Re: [petsc-users] Using MatCreateSBAIJ and MatZeroRowsColumns in parallel

On Fri, Dec 2, 2022 at 7:48 AM Karthikeyan Chockalingam - STFC UKRI via petsc-users wrote: > Hello, > > > > I have system matrix which is symmetric and thought I could make use of > MatCreateSBAIJ. > I don’t understand how to set the blocksize bs. I believe it has taken > into account, when havi

Re: [petsc-users] DMPlex Traversal

On Fri, Dec 2, 2022 at 5:16 AM Nicholas Arnold-Medabalimi < narno...@umich.edu> wrote: > Hi Petsc Users > > I have become familiar with usage of DMPlexGet(Restore)TransitiveClosure > as well as general traversal of the graph using DMPlexGetCone and > GetSupport. > > I was wondering if there is a m

Re: [petsc-users] Compile error on petsc-3.17

On Thu, Dec 1, 2022 at 9:53 AM Jake Lee wrote: > Dear Petsc Project Manager, > > I am Jake Lee with the Advanced Institute of Convergence Technology in > South Korea. > I'm programming with Petsc-3.17 and I encountered the following two > errors. > PETSC_FUNCTION_NAME_CXX and PETSC_RESTRICT macro

Re: [petsc-users] Speed of matrix assembly

On Thu, Dec 1, 2022 at 2:32 AM 김성익 wrote: > Hello, > > > I set a large-sized global matrix through matsetsize and proceed with the > process of assembling multiple local-sized matrices into a global matrix > (By using MatSetValue). > > However, only using matsetsize much less than expected perfor

Re: [petsc-users] About MatMumpsSetIcntl function

On Wed, Nov 30, 2022 at 10:03 AM Pierre Jolivet wrote: > > > On 30 Nov 2022, at 3:54 PM, Matthew Knepley wrote: > > On Wed, Nov 30, 2022 at 9:31 AM 김성익 wrote: > >> After folloing the comment, ./app -pc_type lu -ksp_type preonly >> -ksp_monitor_true_residual -

Re: [petsc-users] About MatMumpsSetIcntl function

(after analysis: estimated size of all MUMPS > internal data for running BLR out-of-core - sum over all processors): 0 > linear system matrix = precond matrix: > Mat Object: 1 MPI process > type: seqaij > rows=24, cols=24 > total: nonzeros=576, allocated nonzero

Re: [petsc-users] About MatMumpsSetIcntl function

output so we can see what the solver is. Thanks, Matt 2022년 11월 30일 (수) 오후 11:16, Matthew Knepley 님이 작성: > >> On Wed, Nov 30, 2022 at 9:10 AM 김성익 wrote: >> >>> When I adopt icntl by using option, the outputs are as below. >>> >>> WARNING! There are o

Re: [petsc-users] About MatMumpsSetIcntl function

-mat_mumps_icntl_7 value: 5 > > Is it work?? > Are you calling KSPSetFromOptions() after the PC is created? -pc_type lu -pc_factor_mat_solver_type mumps -mat_mumps_icntl_7 3 Thanks, Matt > Thanks, > Hyung Kim > > 2022년 11월 30일 (수) 오후 11:04, Matthew Knepley 님이 작성: &

Re: [petsc-users] About MatMumpsSetIcntl function

t; just before kspsolve. > However there is error because of 'pcfactorgetmatrix' and > 'matmumpsseticntl'. > > How can I fix this? > Give the Icntrl as an option. Thanks, Matt > Thanks, > Hyung Kim > > 2022년 11월 30일 (수) 오후 10:44, Matthew Knepley 님이

Re: [petsc-users] Loading labels from a hdf5 mesh file in parallel

On Thu, Mar 3, 2022 at 10:33 PM Yi Jiang wrote: > Dear Petsc developers, > We are trying to use the HDF5_XDMF parallel I/O feature to read/write > unstructured meshes. By trying some tests, we found that the topology and > geometry data (i.e., cells and vertices) can be efficiently loaded in a >

Re: [petsc-users] About Q3 tensor product Hermite element

On Wed, Oct 5, 2022 at 4:39 PM Duan Junming via petsc-users < petsc-users@mcs.anl.gov> wrote: > Dear all, > I'm sorry. This email got lost in my inbox. > I need to use Q3 tensor product Hermite element in 2D (point value, > gradient, and mixed derivative at 4 vertices in a cell as unknowns). >

Re: [petsc-users] About MatMumpsSetIcntl function

On Wed, Nov 30, 2022 at 8:40 AM 김성익 wrote: > Following your comments, > > After matrix assembly end, > PetscCall(KSPGetPC(ksp,&pc)); > PetscCall(KSPSetFromOptions(ksp)); > PetscCall(KSPSetUp(ksp)); > PetscCall(PCFactorGetMatrix(pc,&xGK)); > > However there is another error as below. > [0]PETSC ER

Re: [petsc-users] localToGlobal with MIN_VALUES ?

On Wed, Nov 30, 2022 at 8:22 AM Matteo Semplice < matteo.sempl...@uninsubria.it> wrote: > Hi. > > In DMLocalToGlobal only INSERT_VALUES or ADD_VALUES appear to be allowed. > > Is there a way to perform localToGlobal (or localtolocal) communications > inserting the minimum value instead? > It coul

Re: [petsc-users] Question About Assembly matrix and declaration of KSP & pc

anged. > If you just change values in the matrix, you do not have to call it again. Thanks, Matt > Thanks, > Hyung Kim > > > 2022년 11월 30일 (수) 오후 10:00, Matthew Knepley 님이 작성: > >> On Wed, Nov 30, 2022 at 7:51 AM 김성익 wrote: >> >>> Thank you for y

Re: [petsc-users] Question About Assembly matrix and declaration of KSP & pc

On Wed, Nov 30, 2022 at 7:51 AM 김성익 wrote: > Thank you for your comments. > However, I have more questions. > > 1. Generally, (KSPCreate, KSPSetOperators, KSPGetPC, PCSetType, > PCFactorSetMatSolverType, KSPSetFromOptions ) > above functions are should be called after each "MatassemblyEnd??" >

Re: [petsc-users] Petsc Section in DMPlex

On Sun, Nov 27, 2022 at 10:22 PM Nicholas Arnold-Medabalimi < narno...@umich.edu> wrote: > Hi Petsc Users > > I have a question about properly using PetscSection to assign state > variables to a DM. I have an existing DMPlex mesh distributed on 2 > processors. My goal is to have state variables se

Re: [petsc-users] Different solution while running in parallel

(iv) Can I set ksp type, pc type, ksp monitor etc using > PETScOptionsSetValue instead of code? In that case how would the above code > translate to? That will be very helpful. > Yes, you can use SetValue(). I do not understand the rest of the question. Thanks, Matt

Re: [petsc-users] make error on cluster

On Fri, Nov 25, 2022 at 11:49 PM Sijie Zhang wrote: > Hi, > > > > When I try to install petsc, I got the following error. Can you help me > with that? > This is an issue with your MPI, which I am guessing was installed by the admin. I would send them this output. However, I did find a suggestion

Re: [petsc-users] Petsc Fortran Memory stack trace

On Mon, Nov 21, 2022 at 2:44 PM Nicholas Arnold-Medabalimi < narno...@umich.edu> wrote: > I have been using valgrind with the mem checker. I should have mentioned > that. My question was probably ill posed. I'm more asking about is how > linking petsc affects the stack trace provided by the compil

Re: [petsc-users] Question on Hypre customization within a split

On Sun, Nov 20, 2022 at 5:21 AM Edoardo alinovi wrote: > Hello Barry/Matt/Jed, > > I am going on with testing and now the field split works great. Thanks a > lot for the support! > > I have a question today about Hypre customization for a target split. > let's say that my split 1 use hypre: * -UP

Re: [petsc-users] Different solution while running in parallel

t boundary conditions by > zeroing the entries in the matrix corresponding to the boundary nodes. > > > Please please please run the original thing with the options I suggested: -pc_type svd -pc_svd_monitor This will print out all the singular values of the matrix and solve it using

Re: [petsc-users] Different solution while running in parallel

outputs from both the runs. As before, I am also > printing A, b, and x. > > > > I wonder if it is a memory issue related to mpi library employed. I am > currently using openmpi – should I instead use mpich? > > > > Kind regards, > > Karthik. > > >

Re: [petsc-users] Build error with slepc: Unable to locate PETSc BAMG dynamic library

Your make.log is partial. It looks like you tried to build things and it failed, and then you tried again, but things were in a broken state. I would remove the whole source directory and start over. Thanks, Matt On Thu, Nov 17, 2022 at 9:21 AM Zongze Yang wrote: > Hello, I tried to bui

Re: [petsc-users] Different solution while running in parallel

On Wed, Nov 16, 2022 at 9:07 PM Zhang, Hong via petsc-users < petsc-users@mcs.anl.gov> wrote: > Karhik, > Can you find out the condition number of your matrix? > Also, run using -ksp_view -ksp_monitor_true_residual -ksp_converged_reason and send the two outputs. Thanks, Matt > Hon

Re: [petsc-users] Reading Vectors from a PETSc Vec

t; %12g\n",(double)re,(double)error1)); > eval(i) = re; > VecGetValues(xr, tdof, ei, eveci); > for (int j = 0; j < tdof; j++) > { > evec(j, i) = eveci[j]; > } > } > PetscCall(PetscPrintf(PET

Re: [petsc-users] Reading Vectors from a PETSc Vec

On Mon, Nov 14, 2022 at 7:39 PM Mohammad Ali Yaqteen wrote: > I am using the following procedure to read from Vec, but it keeps giving > me the same values! I was told that using VecGetValues gives wrog output. > By who? It does not give the wrong output. You do not show where in the code you d

Re: [petsc-users] Reference element in DMPlexComputeCellGeometryAffineFEM

1, 1, -1) -- (1, -1, -1) -- (-1, -1, 1) that way the first face has an outward normal. Matt > Blaise > > > On Nov 10, 2022, at 6:42 PM, Matthew Knepley wrote: > > On Thu, Nov 10, 2022 at 3:46 PM Blaise Bourdin > wrote: > >> I am not sure I am buying this… If th

Re: [petsc-users] Use Vectors and Scalars in MatNest matrices

On Mon, Nov 14, 2022 at 8:59 AM Thomas Hisch wrote: > Hi! > > I would like to ask if it is possible to create a MatNest matrix that > contains matrices, vectors and scalars. > No, You would turn everything into a type of matrix, but you can get the effect you want. Vectors can be easily used to

Re: [petsc-users] Use of LSC preconditioning

On Fri, Nov 11, 2022 at 5:57 PM Alexander Lindsay wrote: > Under what conditions can I use LSC preconditioning for field split > problems with Schur? Let's imagine that all I've done is called > SNESetJacobian with global A and P and provided the index sets for 0 and 1. > Based off of the documen

Re: [petsc-users] Reference element in DMPlexComputeCellGeometryAffineFEM

tet > which I was naively assuming was either the unit simplex, or the simplex > with vertices at (-1,-1,-1), (-1,0,-1), (0, -1, -1), and (-1,-1,1) not > necessarily in this order. In order to build my FE basis functions on the > reference element, I really need to know what this element i

Re: [petsc-users] Get solution and rhs in the ts monitor

On Thu, Nov 10, 2022 at 3:18 AM Tang, Qi wrote: > Hi, > > How could I get rhs and solution in a ksp solve of ts? > > I am testing a linear problem (TS_Linear) using a bdf integrator. I tried > to get the operator, rhs, and solution in the ts monitor through TSGetKSP > and KSPGet***. But r = Ax-b

Re: [petsc-users] Reference element in DMPlexComputeCellGeometryAffineFEM

On Wed, Nov 9, 2022 at 10:46 AM Blaise Bourdin wrote: > > > On Nov 9, 2022, at 10:04 AM, Matthew Knepley wrote: > > On Tue, Nov 8, 2022 at 9:14 PM Blaise Bourdin wrote: > > Hi, > > What reference simplex is DMPlexComputeCellGeometryAffineFEM using in 2 > and 3

Re: [petsc-users] Local columns of A10 do not equal local rows of A00

ocal size 15337 on processor 15 >> Split '0' has local size 14849 on processor 19 >> Split '0' has local size 15660 on processor 23 >> Split '0' has local size 14728 on processor 26 >> Split '0' has local size 15724 on processor 28

Re: [petsc-users] Reference element in DMPlexComputeCellGeometryAffineFEM

On Tue, Nov 8, 2022 at 9:14 PM Blaise Bourdin wrote: > 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 simple

Re: [petsc-users] On PCFIELDSPLIT and its implementation

That would be fine. Thanks, Matt On Wed, Nov 9, 2022 at 9:19 AM Edoardo alinovi wrote: > I am copying this example: > https://petsc.org/release/src/ksp/ksp/tutorials/ex42.c.html > lines > 2040'2042 > -- What most experimen

Re: [petsc-users] On PCFIELDSPLIT and its implementation

On Wed, Nov 9, 2022 at 9:17 AM Edoardo alinovi wrote: > Thanks, > > the stuff I am doing is within my code, so I am not sure you can reproduce > it. > How about just making a small code that fills those nonzeros with 1s. We just want to figure out why your sparsity pattern is not working. We hav

Re: [petsc-users] On PCFIELDSPLIT and its implementation

On Wed, Nov 9, 2022 at 9:05 AM Edoardo alinovi wrote: > So my cavity has 3x3=9 cells, each cells as a 3x3 block. I get the same > error: [0]PETSC ERROR: Local column sizes 6 do not add up to total number > of columns 9 > > However I do not define any IS, I just pass an array > to PCFieldSplitSetF

Re: [petsc-users] On PCFIELDSPLIT and its implementation

On Wed, Nov 9, 2022 at 8:09 AM Edoardo alinovi wrote: > Sure, > > I'll try on a 3x3 cavity. How can I print the ISs? > ISView() or PetscObjectViewFromOptions() Thanks, Matt > Il Mer 9 Nov 2022, 14:07 Matthew Knepley ha scritto: > >> On Wed, Nov 9, 20

Re: [petsc-users] On PCFIELDSPLIT and its implementation

blem so that you can print them to the screen? Thanks, Matt > Il Mer 9 Nov 2022, 13:54 Edoardo alinovi ha > scritto: > >> Even in the fortran interface? >> >> Il Mer 9 Nov 2022, 13:52 Matthew Knepley ha scritto: >> >>> Fields are numbered from

Re: [petsc-users] On PCFIELDSPLIT and its implementation

Fields are numbered from 0. Thanks, Matt On Wed, Nov 9, 2022 at 2:20 AM Edoardo alinovi wrote: > Hello guys, > > I am getting this error while using fieldsplit: > > [3]PETSC ERROR: - Error Message > -- > > *

Re: [petsc-users] On PCFIELDSPLIT and its implementation

On Tue, Nov 8, 2022 at 12:05 PM Edoardo alinovi wrote: > Hello Guys, > > Thanks to your suggestions on the block matrices, my fully coupled solver > is proceeding very well! > > I am now about to take advantage of the block structure of the matrix > using PCFIELDSPLIT. I have learned a bit from t

Re: [petsc-users] [petsc-maint] Issues linking petsc header files and lib from FORTRAN codes

On Tue, Nov 8, 2022 at 10:28 AM Jianbo Long wrote: > I am suspecting something else as well ... > > Could you elaborate more about "mixing c++ codes compiled with > /usr/bin/g++ and compilers in /cluster/software/GCCcore/11.2.0" ? My own > Fortran code does not have any c++ codes, and for some re

Re: [petsc-users] Local columns of A10 do not equal local rows of A00

, it should have this many columns as well. However A10 has 4137 local columns. How big is IS_0, on each process, that you pass in to PCFIELDSPLIT? Thanks, Matt > On Mon, Nov 7, 2022 at 12:33 PM Matthew Knepley wrote: > >> On Mon, Nov 7, 2022 at 2:09 PM Alexander Lindsay

Re: [petsc-users] Local columns of A10 do not equal local rows of A00

else >> { >> dinfo._rembedding = dembedding; >> } >> } >> ierr = PetscObjectReference((PetscObject)(dinfo._rembedding)); >> CHKERRQ(ierr); >> (*islist)[d] = dinfo._rembedding; >> } >&

Re: [petsc-users] Manually setting PetscSF

On Mon, Nov 7, 2022 at 1:15 PM Nicholas Arnold-Medabalimi < narno...@umich.edu> wrote: > Hi Petsc Users, > > > I am working on setting up the star forest to connect my meshes on > different processors. > > For a 2-processor example, I have set up a dmplex object and read in the > coordinates nodes

Re: [petsc-users] petsc crash with float128

On Mon, Nov 7, 2022 at 9:27 AM Gong Ding via petsc-users < petsc-users@mcs.anl.gov> wrote: > Dear petsc developer, > > The petsc linear solver crash with following report > It will make it much easier to debug if you can send your matrix. The easiest way to do this is to give the options -ksp_

Re: [petsc-users] PETSc Windows Installation

f you are planning on running on native Windows, you likely need to build there. Thanks, Matt > Thanks, > > Ali > > > > *From:* Matthew Knepley > *Sent:* Monday, November 7, 2022 7:13 PM > *To:* Mohammad Ali Yaqteen > *Cc:* petsc-users > *Subject:* Re

Re: [petsc-users] PETSc Windows Installation

gt; > -Original Message- > From: Satish Balay > Sent: Monday, November 7, 2022 12:00 AM > To: Matthew Knepley > Cc: Mohammad Ali Yaqteen ; petsc-users@mcs.anl.gov > Subject: Re: [petsc-users] PETSc Windows Installation > > Likely the compilers are not setup correctly a

Re: [petsc-users] Determining maximum number of columns in sparse matrix

On Sun, Nov 6, 2022 at 5:31 PM Alexander Lindsay wrote: > We sometimes overallocate our sparsity pattern. Matrix assembly will > squeeze out allocations that we never added into/set. Is there a convenient > way to determine the size of the densest row post-assembly? I know that we > could iterate

Re: [petsc-users] PETSc Windows Installation

We need to see configure.log to see what is going on. Can you send it? Thanks, Matt On Sun, Nov 6, 2022 at 4:29 AM Mohammad Ali Yaqteen wrote: > Dear Sir/Madam, > > > > I am installing PETSc on windows but it keeps giving me unexpected errors. > I want to use it on MS Visual Studio or C

Re: [petsc-users] locate DMSwarm particles with respect to a background DMDA mesh

On Fri, Nov 4, 2022 at 7:46 AM Matteo Semplice < matteo.sempl...@uninsubria.it> wrote: > On 04/11/2022 02:43, Matthew Knepley wrote: > > On Thu, Nov 3, 2022 at 8:36 PM Matthew Knepley wrote: > >> On Thu, Oct 27, 2022 at 11:57 AM Semplice Matteo < >> mat

Re: [petsc-users] On the usage of MatSetValuesBlocked

On Fri, Nov 4, 2022 at 4:32 AM Edoardo alinovi wrote: > It is working like a charm now! > > Is it mandatory to use VecSetValuesBlocked to assemble the rhs? Does the > Vec need to be of any other type than VECMPI? > SetValuesBlocked() is never required. You can always use the normal versions, but

Re: [petsc-users] locate DMSwarm particles with respect to a background DMDA mesh

On Thu, Nov 3, 2022 at 8:36 PM Matthew Knepley wrote: > On Thu, Oct 27, 2022 at 11:57 AM Semplice Matteo < > matteo.sempl...@uninsubria.it> wrote: > >> Dear Petsc developers, >> I am trying to use a DMSwarm to locate a cloud of points with respect >>

Re: [petsc-users] locate DMSwarm particles with respect to a background DMDA mesh

On Thu, Oct 27, 2022 at 11:57 AM Semplice Matteo < matteo.sempl...@uninsubria.it> wrote: > Dear Petsc developers, > I am trying to use a DMSwarm to locate a cloud of points with respect > to a background mesh. In the real application the points will be loaded > from disk, but I have created a

Re: [petsc-users] Local columns of A10 do not equal local rows of A00

On Thu, Nov 3, 2022 at 7:52 PM Alexander Lindsay wrote: > I have errors on quite a few (but not all) processes of the like > > [1]PETSC ERROR: - Error Message > -- > [1]PETSC ERROR: Nonconforming object sizes > [1]PET

Re: [petsc-users] On the usage of MatSetValuesBlocked

On Thu, Nov 3, 2022 at 12:16 PM Edoardo alinovi wrote: > Hello Jed/Barry/Petsc friends > > I am trying to assemble a block matrix with 3x3 in 2D and 4x4 blocks in 3D > coming from the fully coupled NS equation. > > I am not sure I am understanding the example provided here: > https://petsc.org/ma

Re: [petsc-users] Can I use PETSc DMPlex to output the surface mesh?

On Wed, Nov 2, 2022 at 8:57 AM Gong Yujie wrote: > Dear development team, > > Now I'm doing a project about visualization. In the process of > visualization, the surface mesh is preferred. I have two questions about > the DMPlex mesh. > > >1. Can I output the 3D volume mesh in DMPlex as a .ob

Re: [petsc-users] PETSc Windows Installation

> > > > Thank you > > > > Ali > > > > -Original Message- > > From: Satish Balay > > Sent: Monday, October 31, 2022 10:56 PM > > To: Satish Balay via petsc-users > > Cc: Matthew Knepley ; Mohammad Ali Yaqteen > > > > Su

Re: [petsc-users] PETSc Windows Installation

Thanks, Matt > Your help is highly appreciated. > > Thank you > Ali > > -Original Message- > From: Satish Balay > Sent: Saturday, October 29, 2022 2:11 PM > To: Mohammad Ali Yaqteen > Cc: Matthew Knepley ; petsc-users@mcs.anl.gov > Subject: Re

Re: [petsc-users] KSP on GPU

On Sun, Oct 30, 2022 at 3:52 PM Barry Smith wrote: > >In general you should expect similar but not identical conference > behavior. > > I suggest running with all the monitoring you can. > -ksp_monitor_true_residual > -fieldsplit_0_monitor_true_residual -fieldsplit_1_monitor_true_residual

Re: [petsc-users] PETSc Windows Installation

On Fri, Oct 28, 2022 at 9:11 AM Mohammad Ali Yaqteen wrote: > Dear Sir, > > > > During the Installation of PETSc in windows, I installed Cygwin and the > required libraries as mentioned on your website: > > However, when I install PETSc using the configure commands present on the > petsc website:

Re: [petsc-users] An issue of extraction of factorization matrices in sparse direct solver

Regards, > > Gang > > > -原始邮件- > *发件人:*"Xiaoye S. Li" > *发送时间:*2022-10-25 05:47:15 (星期二) > *收件人:* "Matthew Knepley" > *抄送:* "赵刚" , petsc-users@mcs.anl.gov > *主题:* Re: [petsc-users] An issue of extraction of factorization matrices

Re: [petsc-users] locate DMSwarm particles with respect to a background DMDA mesh

On Thu, Oct 27, 2022 at 11:57 AM Semplice Matteo < matteo.sempl...@uninsubria.it> wrote: > Dear Petsc developers, > I am trying to use a DMSwarm to locate a cloud of points with respect > to a background mesh. In the real application the points will be loaded > from disk, but I have created a

Re: [petsc-users] basis/basisDer/Jac in FE

On Thu, Oct 27, 2022 at 1:20 PM Yann Jobic wrote: > There is this factor also in front of the rectangle, which should 1/4 > for a unit rectangle of dim 2, but it's also 0.5. > Hi Yann, The reference element in Petsc is [-1, -1] to [1, 1]. This matches FEniCS/Firedrake and also makes it easier t

Re: [petsc-users] An issue of extraction of factorization matrices in sparse direct solver

On Sun, Oct 23, 2022 at 2:58 AM 赵刚 wrote: > Dear developers, > > I have another question. How can I get the L and U matrices and store them > in a file when I call SuperLU through PETSc? Thanks. SuperLU stores these matrices in its own format. If you want to do I/O with them, you would probably

Re: [petsc-users] Calling SuperLU_MT in PETSc

On Sun, Oct 23, 2022 at 12:48 AM 赵刚 wrote: > Dear PETSc team, > > I want to call the multithreading sparse direct solver SuperLU_MT in > PETSc, Could I download by "--download-superlu-mt"? Or what is a good way > to support calling SuperLU_MT interface in PETSc? Thank you. Is it a separate pack

Re: [petsc-users] Periodic boundary condition

On Thu, Oct 20, 2022 at 10:27 PM Barry Smith wrote: > > Some of the valgrind information does not appear to make sense > > PetscMemcpy() is not calling SNESSolve() so I suspect there must be some > serious corruption of something to this impossible stack trace > I ran Valgrind on it, and it lo

Re: [petsc-users] Periodic boundary condition

On Thu, Oct 20, 2022 at 6:48 PM Sepideh Kavousi wrote: > Hello, > > I want to solve my 5 PDEs based on finite difference method using > periodic BC in x-direction and non-periodic in y-direction but I run into > error (Segmentation Violation, probably memory access out of range). > > For this, I

Re: [petsc-users] DMPlex adding boundary without PETSc discretization

On Thu, Oct 20, 2022 at 9:42 AM Gong Yujie wrote: > Dear development team, > > I'm trying to write a code to solve a partial differential equation. I > didn't use PETSc's discretization. I have a question about the > implementation of the boundary condition (Dirichlet boundary condition). > When

Re: [petsc-users] Some questions about KSP type and PC type selection

On Wed, Oct 19, 2022 at 1:04 PM Jackie Chan wrote: > Dear All， > > I hope you're having a nice day. > In finite element problems, the stiffness matrix and load vector are > constructed to calculate the displacement vector using DMCreateMatrix and > DMCreateGlobalVector, respectively. Fo

Re: [petsc-users] Question about Sequential & Parallel part

On Wed, Oct 19, 2022 at 9:26 AM 김성익 wrote: > Dear PETSc users, > > > I have a question about structure of programming. > > My blueprint of Finite Element programming with PETSc solver is below. > [image: image.png] > The blue box is whole loop for my FE program. > There is a loop B that performs

Re: [petsc-users] how to reuse Mumps factorization

On Wed, Oct 19, 2022 at 9:13 AM 袁煕 wrote: > Hello, > > I am using Mumps to solve a problem with multiple time steps. The matrix > structure does not change but its value may or may not change during > those steps. That means I should reuse the symbolic factorization but > recall numeric factori

Re: [petsc-users] Issue with single precision complex numbers in petsc4py

.emopt', 'PETSC_ARCH': ''} > Can you show the whole output? Also, did you remember to 'export' it so that it goes to subshells? Matt > Best regards, > Peng Sun > ------ > *From:* Stefano Zampini > *Sent:* Thu

Re: [petsc-users] Issue with single precision complex numbers in petsc4py

regards, > Peng Sun > > > ---------- > *From:* Matthew Knepley > *Sent:* Thursday, October 13, 2022 6:34 AM > *To:* Peng Sun > *Cc:* petsc-users@mcs.anl.gov > *Subject:* Re: [petsc-users] Issue with single precision complex numbers > in petsc4py &

Re: [petsc-users] Issue with single precision complex numbers in petsc4py

First send configure.log so we can see the setup. Thanks, Matt On Thu, Oct 13, 2022 at 12:53 AM Peng Sun wrote: > Dear PETSc community, > > > I have a question regarding the single precision complex numbers of > petsc4py. I configured PETSc with the “--with-scalar-type=complex > --wit

Re: [petsc-users] Laplace Equation preconditioner

On Wed, Oct 12, 2022 at 1:38 PM Alfredo J Duarte Gomez wrote: > Good morning PETSC users, > > I have a current solver that requires the solution of a Laplace equation > to be reused for all future time steps. > > The configuration is axisymmetric with Dirichlet BCs at the top and bottom > boundar

Re: [petsc-users] How to get total subsnes iterations

On Wed, Oct 12, 2022 at 11:04 AM Takahashi, Tadanaga wrote: > Hi. I am using the snes nasm for the global solver and snes newtonls for > the local subdomain solver. I am trying to get the total number of Newton > iterations for just one subdomain. I've tried: > > SNESNASMGetSNES(snes,0,&subsnes);

Re: [petsc-users] DMLocalToLocal with DMPlex in Fortran

On Tue, Oct 11, 2022 at 6:04 PM Mike Michell wrote: > Thank you for the reply and checking. > Indeed, it seems that local-to-local halo is still not implemented for > DMPlex. But I believe this is a very required feature for large 3D > simulations with DMPlex. > It is possible that it will make

Re: [petsc-users] DMLocalToLocal with DMPlex in Fortran

On Mon, Oct 10, 2022 at 10:41 PM Mike Michell wrote: > Hi, I was wondering if there is any comment on the example file that I can > refer to. > I see the problem. Local2Local is not implemented for Plex. I thought we had this automated, but it was only coded for DMDA. It is a fairly mechanical t

Re: [petsc-users] make all check error

On Tue, Oct 11, 2022 at 8:52 AM Barry Smith wrote: > > > https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pci-device-with-non-16bit-domain-mean Ah. Obscure environment variables, not present in the error message, are always the best way to deal with this. Stay classy, h

Re: [petsc-users] make all check error

hwloc is giving this warning on your machine: hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). The PETSc results are fine, so you can use your

Re: [petsc-users] MSPIN

On Mon, Oct 10, 2022 at 5:37 PM Alexander Lindsay wrote: > I know that PETSc has native support for ASPIN. Has anyone tried MSPIN? I > wouldn't be surprised if someone has implemented it in user code. Wondering > what the barriers would be to creating an option like `-snes_type mspin` ? > David

Re: [petsc-users] Slepc, shell matrix, parallel, halo exchange

r of > iterations are different to reach the specified "-eps_tol" and the relative > residuals are also slightly different. Is this normal? I am using the > default Krylov-Schur solver and double precision. > > Thanks, > Feng > -- > *Fr

Re: [petsc-users] Slepc, shell matrix, parallel, halo exchange

y think you are misinterpreting the result. There are many examples, such src/vec/tutorials/ex9.c (and ex9f.F) I would start there and try to change that into the communication you want, since it definitely works. I cannot see a problem with the code snippet above. Thanks, Matt > Than

Re: [petsc-users] Vector field ordering question

On Thu, Oct 6, 2022 at 6:47 AM Gong Yujie wrote: > Dear development team, > > I'm trying to write a code to deal with a multi-field problem. Currently I > find that the vector ordering for the field is (a1,a2,a3,b1,b2,b3), here > assume a1,a2,a3 belongs to one field and bs for another field. *Can

Re: [petsc-users] How to show the x window for cmd `make -f ./gmakefile test ...`?

On Thu, Oct 6, 2022 at 9:16 AM Zongze Yang wrote: > Hi, everyone, > > I am trying to run some test cases with x window, but the x window never > showed up with command `make -f ./gmakefile test ...`. It seems a default > option `-nox` is set. How to disable this option for `make test`? > Yes, we

Re: [petsc-users] Is the results of `DMAdaptLabel` as expected in `src/dm/impls/plex/tests/ex20.c`

On Wed, Oct 5, 2022 at 7:40 AM Zongze Yang wrote: > Matthew Knepley 于2022年10月5日周三 00:33写道： > >> On Tue, Oct 4, 2022 at 3:19 PM Zongze Yang wrote: >> >>> Hi everyone, >>> >>> I am learning how to use the `DMAdaptLabel` for `DMPlex`, and found th

Re: [petsc-users] Is the results of `DMAdaptLabel` as expected in `src/dm/impls/plex/tests/ex20.c`

On Tue, Oct 4, 2022 at 3:19 PM Zongze Yang wrote: > Hi everyone, > > I am learning how to use the `DMAdaptLabel` for `DMPlex`, and found the > example `src/dm/impls/plex/tests/ex20.c` which label one cell to refine. > > 1. This example is just a uniform refinement when using the following > comma

Re: [petsc-users] DMLocalToLocal with DMPlex in Fortran

On Sat, Oct 1, 2022 at 8:51 PM Mike Michell wrote: > Thank you for the reply. There is that file in src/dm/interface/ftn-auto/ > for me, instead of the path you mentioned. > > After "make allfortranstubs" was done and, PETSc reconfigured and > reinstalled. > > However, I still have the same probl

Re: [petsc-users] DMLocalToLocal with DMPlex in Fortran

On Fri, Sep 30, 2022 at 4:14 PM Mike Michell wrote: > Hi, > > As a follow-up to this email thread, > https://www.mail-archive.com/petsc-users@mcs.anl.gov/msg44070.html > > Are DMLocalToLocalBegin() and DMLocalToLocalEnd() really available for > DMPlex with Fortran on the latest version of PETSc (

Re: [petsc-users] PETSc usage issues

On Wed, Sep 28, 2022 at 2:27 PM wangzj997 wrote: > Dear PETSc development team： > > Currently, I am learning and trying to use PETSc's KSP to solve > large-scale sparse linear systems Ax= b, where A is symmetric positive > definite > How do you know it is positive definite? This is unusual when

Re: [petsc-users] Strange mpi timing and CPU load when -np > 2

On Mon, Sep 26, 2022 at 12:40 PM Duan Junming via petsc-users < petsc-users@mcs.anl.gov> wrote: > Dear all, > > I am using PETSc 3.17.4 on a Linux server, compiling > with --download-exodus --download-hdf5 --download-openmpi > --download-triangle --with-fc=0 --with-debugging=0 > PETSC_ARCH=arch-li

Re: [petsc-users] Problem solving Ax=b with rectangular matrix A

On Mon, Sep 26, 2022 at 8:52 AM fujisan wrote: > Ok, Thank you. > I didn't know about MatCreateNormal. > > In terms of computer performance, what is best to solve Ax=b with A > rectangular? > Is it to keep A rectangular and use KSPLSQR along with PCNONE or > to convert to normal equations using M

Re: [petsc-users] Solve Linear System with Field Split Preconditioner

Another option are the PCPATCH solvers for multigrid, as shown in this paper: https://arxiv.org/abs/1912.08516 which I believe solves incompressible elasticity. There is an example in PETSc for Stokes I believe. Thanks, Matt On Mon, Sep 26, 2022 at 5:20 AM 晓峰 何 wrote: > Are there other

Re: [petsc-users] Slepc, shell matrix, parallel, halo exchange

what you mean? > Yes Matt > Thanks, > Feng > > -- > *From:* Jose E. Roman > *Sent:* 21 September 2022 13:07 > *To:* feng wang > *Cc:* Matthew Knepley ; petsc-users@mcs.anl.gov < > petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] Slepc, shell matrix

Re: [petsc-users] Slepc, shell matrix, parallel, halo exchange

On Wed, Sep 21, 2022 at 7:41 AM feng wang wrote: > Hello, > > I am using Slepc with a shell matrix. The sequential version seems working > and now I am trying to make it run in parallel. > > The partition of the domain is done, I am not sure how to do the halo > exchange in the shell matrix in Sl

Re: [petsc-users] Read and write HDF5 files

On Thu, Sep 8, 2022 at 7:44 AM Quentin Chevalier < quentin.cheval...@polytechnique.edu> wrote: > Hello PETSc users ! > > I'm trying to use PETSc routine to read and write complex vectors to > binary files in parallel. > > I'm using dolfinx and petsc4py inside a docker container. My end goal is > t

Re: [petsc-users] DMLabel Synchronize

ell, with the rule that face labels cause any cell in the support to be labeled, and labeling a cell also labels its faces 2) Partition with a cell overlap Thanks, Matt > [image: image.png] > > > Sincerely > Nicholas > > > > On Fri, Sep 2, 2022 at 7:27 AM Mat

Re: [petsc-users] DMLabel Synchronize

noldm/code/solver-playground/version_upgrade/version_debug.cpp:35 > application called MPI_Abort(MPI_COMM_SELF, 77) - process 0 > [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=77 > : > system msg for write_line failure : Bad file descriptor > > > > On Thu, Se

Re: [petsc-users] DMLabel Synchronize

lopment work. Thanks, Matt > Thanks > Nicholas > > On Wed, Aug 31, 2022 at 7:45 AM Matthew Knepley wrote: > >> On Tue, Aug 30, 2022 at 6:37 PM Nicholas Arnold-Medabalimi < >> narno...@umich.edu> wrote: >> >>> Hi >>> >>> Tha

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