Re: [petsc-users] 3.16.4 amd blis libflame linking problem

On Fri, Feb 4, 2022 at 11:35 AM Anton Popov wrote: > Hi Satish, > > I just discovered that PETSc 3.16.4 fails to link against the latest AMD > BLIS and LibFLAME libraries on a Linux box. > > > --- > You set a value for

Re: [petsc-users] Is it possible to enforce some mesh entities owned by the same CPU?

On Wed, Feb 2, 2022 at 7:32 PM 袁煕 wrote: > Hello everyone > > I need to enforce some specific nodes, for example, two nodes i,j in my > finite element mesh, to be owned by the same CPU when doing DMPlex > partition. Are there any means to implement it? > It might be possible using edge weights

Re: [petsc-users] Using Finite Difference Jacobian with TS

On Wed, Feb 2, 2022 at 6:08 PM Jorti, Zakariae via petsc-users < petsc-users@mcs.anl.gov> wrote: > Hello, > > I am using a TS to solve a differential algebraic equation (DAE). > I do not provide the Jacobian matrix but instead set the TS to use a > finite difference jacobian with coloring. > For

Re: [petsc-users] [EXTERNAL] Re: Question about PCFieldSplit

ne. >> Should I still rely on PCFieldSplitSetDetectSaddlePoint in this case? >> Many thanks once again. >> >> >> Kind regards, >> >> >> Zakariae >> -- >> *From:* Patrick Sanan >> *Sent:* Tuesday, January 25, 2022 5:36:

Re: [petsc-users] Error when configuring the PETSC environment

On Tue, Jan 25, 2022 at 5:05 PM Peng, Kang wrote: > The blue word in the last Email is part of the configure.log file, this > time I put the whole file in the attachment. > I actually tried to install it via brew, but it still failed. And I could > follow Pflotran's installation tutorial on my

Re: [petsc-users] Error when configuring the PETSC environment

On Tue, Jan 25, 2022 at 4:59 PM Peng, Kang wrote: > Hi PETSc, > > I am trying to configure the PETSC environment in MacOS (Apple M1 pro > chip, macOS 12.1), but something went wrong when I executing those command > below. I tried many methods but failed to solve it. Could you help me to > solve

Re: [petsc-users] HYPRE AMS - Segmentation Violation with discrete gradient

On Mon, Jan 24, 2022 at 4:42 PM Matthew Knepley wrote: > Okay, I can run your example and get an error. I am looking at it. Not > sure if it is us or Hypre yet. > This is failing inside Hypre. It appears that the A_diag offset array does not match the matrix. Are you giving Hypre a re

Re: [petsc-users] HYPRE AMS - Segmentation Violation with discrete gradient

t; You may find it attached and it can be reproduced with > ./ex10 -fA Amat -fP Pmat -fG Gmat -ksp_type gmres -pc_type hypre > -pc_hypre_type ams > > Thank you! > > Il 21/01/22 16:35, *Matthew Knepley * ha scritto: > > On Fri, Jan 21, 2022 at 9:50 AM Nicolas Alejandro Barnaf

Re: [petsc-users] hypre / hip usage

On Mon, Jan 24, 2022 at 9:24 AM Mark Adams wrote: > What is the fastest way to rebuild hypre? reconfiguring did not work and > is slow. > > I am printf debugging to find this HSA_STATUS_ERROR_MEMORY_FAULT (no > debuggers other than valgrind on Crusher??!?!) and I get to a hypre call: > > >

Re: [petsc-users] HYPRE AMS - Segmentation Violation with discrete gradient

On Fri, Jan 21, 2022 at 9:50 AM Nicolas Alejandro Barnafi < nicolas.barn...@unimi.it> wrote: > Dear community, > > I'm giving the discrete gradient to a PC object (sub PC of a fieldsplit) > but HYPRE internally gives a segmentation violation error. The matrix has > been adequately set, as I have

Re: [petsc-users] Cannot eagerly initialize cuda, as doing so results in cuda error 35 (cudaErrorInsufficientDriver) : CUDA driver version is insufficient for CUDA runtime version

On Thu, Jan 20, 2022 at 6:44 PM Fande Kong wrote: > Thanks, Jed > > On Thu, Jan 20, 2022 at 4:34 PM Jed Brown wrote: > >> You can't create CUDA or Kokkos Vecs if you're running on a node without >> a GPU. > > > I am running the code on compute nodes that do have GPUs. > If you are actually

Re: [petsc-users] Asking examples about solving DAE in python

On Thu, Jan 20, 2022 at 5:45 PM Xiong, Jing via petsc-users < petsc-users@mcs.anl.gov> wrote: > Good afternoon Dr. Smith, > > Thank you for your quick response. > I would like to know more details for "a matrix-free solver for the > Jacobian system or have PETSc build the Jacobian for you with

Re: [petsc-users] Nullspaces

h (and other) units that make the matrix entries about 1. It seems like you are far from this, and it is causing a loss of accuracy (your null vector has a residual of about 1e-7). Thanks, Matt > Thank you very much for your support! > > > > > > Marco Cisternino

Re: [petsc-users] Nullspaces

I made a fix for this: https://gitlab.com/petsc/petsc/-/merge_requests/4729 Thanks, Matt On Tue, Jan 18, 2022 at 3:20 PM Matthew Knepley wrote: > On Thu, Dec 16, 2021 at 11:09 AM Marco Cisternino < > marco.cistern...@optimad.it> wrote: > >> Hello Matthew

Re: [petsc-users] Nullspaces

or of your operator, but it is close, as your can see using -mat_null_space_test_view. Thanks, Matt > Thanks for any help. > > > > Marco Cisternino > > > > > > Marco Cisternino, PhD > marco.cistern...@optimad.it > > __ > >

Re: [petsc-users] PetscFV without ghost boundary conditions

On Mon, Jan 17, 2022 at 10:49 AM Jed Brown wrote: > Thibault Bridel-Bertomeu writes: > > > Sorry I wasn't clear I think. > > I was thinking that for finite volume codes, you have two options: either > > you use ghost cells that you fill up with the appropriate primitive state > > for the

Re: [petsc-users] DMPlex filter with Face Sets

On Fri, Jan 14, 2022 at 9:48 AM Lawrence Mitchell wrote: > > On 14 Jan 2022, at 14:12, Matthew Knepley wrote: > > > > On Fri, Jan 14, 2022 at 9:07 AM Thibault Bridel-Bertomeu < > thibault.bridelberto...@gmail.com> wrote: > > Also, if we still consider my ex

Re: [petsc-users] DMPlex filter with Face Sets

u for your help in this matter ! >> Do you mind posting the link to the gitlab issue when you have the >> occasion to open it ? >> >> Thanks ! >> Thibault >> >> >> Le ven. 14 janv. 2022 à 14:37, Matthew Knepley a >> écrit : >> >&g

Re: [petsc-users] DMPlex filter with Face Sets

On Fri, Jan 14, 2022 at 8:23 AM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > Dear all, > > I have a new question - in relation with my other ongoing thread > "Fluid-Structure interaction with multiple DMPlex" actually. > Is it possible to filter a DMPlex and keep in the

Re: [petsc-users] PCSetCoordinates does not set coordinates of sub PC (fieldsplit) objects

, dim, ndofs_block, coords_block); > CHKERRQ(ierr); > ierr = PetscFree(coords_block); CHKERRQ(ierr); > if(!pc_current) > SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_ORDER,"Setting > coordinates to PCFIELDSPLIT but a subPC is null."); > > ilink_current = ilink_cu

Re: [petsc-users] Parallel DMPlex Local to Global Mapping

On Wed, Jan 12, 2022 at 7:55 PM Ferrand, Jesus A. wrote: > Dear PETSc Team: > > Hi! I'm working on a parallel version of a PETSc script that I wrote in > serial using DMPlex. After calling DMPlexDistribute() each rank is assigned > its own DAG where the points are numbered locally. For example,

Re: [petsc-users] PCSetCoordinates does not set coordinates of sub PC (fieldsplit) objects

On Tue, Jan 11, 2022 at 3:31 PM Barry Smith wrote: > > Nicolas, > > For "simple" PCFIELDSPLIT it is possible to pass down the attached > coordinate information. By simple I mean where the splitting is done by > fields and not by general lists of IS (where one does not have enough >

Re: [petsc-users] Finite difference approximation of Jacobian

Am Mo., 13. Dez. 2021 um 20:17 Uhr schrieb Dave May < > dave.mayhe...@gmail.com>: > >> >> >> On Mon, 13 Dec 2021 at 20:13, Matthew Knepley wrote: >> >>> On Mon, Dec 13, 2021 at 1:52 PM Dave May >>> wrote: >>>

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

On Tue, Jan 11, 2022 at 2:59 PM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > Le mar. 11 janv. 2022 à 16:36, Jed Brown a écrit : > >> Thibault Bridel-Bertomeu writes: >> >> > Hello everybody, >> > >> > So, let's say i have the mesh attached to this email that has 2

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

On Sun, Jan 9, 2022 at 11:16 AM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > Le dim. 9 janv. 2022 à 17:08, Matthew Knepley a > écrit : > >> On Sun, Jan 9, 2022 at 10:53 AM Thibault Bridel-Bertomeu < >> thibault.bridelberto...@gmail.com

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

On Sun, Jan 9, 2022 at 10:53 AM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > Le dim. 9 janv. 2022 à 15:38, Matthew Knepley a > écrit : > >> On Sun, Jan 9, 2022 at 7:49 AM Thibault Bridel-Bertomeu < >> thibault.bridelberto...@gmail.com> w

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

On Sun, Jan 9, 2022 at 7:49 AM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > Le dim. 9 janv. 2022 à 13:05, Matthew Knepley a > écrit : > >> On Sat, Jan 8, 2022 at 2:13 PM Thibault Bridel-Bertomeu < >> thibault.bridelberto...@gmail.com>

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

f the domain, but that just impacts how you do the residual integral. You do assemble a combined residual for all dogs, however, which I think is what you mean. Thanks, Matt > Thanks, > > Thibault > > Le sam. 8 janv. 2022 à 20:00, Matthew Knepley a > écrit : > >> O

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

coupling » road > with a sub-DM is the way. > Can I ask how you proceed in the rocket engine code you are writing ? IMEX > ? > Right now it is IMEX, but we are explicitly substepping particles. Not sure what the final thing will be. Thanks, Matt > Thibault > > Le sam. 8

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

I do not know how. Right now, composable TS does not work all the way. Matt On Sat, Jan 8, 2022 at 1:03 PM Mark Adams wrote: > Can you subcycle with IMEX? > > On Sat, Jan 8, 2022 at 10:58 AM Matthew Knepley wrote: > >> On Sat, Jan 8, 2022 at 3:05 AM Thibau

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

On Sat, Jan 8, 2022 at 3:05 AM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > Le ven. 7 janv. 2022 à 19:45, Thibault Bridel-Bertomeu < > thibault.bridelberto...@gmail.com> a écrit : > >> Le ven. 7 janv. 2022 à 19:23, Matthew Knepley a >> é

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

On Fri, Jan 7, 2022 at 12:58 PM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > > Le ven. 7 janv. 2022 à 14:54, Matthew Knepley a > écrit : > >> On Fri, Jan 7, 2022 at 8:52 AM Thibault Bridel-Bertomeu < >> thibault.bridelberto...@gm

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

On Fri, Jan 7, 2022 at 8:52 AM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > Hi Matthew, > > Le ven. 7 janv. 2022 à 14:44, Matthew Knepley a > écrit : > >> On Fri, Jan 7, 2022 at 5:46 AM Thibault Bridel-Bertomeu < >> thibault.bridelbe

Re: [petsc-users] Fluid-Structure interaction with multiple DMPlex

On Fri, Jan 7, 2022 at 5:46 AM Thibault Bridel-Bertomeu < thibault.bridelberto...@gmail.com> wrote: > Dear all, > > First of, happy new year everyone !! All the best ! > Happy New Year! > I am starting to draft a new project that will be about fluid-structure > interaction: in particular, the

Re: [petsc-users] [EXTERNAL] Re: DM misuse causes massive memory leak?

eir output to assign the dof to the > PetscSection. > This should all take almost no time. There are no expensive operations there. Thanks, Matt > For what is worth, I have my configure set to --with-debugging = 1. > -- > *From:* Matthew Knepley

Re: [petsc-users] [EXTERNAL] Re: DM misuse causes massive memory leak?

On Thu, Jan 6, 2022 at 5:15 PM Ferrand, Jesus A. wrote: > Jed: > > DMPlexLabelComplete() has allowed me to speed up my code significantly > (Many thanks!). > > I did not use DMAddBoundary() though. > I figured I could obtain Index Sets (IS's) from the DAG for different > depths and then IS's for

Re: [petsc-users] NVIDIA HPC SDK and complex data type

On Sat, Dec 18, 2021 at 7:03 PM Junchao Zhang wrote: > I found it is a NVIDIA C/C++ compiler bug. I can reproduce it with > Great find! Matt > #include > #include > #include > > typedef double _Complex PetscScalar; > typedef struct { > int row; > PetscScalar *valaddr; > } MatEntry2; >

Re: [petsc-users] --with-mpi=0

On Sat, Dec 18, 2021 at 9:26 AM Tabrez Ali wrote: > Hi, > > I am trying to compile Fortran code with PETSc 3.16 built without MPI, > i.e., --with-mpi=0, and am getting the following error: > >call MPI_Comm_rank(MPI_COMM_WORLD,rank,ierr) > 1 > Error:

Re: [petsc-users] Finite difference approximation of Jacobian

On Mon, Dec 13, 2021 at 1:52 PM Dave May wrote: > On Mon, 13 Dec 2021 at 19:29, Matthew Knepley wrote: > >> On Mon, Dec 13, 2021 at 1:16 PM Dave May wrote: >> >>> >>> >>> On Sat 11. Dec 2021 at 22:28, Matthew Knepley wrote: >>>

Re: [petsc-users] Finite difference approximation of Jacobian

On Mon, Dec 13, 2021 at 1:16 PM Dave May wrote: > > > On Sat 11. Dec 2021 at 22:28, Matthew Knepley wrote: > >> On Sat, Dec 11, 2021 at 1:58 PM Tang, Qi wrote: >> >>> Hi, >>> Does anyone have comment on finite difference coloring with DMStag? We

Re: [petsc-users] Unstructured mesh

pe given: cusparse > > > > > > *@Matthew Knepley *Usually PETSc -log_view reports > the GPU flops. Alternatively if are using an external package such as > hypre, where gpu flops are not recorded by petsc, profiling using Nvidia’s > nsight captures them. So one could tell if t

Re: [petsc-users] Unstructured mesh

KSPSolve, which I didn’t. > > > > Okay, I will wait for Mark to comment. > > > > Kind regards, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Monday, 13 December 2021 at 13:17 > *To: *"Chockalingam, Karthikeyan (STFC,DL,HC)" < &

Re: [petsc-users] Unstructured mesh

gt; > > Kind regards, > > Karthik. > > > > > > *From: *Mark Adams > *Date: *Sunday, 12 December 2021 at 23:00 > *To: *"Chockalingam, Karthikeyan (STFC,DL,HC)" < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *Matthew Knepley , "pet

Re: [petsc-users] SNES always ends at iteration 0

On Sun, Dec 12, 2021 at 7:48 PM celestechev...@gmail.com < celestechev...@gmail.com> wrote: > Thank you so much for your reply ! > > In fact I didn't know how to set tolerances, so I proceeded without > specifying the tolerances, hoping that this could lead to the > implementation of default

Re: [petsc-users] non-manifold DMPLEX

On Sun, Dec 12, 2021 at 4:36 PM TARDIEU Nicolas wrote: > Dear Patrick and Matthew, > > Thank you very much for your answers. I am gonna try to set up such a test > by assigning cell types. > Shall I open a MR in order to contribute this example ? > Yes, that would be great. Thanks, Matt

Re: [petsc-users] non-manifold DMPLEX

On Sun, Dec 12, 2021 at 6:11 AM Patrick Sanan wrote: > Here you have the following "points": > > - 1 3-cell (the cube volume) > - 7 2-cells (the 6 faces of the cube plus the extra one) > - 16 1-cells (the 12 edges of the cube, plus 3 extra ones from the extra > face, plus the extra edge) > - 11

Re: [petsc-users] Finite difference approximation of Jacobian

On Sat, Dec 11, 2021 at 1:58 PM Tang, Qi wrote: > Hi, > Does anyone have comment on finite difference coloring with DMStag? We are > using DMStag and TS to evolve some nonlinear equations implicitly. It would > be helpful to have the coloring Jacobian option with that. > Since DMStag produces

Re: [petsc-users] Unstructured mesh

gt; Labels: > > celltype: 4 strata with value/size (0 (75), 1 (170), 4 (128), 7 (32)) > > depth: 4 strata with value/size (0 (75), 1 (170), 2 (128), 3 (32)) > > marker: 1 strata with value/size (1 (240)) > > Face Sets: 6 strata with value/size (6 (18), 5

Re: [petsc-users] Unstructured mesh

iew Thanks, Matt > Best, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Friday, 10 December 2021 at 13:04 > *To: *"Chockalingam, Karthikeyan (STFC,DL,HC)" < > karthikeyan.chockalin...@stfc.ac.uk> > *Cc: *"petsc-users@mcs.anl.gov&quo

Re: [petsc-users] Unstructured mesh

orm 1.085975028558e+01 > > 1 SNES Function norm 2.294074693590e-07 > > 2 SNES Function norm 2.491900236077e-14 > You are solving the problem twice, probably because ex56 is in its refinement loop. Thanks, Matt > Kind regards, > > Karthik. > > > >

Re: [petsc-users] Internal memory MUMPS during numerical factorization

On Thu, Dec 9, 2021 at 7:53 PM Alberto F. Martín wrote: > Dear PETSc users, > > I am experiencing the following error during numerical factorization > while using the MUMPS package. > > It seems an internal memory error in the DMUMPS_ALLOC_CB function. Has > anyone experienced this before? Any

Re: [petsc-users] How to read/write a HDF5 file using petsc4py ?

s a time-consuming process. > > Quentin > > > > [image: cid:image003.jpg@01D690CB.3B3FDC10] > > Quentin CHEVALIER – IA parcours recherche > > LadHyX - Ecole polytechnique > > __ > > > On Tue, 7 Dec 2021 at 19:16, Matthew Knepley wrote: &g

Re: [petsc-users] Tips on integrating MPI ksp petsc into my application?

ally distribute the > matrix to the ranks? > You can call https://petsc.org/main/docs/manualpages/Mat/MatCreateSubMatricesMPI.html to distribute the matrix. Thanks, Matt > On Tuesday, December 7, 2021, 10:18:04 PM EST, Matthew Knepley < > knep...@gmail.com> wrote

Re: [petsc-users] Tips on integrating MPI ksp petsc into my application?

On Tue, Dec 7, 2021 at 10:06 PM Faraz Hussain via petsc-users < petsc-users@mcs.anl.gov> wrote: > Thanks, I took a look at ex10.c in ksp/tutorials . It seems to do as you > wrote, "it efficiently gets the matrix from the file spread out over all > the ranks.". > > However, in my application I

Re: [petsc-users] PETSc object creation/destruction with adaptive grid

On Tue, Dec 7, 2021 at 12:54 PM Samuel Estes wrote: > Hi, > > I have a code implementing a finite element method with an adaptive grid. > Rather than destroying the PETSc objects (the Jacobian matrix and RHS > residual vector) every time the code refines the grid, we want to > (over-)allocate

Re: [petsc-users] Nullspaces

On Tue, Dec 7, 2021 at 11:19 AM Marco Cisternino < marco.cistern...@optimad.it> wrote: > Good morning, > > I’m still struggling with the Poisson equation with Neumann BCs. > > I discretize the equation by finite volume method and I divide every line > of the linear system by the volume of the

Re: [petsc-users] How to read/write a HDF5 file using petsc4py ?

t;/usr/lib/python3.9/imp.py", line 242, in load_module > return load_dynamic(name, filename, file) > File "/usr/lib/python3.9/imp.py", line 342, in load_dynamic > return _load(spec) > ImportError: > /usr/local/lib/python3.9/dist-packages/petsc4py/lib/l

Re: [petsc-users] How to read/write a HDF5 file using petsc4py ?

esparse > --download-superlu_dist --with-scalar-type=complex > > > > > > So the HDF5 option is not being specified. > > > > Thanks, > > > > Matt > > > >> Cheers, > >> > >> Quentin > >> > >> > >

Re: [petsc-users] How to read/write a HDF5 file using petsc4py ?

; Quentin CHEVALIER – IA parcours recherche > > LadHyX - Ecole polytechnique > > __ > > > On Mon, 6 Dec 2021 at 21:39, Matthew Knepley wrote: > >> On Mon, Dec 6, 2021 at 3:27 PM Quentin Chevalier < >> quentin.cheval...@polytechnique.edu> wrote: &

Re: [petsc-users] DM/DMPlex Issue from DM vector access

On Mon, Dec 6, 2021 at 6:06 PM Ferrand, Jesus A. wrote: > Dear PETSc Team: > > I am a new PETSc user who is working on an FEA code and ran into an issue > pertaining to DMPlex. > > I have a gmsh mesh file that I import using "DMPlexCreateGmshFromFile()." > I then fetch the XYZ coordinates of the

Re: [petsc-users] How to read/write a HDF5 file using petsc4py ?

rve absolutely no behavioural change > whatsoever. I'm afraid I don't know PETSc well enough to be surprised by > that. > > > > Quentin > > > > > > > > Quentin CHEVALIER – IA parcours recherche > > > > LadHyX - Ecole polytechnique > > >

Re: [petsc-users] CV_CONV_FAILURE with TSSUNDIALS in PETSc

ok for Android <https://aka.ms/AAb9ysg> > ---------- > *From:* Matthew Knepley > *Sent:* Monday, December 6, 2021 1:00:49 PM > *To:* Sanjoy Kumar Mazumder > *Cc:* petsc-users@mcs.anl.gov > *Subject:* Re: [petsc-users] CV_CONV_FAILURE with TSSUNDIALS in

Re: [petsc-users] How to read/write a HDF5 file using petsc4py ?

ame error, so a) You did not reconfigure b) Your new build is somewhere else on the machine Thanks, Matt > I will comment I am running on OpenSUSE. > > Quentin > > On Mon, 6 Dec 2021 at 19:09, Matthew Knepley wrote: > > > > On Mon, Dec 6, 2021 at 1:08 P

Re: [petsc-users] KSPBuildResidual and KSPType compatibility

On Mon, Dec 6, 2021 at 1:07 PM Fischer, Greg A. via petsc-users < petsc-users@mcs.anl.gov> wrote: > With -pc_type none, my value matches the ksp value, but it no longer > converges. > So now it seems like the check with unpreconditioned residuals was not right somehow. THanks, Matt >

Re: [petsc-users] How to read/write a HDF5 file using petsc4py ?

rs recherche > > LadHyX - Ecole polytechnique > > __ > > > > On Mon, 6 Dec 2021 at 19:02, Matthew Knepley wrote: > > > > On Mon, Dec 6, 2021 at 11:28 AM Quentin Chevalier < > quentin.cheval...@polytechnique.edu> wrote: > >> > >> Hello

Re: [petsc-users] How to read/write a HDF5 file using petsc4py ?

On Mon, Dec 6, 2021 at 11:28 AM Quentin Chevalier < quentin.cheval...@polytechnique.edu> wrote: > Hello PETSc users, > > This email is a duplicata of this gitlab issue > , sorry for any > inconvenience caused. > > I want to compute a PETSc vector in

Re: [petsc-users] CV_CONV_FAILURE with TSSUNDIALS in PETSc

On Mon, Dec 6, 2021 at 12:17 PM Sanjoy Kumar Mazumder wrote: > Hi all, > > I am trying to solve a set of coupled stiff ODEs in parallel using > TSSUNDIALS with SUNDIALS_BDF as 'TSSundialsSetType' in PETSc. I am using a > sparse Jacobian matrix of type MATMPIAIJ with no preconditioner. It runs >

Re: [petsc-users] dmplex extruded layers

On Wed, Nov 24, 2021 at 5:45 PM Bhargav Subramanya < bhargav.subrama...@kaust.edu.sa> wrote: > On Wed, Nov 24, 2021 at 8:59 PM Matthew Knepley wrote: > >> On Wed, Nov 24, 2021 at 12:27 PM Bhargav Subramanya < >> bhargav.subrama...@kaust.edu.sa> wrote: >> >&

Re: [petsc-users] Hypre (GPU) memory consumption

On Fri, Dec 3, 2021 at 7:57 AM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalin...@stfc.ac.uk> wrote: > Hello, > > > > I am able to successfully run hypre on gpus but the problem seems to > consumption a lot of memory. I ran ksp/ksp/tutorial/ex45 on a grid of 320 > x 320 x 320 using

Re: [petsc-users] Unstructured mesh

On Thu, Dec 2, 2021 at 3:33 AM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalin...@stfc.ac.uk> wrote: > Hello, > > > > Are there example tutorials on unstructured mesh in ksp? Can some of them > run on gpus? > There are many unstructured grid examples, e.g. SNES ex13, ex17, ex56. The

Re: [petsc-users] Output data using ExodusIIViewer

Blaise, is that stuff we should be doing in the viewer? Thanks, Matt On Wed, Dec 1, 2021 at 2:48 PM Blaise Bourdin wrote: > David, > > Here is a modified example. > Exodus needs some additional work prior to saving fields. See the attached > modified example. > > Blaise > > > On Dec 1,

Re: [petsc-users] Communication in parallel MatMatMult

On Wed, Dec 1, 2021 at 9:32 AM Barry Smith wrote: > > PETSc uses Elemental to perform such operations. > > PetscErrorCode MatMatMultNumeric_Elemental(Mat A,Mat B,Mat C) > { > Mat_Elemental*a = (Mat_Elemental*)A->data; > Mat_Elemental*b = (Mat_Elemental*)B->data; > Mat_Elemental

Re: [petsc-users] PETSc Ordering for vectors generated by DMCreateGlobalVector

On Sun, Nov 28, 2021 at 8:05 AM 袁煕 wrote: > Hi all, > > Application Ordering of a vector is generally different from its PETSc > one. In my application, I wish to retrieve the value of a vector generated > by DMCreateGlobalVector into its original application order. I know there > are some

Re: [petsc-users] DMPlex shared node indexing

On Fri, Nov 26, 2021 at 12:49 AM 袁煕 wrote: > Dear PETSc-team, > > When the mesh is distributed, the vertices are renumbered and some > vertices are shared by neighboring CPUs. My question is: > > 1. How to check which vertice is a ghost one? > It is present in the PetscSF describing the

Re: [petsc-users] How to set boundary conditions for a structured finite volume (FV) discretization when using TS/SNES?

What we do in the FVM examples is to use ghost cells around the boundary. Then the state in these cells is set so that the flux on the boundary surface is exactly what you want. You could also prescribe the fluxes directly, but that is not as natural in the setup I have used for FVM. Thanks,

Re: [petsc-users] configure error with fftw and without mpi

On Thu, Nov 25, 2021 at 2:29 PM Fabio Rossi via petsc-users < petsc-users@mcs.anl.gov> wrote: > Thanks for the reply. > > I am using the system fftw which is provided by the distribution so I am > not going to install it by using PETSC's install scripts. > > I am sorry but I am not confident with

Re: [petsc-users] GAMG memory consumption

On Wed, Nov 24, 2021 at 12:26 PM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalin...@stfc.ac.uk> wrote: > Hello, > > > > I would like to understand why more memory is consumed by -pc_type gamg > compared to -pc_type mg for the same problem size > > > > ksp/ksp/tutorial: ./ex45

Re: [petsc-users] dmplex extruded layers

On Wed, Nov 24, 2021 at 12:27 PM Bhargav Subramanya < bhargav.subrama...@kaust.edu.sa> wrote: > Dear Matt and Mark, > > Thank you very much for your reply. Your inputs are very useful to me. > > On Mon, Nov 22, 2021 at 9:38 PM Matthew Knepley wrote: > >> On Mon, No

Re: [petsc-users] Issues with log_view on windows

The user would be responsible for escaping the semicolon if used in the shell unfortunately. Thanks, Matt > Satish > > > On Mon, 22 Nov 2021, Matthew Knepley wrote: > > > On Mon, Nov 22, 2021 at 11:57 AM Barry Smith wrote: > > > > > > > > What do

Re: [petsc-users] hypre on gpus

On Mon, Nov 22, 2021 at 12:41 PM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalin...@stfc.ac.uk> wrote: > @Matthew Knepley Yes, it works with main build! > That is good. I think we might need to push up the next point release then, since we have a Hypre bug for which

Re: [petsc-users] Issues with log_view on windows

rs < > petsc-users@mcs.anl.gov> wrote: > > Well our build tools use cygwin - but the library is built with MS/Intel > compilers - they use paths in windows notation. > > I'm not sure if there is a way to get windows PATHs without ':' > > Satish > > On Mon, 22 Nov 2021,

Re: [petsc-users] Issues with log_view on windows

solute paths, I had also tried to use cygwin > paths (`/cygdrive/c/...`) but that does not work either. > Hmm, that should work I think. Satish, do we have a machine to login and test something like this? Thanks, Matt > Best, > Milan > > ‐‐‐ Original Message ‐‐‐

Re: [petsc-users] hypre on gpus

> [0]PETSC ERROR: -mat_type hypre > > [0]PETSC ERROR: -pc_type hypre > > *[0]PETSC ERROR: End of Error Message ---send entire > error message to petsc-ma...@mcs.anl.gov------* > > -

Re: [petsc-users] hypre on gpus

gt; [0]PETSC ERROR: -use_gpu_aware_mpi 0 > > *[0]PETSC ERROR: End of Error Message ---send entire > error message to petsc-ma...@mcs.anl.gov--* > > ---------- > > > > I have also attached the make.log. Thank you for having a look. > > > > Best,

Re: [petsc-users] hypre on gpus

On Mon, Nov 22, 2021 at 6:47 AM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalin...@stfc.ac.uk> wrote: > Thank you for your response. I tried to run the same example > > > > petsc/src/ksp/ksp/tutorials$ *./ex4 -ksp_type cg -mat_type hypre > -ksp_view -pc_type hypre* > > > > but it

Re: [petsc-users] Issues with log_view on windows

On Mon, Nov 22, 2021 at 5:38 AM Milan Pelletier via petsc-users < petsc-users@mcs.anl.gov> wrote: > Dear PETSc team, > > The way some options are passed to PETSc can be an issue on Windows, in > particular regarding the "log_view" option. > Since the colon ':' character is used as a separator, I

Re: [petsc-users] How to apply boundary conditions when using TS?

On Mon, Nov 15, 2021 at 10:24 PM zhfreewill wrote: > Hi, > I'm new to PETSc. I have been confused about how to apply boundary > conditions (BCs) (e.g., the Dirichlet and the Neumann type) when using the > time-stepping (TS) object of PETSc. > > I have read the example codes ( >

Re: [petsc-users] Error running make on MUMPS

namely that one shell thing failed (ln) and then the make reports an error. Thanks, Matt > Thanks, > Fande > > On Thu, Nov 11, 2021 at 1:29 PM Matthew Knepley wrote: > >> On Thu, Nov 11, 2021 at 3:25 PM Fande Kong wrote: >> >>> Thanks, Satish >>> &

Re: [petsc-users] Error running make on MUMPS

On Thu, Nov 11, 2021 at 3:25 PM Fande Kong wrote: > Thanks, Satish > > "--with-make-np=1" did help us on MUMPS, but we had new trouble with > hypre now. > > It is hard to understand why "gmake install" even failed. > Because HYPRE thinks it is better to use 'ln' than the 'install' script that

Re: [petsc-users] dmplex extrude in parallel

t; [1]PETSC ERROR: ----End of Error Message ---send entire > error message to petsc-ma...@mcs.anl.gov-- > application called MPI_Abort(MPI_COMM_WORLD, 60) - process 1 > > Thanks, > Bhargav > > On Wed, Nov 10, 2021 at 4:33 PM Matthew Knepley wrote: >

Re: [petsc-users] Is it possible to keep track of original elements # after a call to DMPlexDistribute ?

gitlab/knepley/fix-plex-g2n branch will find it's > way into next or main? ;) > Put in the MR today. Thanks, Matt > Thanks, > > Eric > > On 2021-11-10 3:26 p.m., Matthew Knepley wrote: > > Okay, so the PETSC_DEFAULT one is what is used for topology. There are >

Re: [petsc-users] matrix-vector and matrix-matrix products in PETSc

On Thu, Nov 11, 2021 at 3:00 AM Majid Rasouli wrote: > Dear all, > > I'm trying to find a brief explanation about the parallel (MPI) > implementation of matrix-vector multiplication and matrix-matrix > multiplication in PETSc. I have used them for some experiments for a > research paper and I

Re: [petsc-users] How to compute the condition number of SchurComplementMat preconditioned with PCSHELL.

On Wed, Nov 10, 2021 at 8:42 AM Vladislav Pimanov < vladislav.pima...@skoltech.ru> wrote: > Dear PETSc community, > > > I wonder if you could give me a hint on how to compute the condition > number of a preconditioned matrix in a proper way. > > I have a *MatSchurComplement* matrix S and a

Re: [petsc-users] dmplex extrude in parallel

t; Thanks, > Bhargav > > On Wed, Nov 10, 2021 at 12:56 AM Matthew Knepley > wrote: > >> On Tue, Nov 9, 2021 at 9:54 AM Bhargav Subramanya < >> bhargav.subrama...@kaust.edu.sa> wrote: >> >>> Dear All, >>> >>> I want to generate a pris

Re: [petsc-users] Fwd: SNES with Fieldsplit + MatNest in parallel

On Tue, Nov 9, 2021 at 6:52 AM Nicolas Barnafi wrote: > Thanks for the help Matthew. > > > The next step would be to verify that the operators you get in those slots > are correct in parallel. I normally just print out the matrix > for a small problem. This is the only way I know to debug

Re: [petsc-users] Fwd: SNES with Fieldsplit + MatNest in parallel

On Tue, Nov 9, 2021 at 6:18 AM Nicolas Barnafi wrote: > Whoops, I think the notation wasn't very good, sorry. This should have > been my previous message: > > Rank-0, is_0: [0 1 2] ... [633 634 635] > Rank-0, is_1 [636 637 638] ... [729 730 731] > Rank-1, is_0: [732 733 734] ... [1368 1369 1370]

Re: [petsc-users] Fwd: SNES with Fieldsplit + MatNest in parallel

On Tue, Nov 9, 2021 at 4:24 AM Nicolas Barnafi wrote: > > I am not adept enough at FEniCS to look at the code and debug. However, > I would make a very small problem for 2 processes, say two cells on each, > and then print out is_0 and is_1. That should tell you if you have the > right >

Re: [petsc-users] Problem with using make

On Mon, Nov 8, 2021 at 9:57 PM Yaswanth Narayana wrote: > Hello > > My name is Yaswanth Narayana. I am using PETSc as part of my course HPC1. > When trying to use make I am getting the following error. What should I do? > > makefile:8: /lib/petsc/conf/rules: No such file or directory > make: ***

Re: [petsc-users] Fwd: SNES with Fieldsplit + MatNest in parallel

On Mon, Nov 8, 2021 at 11:00 AM barnafi wrote: > Hi PETSc users, > > I am testing a block preconditioner for a nonlinear problem using > fenics for matrix assembly, and I obtain correcet results in serial > only (parallel diverges). The difficulty lies in using Nest matrices, > as I want a

Re: [petsc-users] How to construct DMPlex of cells with different topological dimension?

On Wed, Nov 3, 2021 at 8:06 AM TARDIEU Nicolas wrote: > Dear Matt, > > Thank you for the additional information. > I do agree that I will have to write code to describe the interpolation I > need for a multi-model problem. > Let me try to illustrate my point on the simple mesh I have attached to

<    5   6   7   8   9   10   11   12   13   14   >