it gets faces?). Is there an elegant way to do this, or an example I can follow? Ellen On 10/13/2018 04:26 AM, Matthew Knepley wrote: > On Fri, Oct 12, 2018 at 6:00 PM Ellen M. Price > mailto:ellen.pr...@cfa.harvard.edu>> wrote: > > Hi Matt, > >

Re: [petsc-users] DMPLEX project function error

but I get some kind of error no matter what I do (presumably I'm not giving the right input), and there aren't any examples in the docs. Ellen On 10/12/2018 11:31 AM, Matthew Knepley wrote: > On Fri, Oct 12, 2018 at 11:12 AM Ellen M. Price > mailto:ellen.pr...@cfa.harvard.edu>

Re: [petsc-users] DMPLEX project function error

eciated. Ellen On 10/11/2018 05:41 PM, Matthew Knepley wrote: > On Thu, Oct 11, 2018 at 4:39 PM Ellen M. Price > mailto:ellen.pr...@cfa.harvard.edu>> wrote: > > I was working with a DMPLEX and FEM, following SNES example 12. I get > the following error when I call DMPr

[petsc-users] DMPLEX project function error

I was working with a DMPLEX and FEM, following SNES example 12. I get the following error when I call DMProjectFunction, but I don't know what it means. Can anyone explain where I might have gone wrong, or at least what this error is telling me? I think the point closure size is correct, since my m

Re: [petsc-users] Implementing FEM with PLEX/DS/SNES

tion (on a nontrivial mesh and with a nontrivial, non-analytic mass density function). Ellen On 10/08/2018 06:28 PM, Matthew Knepley wrote: > On Mon, Oct 8, 2018 at 5:50 PM Ellen M. Price > mailto:ellen.pr...@cfa.harvard.edu>> wrote: > > Can anyone shed some light on SNES e

[petsc-users] Implementing FEM with PLEX/DS/SNES

Can anyone shed some light on SNES example 12? https://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex12.c.html I am solving a Poisson problem, but with a source term defined on mesh points, so I don't have an analytic form. The part I am confused about is the role of the funct

[petsc-users] Question about HDF5 viewer groups

Hi there, I'm running a complex PETSc program that outputs a LOT of data to an HDF5 file. As such, I'd like to separate my output into groups to make it easier to traverse in the analysis phase. I'm either confused about the nomenclature or the usage of PetscViewerHDF5PushGroup/PetscViewerHDF5Pop

[petsc-users] Debugging SNES when "everything" looks okay

Hi PETSc users, I'm having trouble applying SNES to a new problem I'm working on. I'll try to be as complete as possible but can't post the full code because it's ongoing research and is pretty long anyway. The nonlinear problem arises from trying to solve a set of two coupled ODEs using a Galerk

[petsc-users] Errors encountered when linking against a successful build including MUMPS

I just successfully (re)-compiled petsc-3.9.2 to use my MUMPS install. The PETSc build process completed with no errors and I installed my new shared libs. However, when I tried linking against the new libraries, I get the following errors: /home/eprice/software/petsc-opt/lib/libpetsc.so: undefine

Re: [petsc-users] What does DMPlexDistribute actually do?

pe: plex Parallel Mesh in 3 dimensions: 0-cells: 445 445 445 445 1-cells: 1196 1196 1196 1196 2-cells: 1072 1072 1072 1072 3-cells: 320 320 320 320 Labels: depth: 4 strata with value/size (0 (445), 1 (1196), 2 (1072), 3 (320)) Ellen Price On 03/25/2018 07:29 PM, Matthew Knepley wrote:

[petsc-users] What does DMPlexDistribute actually do?

I am trying to understand some unusual behavior (at least, given my current understanding) in DMPlexDistribute. I have created a hex mesh and distributed it using the following snippet: /* "-refine" is an option set at runtime */ PetscOptionsGetInt(NULL, NULL, "-refine", &refine, NULL); ierr = DMP