Re: [petsc-users] Calling PETSc functions from Python using petsc4py

No, these are not part of the PETSc library so they would need to be compiled and called separately (you can do that, but it isn't part of petsc4py). "Larson, Jeffrey M." writes: > Hello, > > Is there a way to call a function in a PETSc example file from python? > >

Re: [petsc-users] GAMG for the unsymmetrical matrix

> On Apr 6, 2017, at 9:39 AM, Kong, Fande wrote: > > Thanks, Mark and Barry, > > It works pretty wells in terms of the number of linear iterations (using > "-pc_gamg_sym_graph true"), but it is horrible in the compute time. I am > using the two-level method via

[petsc-users] EPSViewer in SLEPc

Hi All, The EPSViewer in SLEPc looks weird. I do not understand the viewer logic. For example there is a piece of code in SLEPc (at line 225 of epsview.c): *if (!ispower) { if (!eps->ds) { ierr = EPSGetDS(eps,>ds);CHKERRQ(ierr); } ierr = DSView(eps->ds,viewer);CHKERRQ(ierr);

[petsc-users] Calling PETSc functions from Python using petsc4py

Hello, Is there a way to call a function in a PETSc example file from python? Explicitly, I'd like to call EvaluateFunction and EvaluateJacobian (resp. lines 123 and 147) of https://www.mcs.anl.gov/petsc/petsc-current/src/tao/leastsquares/examples/tutorials/chwirut1.c.html from Python. Can

[petsc-users] Using same DMPlex for solving two different problems

I am solving a time-dependent problem using DMNetwork (uses DMPlex internally) to manage the network. To find the initial conditions, I need to solve a nonlinear problem on the same network but with different number of dofs on the nodes and edges. Question: Can I reuse the same DMNetwork (DMPlex)

Re: [petsc-users] examples of DMPlex*FVM methods

Matthew Knepley writes: > On Thu, Apr 6, 2017 at 8:32 AM, Jed Brown wrote: > >> Matthew Knepley writes: >> > Okay, that makes sense. If I do not have fluxes matching the sources, I >> do >> > not >> > preserve montonicity for an advected

Re: [petsc-users] Understanding DMPlexDistribute overlap

Hi Michael, thank you for verifying that the test works. I actually was on `maint`, as per https://www.mcs.anl.gov/petsc/download/index.html. Now that I switched to `master ` everything works as expected, both my test example and the DMPlex test ex12, which I can now build without issue. I

Re: [petsc-users] GAMG for the unsymmetrical matrix

On Thu, Apr 6, 2017 at 7:39 AM, Kong, Fande wrote: > Thanks, Mark and Barry, > > It works pretty wells in terms of the number of linear iterations (using > "-pc_gamg_sym_graph true"), but it is horrible in the compute time. I am > using the two-level method via "-pc_mg_levels

Re: [petsc-users] GAMG for the unsymmetrical matrix

Thanks, Mark and Barry, It works pretty wells in terms of the number of linear iterations (using "-pc_gamg_sym_graph true"), but it is horrible in the compute time. I am using the two-level method via "-pc_mg_levels 2". The reason why the compute time is larger than other preconditioning options

Re: [petsc-users] GAMG for the unsymmetrical matrix

On Tue, Apr 4, 2017 at 10:10 AM, Barry Smith wrote: > >> Does this mean that GAMG works for the symmetrical matrix only? > > No, it means that for non symmetric nonzero structure you need the extra > flag. So use the extra flag. The reason we don't always use the flag is >

Re: [petsc-users] examples of DMPlex*FVM methods

On Thu, Apr 6, 2017 at 8:32 AM, Jed Brown wrote: > Matthew Knepley writes: > > Okay, that makes sense. If I do not have fluxes matching the sources, I > do > > not > > preserve montonicity for an advected field. I might need this to machine > > precision >

Re: [petsc-users] examples of DMPlex*FVM methods

Matthew Knepley writes: > Okay, that makes sense. If I do not have fluxes matching the sources, I do > not > preserve montonicity for an advected field. I might need this to machine > precision > because some other equations cannot tolerate a negative number there. I will >

Re: [petsc-users] examples of DMPlex*FVM methods

On Thu, Apr 6, 2017 at 7:04 AM, Jed Brown wrote: > Matthew Knepley writes: > > > On Wed, Apr 5, 2017 at 9:57 PM, Jed Brown wrote: > > > >> Matthew Knepley writes: > >> > >> > On Wed, Apr 5, 2017 at 1:13 PM, Jed Brown

Re: [petsc-users] Configuring PETSc for KNL

Lawrence Mitchell writes: > On 06/04/17 12:25, Matthew Knepley wrote: >> I'm not sure whether getting the Intel acronyms mixed up (KNL vs MKL) >> makes the quote above better or worse. >> >> >> Too cryptic. Are you saying that this cannot be what is

Re: [petsc-users] examples of DMPlex*FVM methods

Matthew Knepley writes: > On Wed, Apr 5, 2017 at 9:57 PM, Jed Brown wrote: > >> Matthew Knepley writes: >> >> > On Wed, Apr 5, 2017 at 1:13 PM, Jed Brown wrote: >> > >> >> Matthew Knepley writes:

Re: [petsc-users] examples of DMPlex*FVM methods

Ingo Gaertner writes: > By transport equation I mean the advection-diffusion equation. This is > always parabolic, independent of whether it is advection dominated or > diffusion dominated. This is true from an analysis perspective, but nearly meaningless from the

Re: [petsc-users] examples of DMPlex*FVM methods

On Wed, Apr 5, 2017 at 9:57 PM, Jed Brown wrote: > Matthew Knepley writes: > > > On Wed, Apr 5, 2017 at 1:13 PM, Jed Brown wrote: > > > >> Matthew Knepley writes: > >> > >> > On Wed, Apr 5, 2017 at 12:03 PM, Jed Brown

Re: [petsc-users] Configuring PETSc for KNL

On 06/04/17 12:25, Matthew Knepley wrote: > I'm not sure whether getting the Intel acronyms mixed up (KNL vs MKL) > makes the quote above better or worse. > > > Too cryptic. Are you saying that this cannot be what is happening? How > would you explain > the drop off in performance? >

Re: [petsc-users] Configuring PETSc for KNL

On Wed, Apr 5, 2017 at 10:26 PM, Jed Brown wrote: > Matthew Knepley writes: > > > On Wed, Apr 5, 2017 at 12:23 PM, Justin Chang > wrote: > > > >> I simply ran these KNL simulations in flat mode with the following > options: > >> > >>

Re: [petsc-users] Understanding DMPlexDistribute overlap

Hi Francesco, Ok, I can confirm that your test runs fine for me with the latest master branch. I'm attaching the log for two processes up to overlap 7, where the entire mesh is effectively replicated on each partition. The command I ran was: for OL in 1 2 3 4 5 6 7; do mpiexec -np 2 python

Re: [petsc-users] Understanding DMPlexDistribute overlap

Dear Matt, thanks for your reply. On mercoledì 5 aprile 2017 21:09:43 CEST Matthew Knepley wrote: > On Wed, Apr 5, 2017 at 6:03 AM, Francesco Caimmi >[...] > > the program fails with the error message captured in the attached file > > error.log. Changing the number

Re: [petsc-users] examples of DMPlex*FVM methods

There are many flavors of FEM and FVM. If by FEM you mean the Continuous Galerkin FEM, then yes it is a far from ideal method for solving advection-diffusion equations, especially when advection is the dominating effect. The Discontinuous Galerkin (DG) FEM on the other hand is much better for

Re: [petsc-users] examples of DMPlex*FVM methods

2017-04-05 19:56 GMT+02:00 Jed Brown : > Ingo Gaertner writes: > > > Hi Matt, > > I don't care if FV is suboptimal to solve the Poisson equation. I only > want > > to better understand the method by getting my hands dirty, and also > > implement the