Re: [petsc-users] Inquiry about the definitely lost memory

2023-06-09 Thread Matthew Knepley
On Fri, Jun 9, 2023 at 12:04 PM neil liu wrote: > Dear Petsc developers, > > I am using valgrind to check the memory leak. It shows, > [image: image.png] > Finally, I found that DMPlexrestoretrasitiveclosure can resolve this > memory leak. > > My question is from the above screen shot, it seems

Re: [petsc-users] Behavior of KSP iterations when using Restart

2023-06-09 Thread Matthew Knepley
_type lu Thanks, Matt > ------ > *De:* Matthew Knepley > *Enviado:* viernes, 9 de junio de 2023 4:13:35 > *Para:* Nicolas Garcia Guzman > *Cc:* petsc-users@mcs.anl.gov > *Asunto:* Re: [petsc-users] Behavior of KSP iterations when using Restart > &

Re: [petsc-users] Behavior of KSP iterations when using Restart

2023-06-08 Thread Matthew Knepley
On Thu, Jun 8, 2023 at 9:13 PM Nicolas Garcia Guzman wrote: > Hello, > > > I am solving a linear system using petsc4py, with the following command: > > > python main.py -ksp_type gmres -ksp_gmres_restart 16 -ksp_max_it 18 > -ksp_monitor -ksp_converged_reason -ksp_rtol 1e-15 -pc_type asm >

Re: [petsc-users] Gauss-Lobatto-Legendre Element Gradient -- Caught signal number 11 SEGV

2023-06-01 Thread Matthew Knepley
On Thu, Jun 1, 2023 at 1:46 AM Duan Junming via petsc-users < petsc-users@mcs.anl.gov> wrote: > Dear all, > > > I have a simple demo code attached below, which gives a segmentation > violation error. > > Can you help me with this problem? I think the problem is due to the > destroy function. > >

Re: [petsc-users] PetscSF "One-Sided" vs. "Two-Sided"

2023-05-31 Thread Matthew Knepley
On Wed, May 31, 2023 at 6:37 PM Ferrand, Jesus A. wrote: > Dear PETSc team: > > For one of my applications, I need to know which owned DAG points in a > (DMPlex) are other ranks' ghosts. > Say, rank-0 has some point "x" (which it owns) and it shows up in, say, > rank-1 as a ghost numbered "y".

Re: [petsc-users] Using SNESSHELL as a wrapper for a CFD solver.

2023-05-31 Thread Matthew Knepley
d for consistency and comparison to these other (more appropriate!) uses > of PETSc. > > Thanks. > Kenneth > > > > *From: *Matthew Knepley > *Date: *Wednesday, May 31, 2023 at 3:48 PM > *To: *Kenneth C Hall > *Cc: *petsc-users@mcs.anl.gov > *Subject: *Re: [pe

Re: [petsc-users] Using SNESSHELL as a wrapper for a CFD solver.

2023-05-31 Thread Matthew Knepley
On Wed, May 31, 2023 at 3:21 PM Kenneth C Hall wrote: > Hi, > > > > I am doing a number of problems using PETSc/SLEPc, but I also work on some > non-PETSc/SLEPc flow solvers. I would like to use PETSc as a wrapper for > this non-PETSc flow solver for compatibility, so I can use the tolerance

Re: [petsc-users] Multiple points constraint in parallel

2023-05-31 Thread Matthew Knepley
On Wed, May 31, 2023 at 2:43 PM YuSh Lo wrote: > Matthew Knepley 於 2023年5月31日 週三 下午1:02寫道: > >> On Wed, May 31, 2023 at 1:53 PM YuSh Lo wrote: >> >>> Hi Matthew, >>> >>> Matthew Knepley 於 2023年5月31日 週三 上午5:08寫道: >>> >>>

Re: [petsc-users] Multiple points constraint in parallel

2023-05-31 Thread Matthew Knepley
On Wed, May 31, 2023 at 1:53 PM YuSh Lo wrote: > Hi Matthew, > > Matthew Knepley 於 2023年5月31日 週三 上午5:08寫道: > >> On Wed, May 31, 2023 at 1:25 AM YuSh Lo wrote: >> >>> Hi, >>> >>> I have some multiple points constraint input as follows, &

Re: [petsc-users] [petsc-maint] Error during compile

2023-05-31 Thread Matthew Knepley
th exit code 1 (use -v to see > invocation)* > > > > > > I attach the complete log file. > > > > Thanks a lot for your help. > > > > Best regards, > > > > Joauma > > > > *De : *Matthew Knepley > *Date : *mercredi, 31 mai 2023 à 12:03 >

Re: [petsc-users] Multiple points constraint in parallel

2023-05-31 Thread Matthew Knepley
On Wed, May 31, 2023 at 1:25 AM YuSh Lo wrote: > Hi, > > I have some multiple points constraint input as follows, > > A_1 a_4 > B_2 b_5 > C_3 c_6 > > each columns are stored in different IS. > So one IS lists the capital letter and one lists the lowercase? > After dmplex distribute, they will

Re: [petsc-users] [petsc-maint] Error during compile

2023-05-31 Thread Matthew Knepley
On Wed, May 31, 2023 at 5:25 AM Joauma Marichal < joauma.maric...@uclouvain.be> wrote: > Hello, > > > > I am writing to you as I am trying to compile petsc on my mac. > > > > I used: > > $ export >

Re: [petsc-users] Get global offset in global vector for the points not owned by this processor.

2023-05-29 Thread Matthew Knepley
On Mon, May 29, 2023 at 5:47 PM YuSh Lo wrote: > Hi, > > How to get the offset in global vector for the points not owned by this > processor? > I have a parallel DMPlex and a section assigned to it. > GetSectionGetOffset with a global section returns -1 for the points not > owned by this

Re: [petsc-users] reading and writing periodic DMPlex to file

2023-05-24 Thread Matthew Knepley
Checking back. What does not work? Thanks, Matt On Tue, Jan 24, 2023 at 11:26 AM Matthew Knepley wrote: > On Tue, Jan 24, 2023 at 10:39 AM Berend van Wachem < > berend.vanwac...@ovgu.de> wrote: > >> Dear Matt, >> >> I have been working on this now

Re: [petsc-users] DMLabel to extract height-0 points by their DMPolytope value

2023-05-24 Thread Matthew Knepley
On Tue, May 23, 2023 at 8:44 PM Ferrand, Jesus A. wrote: > Dear PETSc team: > > I am trying to use DMPlex and DMLabel to develop an API to write plexes to > .cgns format in parallel. > To that end, I need a way to extract the height-0 points and sort them by > topological type (i.e., chunk of

Re: [petsc-users] MPI_Iprobe Error with MUMPS Solver on Multi-Nodes

2023-05-23 Thread Matthew Knepley
y. If this >> amount of memory is sufficient for solving the matrix with approximately 3 >> million degrees of freedom? >> >> Thanks! >> Zongze >> >> Il giorno lun 22 mag 2023 alle ore 20:03 Zongze Yang < >>> yangzon...@gmail.com> ha scri

Re: [petsc-users] MPI_Iprobe Error with MUMPS Solver on Multi-Nodes

2023-05-23 Thread Matthew Knepley
ees of freedom? > It really depends on the fill. Suppose that you get 1% fill, then (3e6)^2 * 0.01 * 8 = 1e12 B and you have 1.5e12 B, so I could easily see running out of memory. Thanks, Matt > Thanks! > Zongze > > Il giorno lun 22 mag 2023 alle ore 20:03 Zongze Yan

Re: [petsc-users] MPI_Iprobe Error with MUMPS Solver on Multi-Nodes

2023-05-22 Thread Matthew Knepley
On Mon, May 22, 2023 at 11:07 AM Zongze Yang wrote: > Hi, > > I hope this letter finds you well. I am writing to seek guidance regarding > an error I encountered while solving a matrix using MUMPS on multiple nodes: > Iprobe is buggy on several MPI implementations. PETSc has an option for

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-22 Thread Matthew Knepley
llCoordinatesLocal and CoordinatesLocal works. > > Best regards, Berend. > > Many thanks and best regards, Berend. > > On 5/17/23 23:04, Matthew Knepley wrote: > > On Wed, May 17, 2023 at 2:01 PM Berend van Wachem > > mailto:berend.vanwac...@ovgu.de>> wrote: > > > >

Re: [petsc-users] Using dmplexdistribute do parallel FEM code.

2023-05-18 Thread Matthew Knepley
t; 2 13 0 0 > 2 21 0 0 > 2 26 0 0 > 3 1 0 0 > $EndNodes > $Elements > 5 24 1 24 > 2 1 2 2 > 1 1 2 4 > 2 4 2 3 > 2 13 2 4 > 3 9 1 2 > 4 9 2 10 > 5 5 9 10 > 6 5 10 6 > 2 21 2 4 > 7 11 3 4 > 8 11 4 12 > 9 7 11 12 > 10 7 12 8 > 2 26 2 2 >

Re: [petsc-users] Using dmplexdistribute do parallel FEM code.

2023-05-17 Thread Matthew Knepley
On Wed, May 17, 2023 at 6:58 PM neil liu wrote: > Dear Petsc developers, > > I am writing my own code to calculate the FEM matrix. The following is my > general framework, > > DMPlexCreateGmsh(); > MPI_Comm_rank (Petsc_comm_world, ); > DMPlexDistribute (.., .., ); > > dm = dmDist; > //This can

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Matthew Knepley
should be 1.0. > > Am I doing something wrong? > Quickly, I see that a *= 10.0 + 1.0; is the same as a *= 11.0; not multiply by 10 and add 1. I will send it back when I get everything the way I want. Thanks, Matt > Thanks and best regards, > > Berend. > > On 5/

Re: [petsc-users] Nested field split

2023-05-17 Thread Matthew Knepley
On Wed, May 17, 2023 at 3:23 PM Matthew Knepley wrote: > On Wed, May 17, 2023 at 2:59 PM Barry Smith wrote: > >> >> Absolutely, that is fundamental to the design. >> >> In the simple case where all the degrees of freedom exist at the same >> grid po

Re: [petsc-users] Nested field split

2023-05-17 Thread Matthew Knepley
On Wed, May 17, 2023 at 2:59 PM Barry Smith wrote: > > Absolutely, that is fundamental to the design. > > In the simple case where all the degrees of freedom exist at the same > grid points, hence storage is like u,v,t,p in the vector the nesting is > trivial. You indicate the fields

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Matthew Knepley
DMSetCoordinatesLocal(dm, xl); DMGetCellCoordinatesLocal(dm, ); VecScale(xl, scale); DMSetCellCoordinatesLocal(dm, xl); Does this not work? Thanks, Matt Best regards, Berend. > > On 5/17/23 16:35, Matthew Knepley wrote: > > On Wed, May 17, 2023 at 10:21 AM Berend van Wachem < > berend.va

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Matthew Knepley
to push in an API for "just" scaling, but I could be convinced the other way. Thanks, Matt > Thanks, Berend. > > On 5/17/23 16:10, Matthew Knepley wrote: > > On Wed, May 17, 2023 at 10:02 AM Berend van Wachem > > mailto:berend.vanwac...@ovgu.de>> wrote: &g

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Matthew Knepley
On Wed, May 17, 2023 at 10:02 AM Berend van Wachem wrote: > Dear PETSc Team, > > We are using DMPlex, and we create a mesh using > > DMPlexCreateBoxMesh ( ); > > and get a uniform mesh. The mesh is periodic. > > We typically want to "scale" the coordinates (vertices) of the mesh, and > to

Re: [petsc-users] Large MATMPIAIJ - 32bit integer overflow in nz value

2023-05-17 Thread Matthew Knepley
On Wed, May 17, 2023 at 9:02 AM Fleischli Benno HSLU T < benno.fleisc...@hslu.ch> wrote: > Dear PETSc developers > > I am creating a very large parallel sparse matrix (MATMPIAIJ) with PETSc. > I write this matrix to disk. > The number of non-zeros exceeds the maximum number a 32-bit integer can >

Re: [petsc-users] SNESDMDASNESSetFunctionLocal in Fortran

2023-05-16 Thread Matthew Knepley
s, Matt > Thank you for your patience! I am still new to PETSc and learning how to > use it. > > > > *From:* Matthew Knepley > *Sent:* Sunday, May 14, 2023 12:24 PM > *To:* Khaled Nabil Shar Abdelaziz > *Cc:* petsc-users@mcs.anl.gov > *Subject:* Re: [petsc-

Re: [petsc-users] Interpolation between nodal and elemental field

2023-05-16 Thread Matthew Knepley
in each direction for cell (i, j, k). Thanks, Matt > > > Hope I make it clear, thanks! > > > > Regards, > > Kai > > Matthew Knepley 于2023年5月16日周二 16:29写道: > >> On Tue, May 16, 2023 at 10:27 AM K. Wu wrote: >> >>> Hi all, >&

Re: [petsc-users] Interpolation between nodal and elemental field

2023-05-16 Thread Matthew Knepley
On Tue, May 16, 2023 at 10:27 AM K. Wu wrote: > Hi all, > > Good day! > > I am currently working on interploating the nodal field vector I obtained > to its corresponding elemental field vector. I am doing it in a simple way > by using structured mesh, the element value is just the average of

Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers and OpenMPI

2023-05-15 Thread Matthew Knepley
ther, broken build. I would completely clean out your PETSc installation and start from scratch. Thanks, Matt > Thanks! > Marcos > ---------- > *From:* Matthew Knepley > *Sent:* Monday, May 15, 2023 12:53 PM > *To:* Vanella, Marcos (Fed) > *Cc

Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers and OpenMPI

2023-05-15 Thread Matthew Knepley
sing > the job to be terminated. The first process to do so was: > > Process name: [[48108,1],0] > Exit code:174 > -- > Completed test examples > Error while running make check > make[1]: *** [c

Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers and OpenMPI

2023-05-15 Thread Matthew Knepley
On Mon, May 15, 2023 at 11:19 AM Vanella, Marcos (Fed) via petsc-users < petsc-users@mcs.anl.gov> wrote: > Hello, I'm trying to compile the PETSc library version 3.19.1 with OpenMPI > 4.1.4 and the OneAPI 2022 Update 2 Intel Compiler suite on a Mac with OSX > Ventura 13.3.1. > I can compile PETSc

Re: [petsc-users] How to find the map between the high order coordinates of DMPlex and vertex numbering?

2023-05-15 Thread Matthew Knepley
On Mon, May 15, 2023 at 9:55 AM Zongze Yang wrote: > On Mon, 15 May 2023 at 17:24, Matthew Knepley wrote: > >> On Sun, May 14, 2023 at 7:23 PM Zongze Yang wrote: >> >>> Could you try to project the coordinates into the continuity space

Re: [petsc-users] Issues creating DMPlex from higher order mesh generated by gmsh

2023-05-15 Thread Matthew Knepley
On Mon, May 15, 2023 at 9:30 AM Jed Brown wrote: > Matthew Knepley writes: > > > On Fri, May 5, 2023 at 10:55 AM Vilmer Dahlberg via petsc-users < > > petsc-users@mcs.anl.gov> wrote: > > > >> Hi. > >> > >> > >> I'm tryin

Re: [petsc-users] Issues creating DMPlex from higher order mesh generated by gmsh

2023-05-15 Thread Matthew Knepley
On Fri, May 5, 2023 at 10:55 AM Vilmer Dahlberg via petsc-users < petsc-users@mcs.anl.gov> wrote: > Hi. > > > I'm trying to read a mesh of higher element order, in this example a mesh > consisting of 10-node tetrahedral elements, from gmsh, into PETSC. But It > looks like the mesh is not properly

Re: [petsc-users] How to find the map between the high order coordinates of DMPlex and vertex numbering?

2023-05-15 Thread Matthew Knepley
t; > > On Mon, 15 May 2023 at 04:24, Matthew Knepley wrote: > >> On Sun, May 14, 2023 at 12:27 PM Zongze Yang >> wrote: >> >>> >>> >>> >>> On Sun, 14 May 2023 at 23:54, Matthew Knepley wrote: >>> >>>> On Sun, May

Re: [petsc-users] How to find the map between the high order coordinates of DMPlex and vertex numbering?

2023-05-14 Thread Matthew Knepley
On Sun, May 14, 2023 at 12:27 PM Zongze Yang wrote: > > > > On Sun, 14 May 2023 at 23:54, Matthew Knepley wrote: > >> On Sun, May 14, 2023 at 9:21 AM Zongze Yang wrote: >> >>> Hi, Matt, >>> >>> The issue has been resolved whil

Re: [petsc-users] SNESDMDASNESSetFunctionLocal in Fortran

2023-05-14 Thread Matthew Knepley
On Sun, May 14, 2023 at 12:06 PM Khaled Nabil Shar Abdelaziz < kabde...@purdue.edu> wrote: > Hey there, > > > > I'm having a problem with the DMDASNESSetFunctionLocal() function in C and > its Fortran counterpart. The thing is, in C, you can pass a bunch of > variables using the ctx parameter,

Re: [petsc-users] How to find the map between the high order coordinates of DMPlex and vertex numbering?

2023-05-14 Thread Matthew Knepley
gt; my previous oversight. > Great! If you make an MR for this, you will be included on the next list of PETSc contributors. Otherwise, I can do it. Thanks, Matt > Best wishes, > Zongze > > > On Sun, 14 May 2023 at 16:44, Matthew Knepley wrote: > >> On Sat, May 13, 2

Re: [petsc-users] How to find the map between the high order coordinates of DMPlex and vertex numbering?

2023-05-14 Thread Matthew Knepley
for some references on the order of >> the dofs on PETSc's FE Space (especially high order elements)? >> >> Thanks, >> >> Zongze >> >> Matthew Knepley 于2022年6月18日周六 20:02写道: >> >>> On Sat, Jun 18, 2022 at 2:16 AM Zongze Yang >>> w

Re: [petsc-users] DMSWARM particle coordinates per rank

2023-05-12 Thread Matthew Knepley
f New Hampshire > matthew.yo...@unh.edu > == > > > On Fri, May 12, 2023 at 10:05 AM Matthew Knepley > wrote: > >> On Fri, May 12, 2023 at 9:40 AM Matthew Young < >> myoung.space.scie...@gmail.com> wrote: >> >>> Got it.

Re: [petsc-users] DMSWARM particle coordinates per rank

2023-05-12 Thread Matthew Knepley
t; --Matt > == > Matthew Young, PhD (he/him) > Research Scientist II > Space Science Center > University of New Hampshire > matthew.yo...@unh.edu > ========== > > > On Fri, May 12, 2023 at 5:15 AM Matthew Knepley wrote: > >

Re: [petsc-users] DMSWARM particle coordinates per rank

2023-05-12 Thread Matthew Knepley
On Thu, May 11, 2023 at 9:15 PM Matthew Young < myoung.space.scie...@gmail.com> wrote: > Does setting up a PIC-type DMSWARM with an associated cell DM guarantee > that each MPI rank will own the particles with coordinates inside the > bounds of the portion of the grid it owns? > There is a

Re: [petsc-users] About case ksp/tutorial/ex36.cxx

2023-05-09 Thread Matthew Knepley
On Tue, May 9, 2023 at 3:12 PM neil liu wrote: > Hello, Petsc Developers, > I am trying to compile ksp/tutorial/ex36.cxx like make ex36, > > it shows an error > " Documents/petsc-3.19.1/include/petscdmmoab.h:10:10: fatal error: > moab/Core.hpp: No such file or directory > #include /*I

Re: [petsc-users] Understanding index sets for PCGASM

2023-05-09 Thread Matthew Knepley
On Tue, May 9, 2023 at 10:05 AM LEONARDO MUTTI < leonardo.mutt...@universitadipavia.it> wrote: > Great thanks! I can now successfully run > https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/ksp/tests/ex71f.F90. > > Going forward with my experiments, let me post a new code snippet (very > similar

Re: [petsc-users] Bug report LMVM matrix class

2023-05-09 Thread Matthew Knepley
On Tue, May 9, 2023 at 4:15 AM Stephan Köhler < stephan.koeh...@math.tu-freiberg.de> wrote: > Dear PETSc/Tao team, > > it seems to be that there is a bug in the LMVM matrix class: > > The function MatMultAdd_LMVM, see, e.g., > https://petsc.org/release/src/ksp/ksp/utils/lmvm/lmvmimpl.c.html at

Re: [petsc-users] Scalable Solver for Incompressible Flow

2023-05-08 Thread Matthew Knepley
rk is patch smoothing (I gave a paper reference). It could be that we have a bug in LSC, but I thought we verified it with the Shuttleworth paper. THanks, Matt > Mark > > >> >> Thanks a lot, >> Sebastian >> >> On 03.05.2023 09:07, Sebastian Blauth wrote: >> &

Re: [petsc-users] Step size setting in TS

2023-05-07 Thread Matthew Knepley
it is doing something morally similar. Thanks, Matt > Qi > > On May 6, 2023, at 7:35 PM, Matthew Knepley wrote: > >  > On Sat, May 6, 2023 at 7:25 PM Jorti, Zakariae via petsc-users < > petsc-users@mcs.anl.gov> wrote: > >> Hello, >> >> >&g

Re: [petsc-users] Help with KSPSetConvergenceTest

2023-05-07 Thread Matthew Knepley
On Sun, May 7, 2023 at 10:02 AM Edoardo alinovi wrote: > Thanks, > > Is this a reasonable thing to do if I want to replicate what KSP is doing > by default? > Yes. The other option is to pass along 'dummy' Thanks, Matt -- What most experimenters take for granted before they begin

Re: [petsc-users] Help with KSPSetConvergenceTest

2023-05-07 Thread Matthew Knepley
On Sun, May 7, 2023 at 9:42 AM Edoardo alinovi wrote: > Hi Matt, > > h, what if I do: > > KSPConvergedDefault(ksp, n, rnorm, flag, PETSC_NULL_FUNCTION, ierr) > > That looks to behave OK, but I am not sure about what I am doing -.- > You are saying that no convergence context was passed in

Re: [petsc-users] Help with KSPSetConvergenceTest

2023-05-07 Thread Matthew Knepley
On Sun, May 7, 2023 at 9:21 AM Edoardo alinovi wrote: > Hello guys, > > Today I am about to write a custom convergence test for KSP doing the > following job: > > - if the number of ksp iterations is less than a given threshold, iterate > until that threshold is met > - if the number of ksp

Re: [petsc-users] Step size setting in TS

2023-05-06 Thread Matthew Knepley
On Sat, May 6, 2023 at 7:25 PM Jorti, Zakariae via petsc-users < petsc-users@mcs.anl.gov> wrote: > Hello, > > > I have a time-dependent model that I solve using TSSolve. > > And I am trying to adaptively change the step size (dt). > > I found that there are some TSAdapt schemes already available.

Re: [petsc-users] question about leap-frog for wave equation in petsc

2023-05-06 Thread Matthew Knepley
On Sat, May 6, 2023 at 11:47 AM Huidong Yang wrote: > Hi Petsc developer. > > may I ask if there is any available implementations in petsc > using leap-frog scheme? > I don't think we have leapfrog, but we do have Stormer-Verlet, which is also a 2nd order symplectic method. Thanks,

Re: [petsc-users] Understanding index sets for PCGASM

2023-05-05 Thread Matthew Knepley
time index on the inside. >> Then the blocks would be over all time, but limited space, which is more >> the spirit of ASM I think. >> >> Have you considered waveform relaxation for this problem? >> >>Thanks, >> >> Matt >> >> >>

Re: [petsc-users] issues with VecSetValues in petsc 3.19

2023-05-05 Thread Matthew Knepley
On Fri, May 5, 2023 at 5:13 AM Edoardo alinovi wrote: > Hi Matt, > > I have some more questions on the fieldsplit saga :) > > I am running a 1M cell ahmed body case using the following options: > > "solver": "fgmres", > "preconditioner": "fieldsplit", > "absTol": 1e-6, >

Re: [petsc-users] parallel computing error

2023-05-05 Thread Matthew Knepley
목) 오후 12:08, Barry Smith 님이 작성: >> >>> >>> You can configure with MUMPS ./configure --download-mumps >>> --download-scalapack --download-ptscotch --download-metis >>> --download-parmetis >>> >>> And then use MatMatSolve() as in src/m

Re: [petsc-users] Understanding index sets for PCGASM

2023-05-04 Thread Matthew Knepley
ing the time index on the inside. Then the blocks would be over all time, but limited space, which is more the spirit of ASM I think. Have you considered waveform relaxation for this problem? Thanks, Matt > Hope this helps. > Best, > Leonardo > > Il giorno gio 4 mag 202

Re: [petsc-users] sources of floating point randomness in JFNK in serial

2023-05-04 Thread Matthew Knepley
ng that >> solver with a sparse matrix. This would give me confidence >> that nothing in the solver is variable. >> >> I could do the sparse finite difference jacobian once, save it to disk, > and then use that system each time. > Yes. That would work. Thanks,

Re: [petsc-users] sources of floating point randomness in JFNK in serial

2023-05-04 Thread Matthew Knepley
stem matrix followed by preconditioner matrix: > Mat Object: 1 MPI process > type: mffd > rows=16384, cols=16384 > Matrix-free approximation: > err=1.49012e-08 (relative error in function evaluation) > Using wp compute h routine >

Re: [petsc-users] Understanding index sets for PCGASM

2023-05-04 Thread Matthew Knepley
On Thu, May 4, 2023 at 11:24 AM LEONARDO MUTTI < leonardo.mutt...@universitadipavia.it> wrote: > Thank you for the help. > Adding to my example: > > > * call PCGASMSetSubdomains(pc,NSub, subdomains_IS, inflated_IS,ierr) > call PCGASMDestroySubdomains(NSub,subdomains_IS,inflated_IS,ierr)*

Re: [petsc-users] sources of floating point randomness in JFNK in serial

2023-05-04 Thread Matthew Knepley
block size is 16 >>> linear system matrix = precond matrix: >>> Mat Object: (sub_) 1 MPI process >>> type: seqbaij >>> rows=16384, cols=16384, bs=16 >>> total: nonzeros=1277952, allocated

Re: [petsc-users] sources of floating point randomness in JFNK in serial

2023-05-04 Thread Matthew Knepley
rows=16384, cols=16384, bs=16 > total: nonzeros=1277952, allocated nonzeros=1277952 > total number of mallocs used during MatSetValues calls=0 > block size is 16 > > On Thu, May 4, 2023 at 8:30 AM Mark Adams wrote: > >> If you are using MG what i

Re: [petsc-users] sources of floating point randomness in JFNK in serial

2023-05-04 Thread Matthew Knepley
On Thu, May 4, 2023 at 8:21 AM Mark Lohry wrote: > Do they start very similarly and then slowly drift further apart? > > > Yes, this. I take it this sounds familiar? > > See these two examples with 20 fixed iterations pasted at the end. The > difference for one solve is slight (final SNES norm

Re: [petsc-users] parallel computing error

2023-05-03 Thread Matthew Knepley
On Wed, May 3, 2023 at 6:05 AM ­권승리 / 학생 / 항공우주공학과 wrote: > Dear developers > > I'm trying to use parallel computing and I ran the command 'mpirun -np 4 > ./app' > > In this case, there are two problems. > > *First,* I encountered error message > /// > [0]PETSC ERROR: [1]PETSC ERROR:

Re: [petsc-users] Scalable Solver for Incompressible Flow

2023-05-02 Thread Matthew Knepley
On Tue, May 2, 2023 at 2:29 PM Jed Brown wrote: > Sebastian Blauth writes: > > > I agree with your comment for the Stokes equations - for these, I have > > already tried and used the pressure mass matrix as part of a (additive) > > block preconditioner and it gave mesh independent results. > >

Re: [petsc-users] Node numbering in parallel partitioned mesh

2023-05-02 Thread Matthew Knepley
blem accessing those nodes > from the wrong partition unless those nodes are ghosted? Maybe I am not > thinking about it correctly. > > > > Kind regards, > > Karthik. > > > > > > *From: *Matthew Knepley > *Date: *Tuesday, 2 May 2023 at 13:35 > *To: *Cho

Re: [petsc-users] Scalable Solver for Incompressible Flow

2023-05-02 Thread Matthew Knepley
On Tue, May 2, 2023 at 9:07 AM Blauth, Sebastian < sebastian.bla...@itwm.fraunhofer.de> wrote: > Hello, > > > > I am having a problem using / configuring PETSc to obtain a scalable > solver for the incompressible Navier Stokes equations. I am discretizing > the equations using FEM (with the

Re: [petsc-users] Node numbering in parallel partitioned mesh

2023-05-02 Thread Matthew Knepley
On Tue, May 2, 2023 at 8:25 AM Karthikeyan Chockalingam - STFC UKRI via petsc-users wrote: > Hello, > > > > This is not exactly a PETSc question. I have a parallel partitioned finite > element mesh. What are the steps involved in having a contiguous but unique > set of node numbering from one

Re: [petsc-users] DMSWARM with DMDA and KSP

2023-04-30 Thread Matthew Knepley
On Sun, Apr 30, 2023 at 1:12 PM Matthew Young < myoung.space.scie...@gmail.com> wrote: > Hi all, > > I am developing a particle-in-cell code that models ions as particles and > electrons as an inertialess fluid. I use a PIC DMSWARM for the ions, which > I gather into density and flux before

Re: [petsc-users] PETSC ERROR in DMGetLocalBoundingBox?

2023-04-30 Thread Matthew Knepley
reporting that. Matt > > > Regards, > > > > Danyang > > > > *From: * > *Date: *Friday, March 17, 2023 at 11:02 AM > *To: *'Matthew Knepley' > *Cc: * > *Subject: *RE: [petsc-users] PETSC ERROR in DMGetLocalBoundingBox? > > > > Hi Matt,

Re: [petsc-users] makefile error

2023-04-26 Thread Matthew Knepley
o there is some reason it is not there. > Is there any way to solve this problem? Or Do I have to reinstall PETSc? > Just rebuild cd $PETSC_DIR make Thanks, Matt > Best regards > Seung Lee Kwon > > 2023년 4월 26일 (수) 오후 7:05, Matthew Knepley 님이 작성: > >> On Wed, Apr 26, 2023 at 6

Re: [petsc-users] makefile error

2023-04-26 Thread Matthew Knepley
On Wed, Apr 26, 2023 at 6:02 AM ­권승리 / 학생 / 항공우주공학과 wrote: > Dear developers > > Could you recommend the error messages below? > > /home/ksl/petsc/arch-linux-c-debug/bin/mpicxx -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch > -fstack-protector

Re: [petsc-users] obtaining estimated Hessian in BQNLS

2023-04-25 Thread Matthew Knepley
On Tue, Apr 25, 2023 at 2:21 PM Suh, Hansol via petsc-users < petsc-users@mcs.anl.gov> wrote: > Actually, let me take that back , about inability to access LMVM. > > You can access LMVM Hessian mat after you are done with TaoSolve, but not > within the iteration. > Good catch. You could do this

Re: [petsc-users] obtaining estimated Hessian in BQNLS

2023-04-25 Thread Matthew Knepley
On Tue, Apr 25, 2023 at 8:53 AM Stefano Carli wrote: > Dear PETSc developers, > > > > I’m using PETSc version 3.14.1 coupled to a Fortran code, and I was > wondering if there is a way of obtaining in output, possibly at each > iteration, the estimated Hessian matrix for the BQNLS method. > It

Re: [petsc-users] Question about linking LAPACK library

2023-04-25 Thread Matthew Knepley
> Alternatively, I want to know how to link the LAPACK library. > > best, > > Seung Lee Kwon > > 2023년 4월 25일 (화) 오후 6:44, Matthew Knepley 님이 작성: > >> On Mon, Apr 24, 2023 at 11:47 PM ­권승리 / 학생 / 항공우주공학과 >> wrote: >> >>> Dear all >>

Re: [petsc-users] Setting up a matrix for Lagrange multiplier

2023-04-25 Thread Matthew Knepley
erShipRange of SubP; I will be able to > parallelize the loop. Is MatGetOwnerShipRange also available for > submatrices as well? > It is a local submatrix, so I would only run over local things (parallelization is implicit). I think I have shown all these operations in the example. TH

Re: [petsc-users] Question about linking LAPACK library

2023-04-25 Thread Matthew Knepley
On Mon, Apr 24, 2023 at 11:47 PM ­권승리 / 학생 / 항공우주공학과 wrote: > Dear all > > It depends on the problem. It can have hundreds of thousands of degrees of > freedom. > Suppose your matrix was dense and had 1e6 dofs. The work to invert a matrix is O(N^3) with a small constant, so it would take 1e18 =

Re: [petsc-users] Fwd: Inquiry about the dual space (PetscFECreateTabulation_Basic)

2023-04-24 Thread Matthew Knepley
n the PetscSpaceEvaluate() function: https://petsc.org/main/manualpages/SPACE/PetscSpaceEvaluate/ You can see pointers to the implementations at the bottom of that page. Thanks, Matt > On Fri, Apr 21, 2023 at 12:37 PM neil liu wrote: > >> Thanks a lot. Very helpful. >>

Re: [petsc-users] Setting up a matrix for Lagrange multiplier

2023-04-24 Thread Matthew Knepley
Solve_Private() at > /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/ksp/ksp/interface/itfunc.c:824* > > *[0]PETSC ERROR: #7 KSPSolve() at > /Users/karthikeyan.chockalingam/AMReX/SRC_PKG/petsc/src/ksp/ksp/interface/itfunc.c:1070* > > *End of program * > > *so

Re: [petsc-users] Setting up a matrix for Lagrange multiplier

2023-04-24 Thread Matthew Knepley
RRQ(ierr); > > ierr = PetscOptionsSetValue(NULL,"-fieldsplit_1_ksp_type", > "preonly"); CHKERRQ(ierr); > > ierr = PetscOptionsSetValue(NULL,"-fieldsplit_1_pc_type", "lu"); > CHKERRQ(ierr);*/ > > > > ierr = Pe

Re: [petsc-users] Setting up a matrix for Lagrange multiplier

2023-04-24 Thread Matthew Knepley
> Karthik. > > > > > > *From: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalin...@stfc.ac.uk> > *Date: *Wednesday, 19 April 2023 at 17:52 > *To: *Matthew Knepley > *Cc: *petsc-users@mcs.anl.gov > *Subject: *Re: [petsc-users] Settin

Re: [petsc-users] Reading user generated Cartesian grid into DMXX

2023-04-24 Thread Matthew Knepley
On Mon, Apr 24, 2023 at 7:33 AM 吉兴洲 wrote: > Dear all, > > I'm solving a fluid problem and it has multiple square cylinders in the > flow area. Unfortunately, I have to use a Cartesian grid (nonuniform) which > can't generated by Gmsh. > > I have noticed that the object *DMDA* and *DMFOREST*

Re: [petsc-users] Fwd: Inquiry about the dual space (PetscFECreateTabulation_Basic)

2023-04-21 Thread Matthew Knepley
\ / x \ / 0 \ / y \ / 0 \ \ 0 / \ 1 / \ 0 / \ x / \ 0 / \ y / six vectors with 2 components each. Thanks, Matt > Thanks, > > Xiaodong > > > > > > > On Fri, Apr 21, 2023 at 10:05 AM Matthew Knepley > wrote: > >> On Fri, Apr 21, 2023 at 10:0

Re: [petsc-users] Fwd: Inquiry about the dual space (PetscFECreateTabulation_Basic)

2023-04-21 Thread Matthew Knepley
On Fri, Apr 21, 2023 at 10:02 AM neil liu wrote: > Hello, Petsc group, > > I am learning the FE structure in Petsc by running case > https://petsc.org/main/src/snes/tutorials/ex12.c.html with -run_type test > -bc_type dirichlet -dm_plex_interpolate 0 -petscspace_degree 1 > -show_initial

Re: [petsc-users] issues with VecSetValues in petsc 3.19

2023-04-21 Thread Matthew Knepley
work for this system. > I did some blind search using gamg/hypre and they look terribile. I guess > i am missing a trick, probaly they are not the way to go? > I believe that trick is that the patches you use have to very specific. Thanks, Matt > Thanks! > > Il Lun 17 Apr

Re: [petsc-users] question about MatSetLocalToGlobalMapping

2023-04-20 Thread Matthew Knepley
On Thu, Apr 20, 2023 at 6:13 AM Karthikeyan Chockalingam - STFC UKRI via petsc-users wrote: > Hello, > > > > I created a new thread, thought would it be more appropriate (and is a > continuation of my previous post). I want to construct the below K matrix > (which is composed of submatrices) > >

Re: [petsc-users] [petsc-maint] DMSwarm with periodic B.C.

2023-04-19 Thread Matthew Knepley
If this is a problem, let's make an example and I can debug it because I thought that this worked. I might have only tested with Plex. Thanks, Matt On Wed, Apr 12, 2023 at 11:32 AM Mark Adams wrote: > First, you don't want a DMShell. Just use da_swarm. > See src/dm/tutorials/ex20.c > >

Re: [petsc-users] [petsc-maint] Lagrangian particle tracking - ghost cells

2023-04-19 Thread Matthew Knepley
On Wed, Apr 19, 2023 at 8:40 AM Joauma Marichal < joauma.maric...@uclouvain.be> wrote: > Hello, > > > > I am using the DMSwarm library in some Eulerian-Lagrangian approach to > have vapor bubbles in water. > > I would like the bubbles to have an impact on the water fields of the same > cells and

Re: [petsc-users] Setting up a matrix for Lagrange multiplier

2023-04-18 Thread Matthew Knepley
this case. Thanks, Matt > Best regards, > > Karthik. > > > > > > > > *From: *Matthew Knepley > *Date: *Tuesday, 18 April 2023 at 11:08 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *petsc-user

Re: [petsc-users] Setting up a matrix for Lagrange multiplier

2023-04-18 Thread Matthew Knepley
On Tue, Apr 18, 2023 at 5:24 AM Karthikeyan Chockalingam - STFC UKRI via petsc-users wrote: > Hello, > > > > I'm solving a problem using the Lagrange multiplier, the matrix has the > form > > > > K = [A P^T > >P 0] > > > > I am familiar with constructing K using MATMPIAIJ. However, I

Re: [petsc-users] PCHPDDM and matrix type

2023-04-17 Thread Matthew Knepley
penmp=1 --with-cxx-dialect=C++11 > --with-fortran-bindings=0 --with-sowing=0 --with-64-bit-indices > --with-make-np=256 --download-hpddm > [1]PETSC ERROR: #1 buildTwo() at > /raid/lindad/moose/petsc/arch-moose/include/HPDDM_schwarz.hpp:1012 > > On Mon, Apr 17, 2023 at 4:55 PM Ma

Re: [petsc-users] PCHPDDM and matrix type

2023-04-17 Thread Matthew Knepley
I don't think so. Can you show the whole stack? THanks, Matt On Mon, Apr 17, 2023 at 6:24 PM Alexander Lindsay wrote: > If it helps: if I use those exact same options in serial, then no errors > and the linear solve is beautiful :-) > > On Mon, Apr 17, 2023 at 4:22 PM Alexander Lindsay

Re: [petsc-users] issues with VecSetValues in petsc 3.19

2023-04-17 Thread Matthew Knepley
On Mon, Apr 17, 2023 at 6:37 AM Edoardo alinovi wrote: > Sure thing, the solver I am working on is this one: > https://gitlab.com/alie89/flubio-code-fvm. > > It is a 3D, collocated, unstructured, finite volume solver for > incompressibility NS. I can run steady, unsteady and I can use SIMPLE,

Re: [petsc-users] issues with VecSetValues in petsc 3.19

2023-04-17 Thread Matthew Knepley
On Mon, Apr 17, 2023 at 6:16 AM Edoardo alinovi wrote: > Do you mean the solver I am messing around? XD > Yes, and what physics it is targeting. THanks, Matt -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results

Re: [petsc-users] issues with VecSetValues in petsc 3.19

2023-04-17 Thread Matthew Knepley
On Mon, Apr 17, 2023 at 6:09 AM Edoardo alinovi wrote: > Thanks Matt, your always there when you need <3 > Glad it's working! Sometime you have to tell me what it is solving. Thanks, Matt -- What most experimenters take for granted before they begin their experiments is infinitely

Re: [petsc-users] issues with VecSetValues in petsc 3.19

2023-04-17 Thread Matthew Knepley
On Mon, Apr 17, 2023 at 6:00 AM Edoardo alinovi wrote: > Hey Matt, > > Thanks for the help. Here is the error: > > [0]PETSC ERROR: - Error Message > -- > [0]PETSC ERROR: Object is in wrong state > [0]PETSC ERROR: Not

Re: [petsc-users] issues with VecSetValues in petsc 3.19

2023-04-17 Thread Matthew Knepley
On Mon, Apr 17, 2023 at 5:36 AM Edoardo alinovi wrote: > Hello Barry, Matt, Jed, > > I have just installed the latest and greatest version of petsc and I am > hitting a problem I did not have in previous releases. > > Here is the error: > > > > > *[1]PETSC ERROR: - Error

Re: [petsc-users] problem with PetscInitialize when moving to 3.19.0

2023-04-15 Thread Matthew Knepley
line is wrong. Let's start with a PETSc example. Can you make Vec ex1f90/F90? cd $PETSC_DIR cd src/vec/vec/tutorials/ make ex1f90 That will also show the correct link line. Thanks, Matt > Danny. > > On 15 Apr 2023, at 13:41, Matthew Knepley wrote: > > On Sat, Apr 15, 2023 a

<    1   2   3   4   5   6   7   8   9   10   >