Re: [petsc-users] Memory leak related to MatSetValue

s called exactly once and also the > matching MPI_Type_free() to determine if the problem is PETSc logic or > MPICH logic. > > Since we test PETSc in our CI with valgrind it is unlikely a PETSc bug > > Barry > > > On Jun 9, 2025, at 7:47 PM, neil liu wrote: > > Dear

[petsc-users] Memory leak related to MatSetValue

Dear Petsc community, Recently, I encountered a memory leak while using Valgrind (3.25.1) with MPI (2 processes, MPICH 4.21.1) to test a PETSc-based code, which is a variant of the pestc's built-in example. *#include * *static char help[] = "Demonstrate PCFIELDSPLIT after MatZeroRowsColumns() insi

Re: [petsc-users] Mixing PETSc Parallelism with Serial MMG3D Workflow

it safe to do things like this? Thanks, Xiaodong On Wed, Apr 23, 2025 at 4:33 PM Pierre Jolivet wrote: > > > On 23 Apr 2025, at 7:28 PM, neil liu wrote: > >  > > *MMG only supports serial execution, whereas ParMMG supports parallel mode > (although ParMMG is not as

Re: [petsc-users] Mixing PETSc Parallelism with Serial MMG3D Workflow

upport parallel communicators, we should handle it > internally in the code, always use commself, and raise an error if there > are two or more processes in the comm that have cEnd - cStart > 0 > > Il giorno mer 23 apr 2025 alle ore 20:05 neil liu ha > scritto: > >> Thanks

Re: [petsc-users] Mixing PETSc Parallelism with Serial MMG3D Workflow

Thanks a lot. Pierre. Do you have any suggestions to build a real serial DM from this gatherDM? I tried several ways, which don't work. DMClone? Thanks, On Wed, Apr 23, 2025 at 11:39 AM Pierre Jolivet wrote: > > > On 23 Apr 2025, at 5:31 PM, neil liu wrote: > > Thanks

Re: [petsc-users] Mixing PETSc Parallelism with Serial MMG3D Workflow

ven 18 apr 2025 alle ore 17:02 neil liu ha > scritto: > >> Dear PETSc developers and users, >> >> I am currently exploring the integration of MMG3D with PETSc. Since MMG3D >> supports only serial execution, I am planning to combine parallel and >> serial comput

[petsc-users] Mixing PETSc Parallelism with Serial MMG3D Workflow

Dear PETSc developers and users, I am currently exploring the integration of MMG3D with PETSc. Since MMG3D supports only serial execution, I am planning to combine parallel and serial computing in my workflow. Specifically, after solving the linear systems in parallel using PETSc: 1. I int

Re: [petsc-users] Inquiry about resetting a petscsection for a dmplex

t 6:12 PM neil liu wrote: > >> Dear Pestc community, >> >> I am currently working on a 3D adaptive vector FEM solver. In my case, I >> need to solve two systems: one for the primal equation using a low-order >> discretization and another for the adjoint equation

[petsc-users] Inquiry about resetting a petscsection for a dmplex

Dear Pestc community, I am currently working on a 3D adaptive vector FEM solver. In my case, I need to solve two systems: one for the primal equation using a low-order discretization and another for the adjoint equation using a high-order discretization. Afterward, I need to reset the section ass

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

Thanks a lot, Blaise. Yes. As you said, I have to define a node set to find the edges we are interested in for Exodus II file. On Sun, Sep 22, 2024 at 9:26 AM Blaise Bourdin wrote: > > > On Sep 21, 2024, at 9:54 AM, neil liu wrote: > > Caution: External email. > > Than

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

Dear Petsc developers and users, I am trying to read an exodus II file from coreform cubit, but without success, Then I used petsc's built-in exodus file, /share/petsc/datafiles/meshes/sevenside.exo. This file can be read by petsc successfully. And I did a test. This file, sevenside.exo, is impor

[petsc-users] Inquiry about reading exodus file for Petsc.

Dear Petsc developers and users, I am trying to import an exodus II file from coreform Cubit. It is a little test.e Description: Binary data

Re: [petsc-users] Inquiry about metric-based adaptation using MMG in petsc

ARG_OUTOFRANGE, "Global metric normalization factor must be in > (0, inf). Is the input metric positive-definite?"); > + PetscCheck(realIntegral > 1.0e-30, PETSC_COMM_SELF, > PETSC_ERR_ARG_OUTOFRANGE, "Global metric normalization factor %g must be in > (0, inf). Is the input

[petsc-users] Inquiry about metric-based adaptation using MMG in petsc

Dear Petsc developers and users, I am trying to explore adaptive mesh refinement (tetradedra) with Petsc. It seems case 12 ($PETSC DIR/src/snes/tutorials/ex12.c, from paper, https://urldefense.us/v3/__https://arxiv.org/pdf/2201.02806__;!!G_uCfscf7eWS!ZEwaHkvYc_IrjycFr8LiNi-nZcFqu0ZpsydAAomxptQ6C0

[petsc-users] Questitons about viewing the mesh from "Meshing for Subsurface Flows in PETSc"

Dear Petsc developers, I am trying to learn about the mesh refinement part. I tried to follow the instructions from the website, "Meshing for Subsurface Flows in PETSc, make -f ./gmakefile test globsearch="dm_impls_plex_tutorials-ex10_0", but it will run many tests and will not deliver " DM

Re: [petsc-users] Strong scaling concerns for PCBDDC with Vector FEM

Thanks a lot for this explanation, Matt. I will explore whether the matrix has the same size and spaisity. On Tue, Aug 20, 2024 at 1:45 PM Matthew Knepley wrote: > On Tue, Aug 20, 2024 at 1:36 PM neil liu wrote: > >> Hi, Matt, >> I think the time listed here represents the

Re: [petsc-users] Strong scaling concerns for PCBDDC with Vector FEM

wrote: > On Tue, Aug 20, 2024 at 1:10 PM neil liu wrote: > >> Thanks a lot for your explanation, Stefano. Very helpful. >> Yes. I am using dmplex to read a tetrahdra mesh from gmsh. With parmetis, >> the scaling performance is improved a lot. >> I will read your paper

Re: [petsc-users] Strong scaling concerns for PCBDDC with Vector FEM

edelec elements, which is done automatically if you > prescribe the discrete gradient operator (see the paper I have linked to in > my previous communication). > > > > Il giorno dom 18 ago 2024 alle ore 00:37 neil liu ha > scritto: > >> Hi, Stefano, >> Please see the atta

[petsc-users] Strong scaling concerns for PCBDDC with Vector FEM

Dear Petsc developers, Thanks for your previous help. Now, the PCBDDC can converge to 1e-8 with, petsc-3.21.1/petsc/arch-linux-c-opt/bin/mpirun -n 8 ./app -pc_type bddc -pc_bddc_coarse_redundant_pc_type svd -ksp_error_if_not_converged -mat_type is -ksp_monitor -ksp_rtol 1e-8 -ksp_gmres_restart

Re: [petsc-users] Question about the memory usage for BDDC preconditioner.

eWS!ZVyzxJb4s9N1kzsS2BV7raG-kJIn8X6skBNtfsvA8aHyjWPm8oYGfzk83j1n0PFstGE6nDCHpOIpMvlI_QH81A$ > > > Il giorno mer 14 ago 2024 alle ore 05:15 neil liu ha > scritto: > >> Hi, Stefano, >> >> Please see the attached for the smaller case(successful with BDDC). >> and the Error_larger

[petsc-users] Question about the memory usage for BDDC preconditioner.

Dear Petsc developers, I am testing PCBDDC for my vector based FEM solver(complex system). It can work well on a coarse mesh(tetrahedra cell #: 6,108; dof # : 39,596). Then I tried a finer mesh (tetrahedra cell #: 32,036; dof # : 206,362). It seems ASM can work well with petsc-3.21.1/petsc/arch-l

Re: [petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

s point call > MatSetBlockSize(A,2) before MatSetUp() > > > On Jul 31, 2024, at 6:01 PM, neil liu wrote: > > Hi, all, > Following Stefano's advice, my code is reorganized as follows, > > *MatCreate(PETSC_COMM_WORLD, &A);* > > > > > > * MatSetType(A, MATI

Re: [petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

ong.liu/Documents/petsc-3.21.1/petsc/src/mat/impls/is/matis.c:2831 [1]PETSC ERROR: #3 MatSetLocalToGlobalMapping() at /home/xiaodong.liu/Documents/petsc-3.21.1/petsc/src/mat/interface/matrix.c:2252 After Mat set local to global mapping! Thanks, On Tue, Jul 30, 2024 at 2:51 PM neil liu wrote: >

Re: [petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

Hi, Stefano, I am trying to understand the example there you mentioned. I have a question, the example always use DMDA there. Does BDDC also work for DMPLEX? Thanks , On Tue, Jul 30, 2024 at 1:47 PM neil liu wrote: > Thanks, Stefano, > > I am trying to modify the code as follows, &g

Re: [petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

N6-FBjxF1G_dSiPtnq7Yj-RlBHZiiQ$ > > or > https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/ksp/tutorials/ex71.c?ref_type=heads__;!!G_uCfscf7eWS!cDRkl4iAuyMeT5FvByDeeIBRUN6lrFt7MnusMnOcqch-xF5D2nGsgMCZN6-FBjxF1G_dSiPtnq7Yj-REAmdXuA$ > > > Il giorno mar

Re: [petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

A, J);* * MatDestroy(&J);* * KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);* * KSPSetFromOptions(ksp);* petsc-3.21.1/petsc/arch-linux-c-debug/bin/mpirun -n 2 ./app -ksp_type cg -pc_type bddc -ksp_monitor -mat_type is Do you have any suggestions? Thanks , Xiaodong On Mon, Jul 29, 2024 at 6:19 PM

Re: [petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

When I compile with real data, it shows the attached error. The data file is in binary format, right? On Mon, Jul 29, 2024 at 5:36 PM Stefano Zampini wrote: > Your PETSc installation is for complex, data is for real > > On Mon, Jul 29, 2024, 23:14 neil liu wrote: > >> I c

Re: [petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

Jul 29, 2024, at 3:55 PM, neil liu wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Dear Petsc developers,, > > I am trying to run > https://urldefense.us/v3/__https://petsc.org/release/src/ksp/ksp

[petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

Dear Petsc developers,, I am trying to run https://urldefense.us/v3/__https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html__;!!G_uCfscf7eWS!ZG4gvmS6hQD8ymbvCUDfAatzRUJHzmWO-hOgp9m0xXuAXgIB-fxe_xspYs3WEPi_Ed0UFLMHKanYuYWrTlQGrA$ with petsc-3.21.1/petsc/arch-linux-c-opt/bin/mpirun -n 2 ./e

Re: [petsc-users] [petsc-maint] Out of memory issue related to KSP.

Thanks, mark. I am using a sparse matrix from a second-oder vector basis FEM. Will this sparse matrix still use a memory similar to a dense matrix? Thanks, Xiaodong On Thu, Jul 18, 2024 at 6:00 PM Mark Adams wrote: > keep on the list. > > > > > On Thu, Jul 18, 2024 at 5:06 

[petsc-users] Out of memory issue related to KSP.

Dear Pestc team, I am trying to solve a complex linear system by Petsc KSP. When I committed out this piece code, no errors came out. Will my coding part affect ksp? I am using a direct solver, -pc_type LU. *PetscErrorCode ElementInfo::solveLinearSystem( ){ * *PetscFunctionBegin; * *KSP ksp; * *K

[petsc-users] About the face orientation.

Dear Petsc developers, I am checking the face orientations for DMPLEX. I found the following rule, edge ordering for face 0 Orientation 0 1 2 0 1 0 2-1 2 1 0-2 0 2 1-3 How about -4 or -5? I am a trying a simple mesh, therefore didn

Re: [petsc-users] About the complex version of gmres.

I run with -ksp_gmres_restart 100 it converges in 75 iterations. > > Barry > > > > > On Jun 7, 2024, at 8:03 PM, neil liu wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Dear Petsc developers, > > I am

[petsc-users] About the complex version of gmres.

Dear Petsc developers, I am using Petsc to solve a complex system ,AX=B. A is complex and B is real. And the petsc was configured with Configure options --download-mpich --download-fblaslapack=1 --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-triangle --with-scalar-type=complex A and

Re: [petsc-users] Can not find the header file for OpenMPI

hould cause no harm to include it in compile > commands. > > Satish > > > On Mon, 13 May 2024, Satish Balay via petsc-users wrote: > > > On Mon, 13 May 2024, neil liu wrote: > > > > > > > I also tried the 2nd way, it didn't work. >

Re: [petsc-users] Can not find the header file for OpenMPI

n > --with-mpi-include=/home/balay/soft/mpich-4.0.1/include > --with-mpi-lib="-L/home/balay/soft/mpich-4.0.1/lib -Wl,-rpath > -Wl,/home/balay/soft/mpich-4.0.1/lib -lmpifort -lmpi" > > Satish > > > > On Mon, 13 May 2024, neil liu wrote: > > > Thanks, I t

[petsc-users] Can not find the header file for OpenMPI

Dear Petsc developers, I am trying to install Petsc with a preinstalled OpenMPi. ./configure --download-fblaslapack --with-mpi-dir=/usr/lib64/openmpi --with-mpi-incdir=/usr/include/openmpi-x86_64 But the final information shows, MPI: Version:3 Includes: -I/usr/lib64/openmpi/include (

[petsc-users] Fwd: Inquiry about DMPlexCreateSection

Hello, Petsc team, Previously, following the function setupseciton in the following case https://petsc.org/main/src/dm/impls/plex/tutorials/ex7.c.html I successfully created a section layout and then imposed the Dirchlet boundary conditions. It seems DMPlexCreateSection is able to replace the abov

Re: [petsc-users] Inquiry about the PetscScalar in Petsc.

Thanks for your explanation so much. On Tue, Jul 11, 2023 at 12:41 PM Barry Smith wrote: > > > On Jul 11, 2023, at 12:16 PM, neil liu wrote: > > I think I understood that. > > 1) In order to save memory, use a larger real system > > >This will save a little

Re: [petsc-users] Inquiry about the PetscScalar in Petsc.

I think I understood that. 1) In order to save memory, use a larger real system 2) vec will store the real part with imaginary part equal to zero in the context of --scalar =complex. But this will not save memory. Right? Thanks, Xiaodong On Tue, Jul 11, 2023 at 12:03 PM neil liu wrote: >

Re: [petsc-users] Inquiry about the PetscScalar in Petsc.

Do you mean that, even if I configure with --scalar=complex, when I use vecGetarray to get the coords, the coords array is still stored in a real manner? Thanks, Xiaodong On Tue, Jul 11, 2023 at 11:54 AM Matthew Knepley wrote: > On Tue, Jul 11, 2023 at 11:48 AM neil liu wrote: > >

Re: [petsc-users] Inquiry about the PetscScalar in Petsc.

only real ones) > > Barry > > > > On Jul 11, 2023, at 11:34 AM, neil liu wrote: > > > > Dear Petsc developers, > > > > My computation involves both real and complex numbers. > > For example, my coordinate is real, but my matrix is complex. > >

[petsc-users] Inquiry about the PetscScalar in Petsc.

Dear Petsc developers, My computation involves both real and complex numbers. For example, my coordinate is real, but my matrix is complex. I use VecGetArray to get the coordinates. But it seems coordinates have to be defined in a complex manner to be consistent with complex matrix. Is there som

[petsc-users] Inquiry about reading the P2 tetrahedron mesh from GMSH

Dear Petsc developers, I am reading P2 mesh from GMSH. And used DMFieldGetClosure_Internal to check the coordinates for each tetrahedron, It seems reasonable. But when I tried DMGetCoordinates (dm, &global), it seems the vector global is not consistent with the node number, Then what is global he

Re: [petsc-users] Inquiry about PetscDTSimplexQuadrature .

Thanks, Matt. It seems DMPlexComputeCellGeometryFEM works well with the quadrature points to deliver Jacobian and inverse one. Will it be a good choice ? Have a good night. Thanks, On Fri, Jun 23, 2023 at 10:33 AM Matthew Knepley wrote: > On Fri, Jun 23, 2023 at 10:28 AM neil liu wr

[petsc-users] Inquiry about PetscDTSimplexQuadrature .

Dear Petsc developers, I am learning *PetscDTSimplexQuadrature *and plan to use it. I found that, in the biunit simplex (tetra), (-1,-1,-1),(1,-1,-1),(-1,1,-1),(-1,-1,1), degree 1: npoints 4, the sum of weights = 4/3(the volume of this simplex) degree 2 : npoints 8; For my previous experience, I

Re: [petsc-users] Inquiry about the c++ destructor and PetscFinalize.

rrect. > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > > > On Jun 21, 2023, at 16:58, neil liu wrote: > > > > It works well for one processor; but when I tried two processors using > mpiexec -n 2 ./ex1, > > there

Re: [petsc-users] Inquiry about the c++ destructor and PetscFinalize.

ith-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack --download-ctetgen [0]PETSC ERROR: #1 DMDestroy() at /home/xiaodong.liu/Documents/petsc-3.19.1/src/dm/interface/dm.c:639 On Tue, Jun 20, 2023 at 12:36 PM neil liu wrote: > Thanks a lot, Constantine. It work

Re: [petsc-users] Inquiry about the c++ destructor and PetscFinalize.

> DMManage objDMManage; > } // objDMManage is destroyed here > > PetscFinalize(); >return 0; > } > > On 6/16/23 14:13, neil liu wrote: > > Dear Petsc developers, > > > > I am trying to use Petsc with C++. And came across one issue. > > Class

[petsc-users] Inquiry about the c++ destructor and PetscFinalize.

Dear Petsc developers, I am trying to use Petsc with C++. And came across one issue. Class DMManage has been defined, one default constructor and destructor has been defined there. The code has a runtime error, "double free or corruption". Finally I found that, this is due to PetscFinalize. If I c

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

lled and completes? > > We'll need the exact PETSc version you are using to know exactly which > MPI object is not being destroyed. > > > Barry > > > > On Jun 9, 2023, at 12:01 PM, neil liu wrote: > > > > Dear Petsc developers, > > > > I am

[petsc-users] Inquiry about the definitely lost memory

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 the leak is related to MPI. How can I relate that reminder to DMP

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

basic [0] Number of roots=15, leaves=5, remote ranks=1 [0] 5 <- (1,2) [0] 6 <- (1,3) [0] 7 <- (1,4) [0] 10 <- (1,8) [0] 11 <- (1,9) [1] Number of roots=15, leaves=0, remote ranks=0 [0] Roots referenced by my leaves, by rank [0] 1: 5 edges [0]5 <- 2 [0]6 &l

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

2 12 10 11 7 23 6 8 7 10 24 10 8 7 12 $EndElements On Wed, May 17, 2023 at 7:30 PM Matthew Knepley wrote: > 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 >

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

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, &rank); DMPlexDistribute (.., .., &dmDist); dm = dmDist; //This can create separate dm s for different processors. (reordering.

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

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 "moab/Core.hpp"I*/ ^~~ compilation termi

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

ld you please direct me to the exact location where the source code has been defined to do the transformation? On Fri, Apr 21, 2023 at 12:37 PM neil liu wrote: > Thanks a lot. Very helpful. > > On Fri, Apr 21, 2023 at 10:57 AM Matthew Knepley > wrote: > >> On Fri, Apr 21

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

Thanks a lot. Very helpful. On Fri, Apr 21, 2023 at 10:57 AM Matthew Knepley wrote: > On Fri, Apr 21, 2023 at 10:36 AM neil liu wrote: > >> When you say "For multicomponent spaces, we currently do not represent it >> as a tensor product over the scalar space, so

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

defined by 1 x y)) [ 1 -0.6667 -0.6667 1 -0.6667 0. 1 0. -0.]. How do you transform from this 1x9 to 3x6x2 there. Thanks, Xiaodong On Fri, Apr 21, 2023 at 10:05 AM Matthew Knepley wrote: > On Fri, Apr 21, 2023 at 10:02 AM neil liu wrote: > >> Hello, Petsc group, &

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

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 -dm_plex_print_fem 1 When I check the subroutine PetscFECreateTabulati

Re: [petsc-users] Questions about the PetscDSSetResidual and Nedelec element.

ou support Hcurl (curl conforming) Nedelec element ? On Tue, Apr 4, 2023 at 10:59 AM Matthew Knepley wrote: > On Tue, Apr 4, 2023 at 10:45 AM neil liu wrote: > >> Hello, >> >> I am learning this case, >> https://petsc.org/release/src/snes/tutorials/ex62.c.html >&

Re: [petsc-users] Questions about the PetscDSSetResidual and Nedelec element.

Thanks, Matt. When you said "P and P minus space" , do you have some references about this terminology to build the Hdiv and Hcurl for triangles or tetrahedra? On Wed, Apr 5, 2023 at 10:12 AM Matthew Knepley wrote: > On Wed, Apr 5, 2023 at 10:00 AM neil liu wrote: > >> T

Re: [petsc-users] Questions about the PetscDSSetResidual and Nedelec element.

Hdiv basis functions? Thanks, On Wed, Apr 5, 2023 at 11:16 AM Matthew Knepley wrote: > On Wed, Apr 5, 2023 at 10:36 AM neil liu wrote: > >> Thanks, Matt. >> When you said "P and P minus space" , do you have some references about >> this terminology to build the Hdi

[petsc-users] Questions about the PetscDSSetResidual and Nedelec element.

Hello, I am learning this case, https://petsc.org/release/src/snes/tutorials/ex62.c.html . And try to make myself familiar with the FEM (PetscFE) there. Then I have several questions. 1) PetscDSSetResidual , For example, line 291, Pet