[petsc-users] Unstructured mesh

Matthew Knepley knepley at gmail.com
Fri Dec 10 20:26:51 CST 2021 

On Fri, Dec 10, 2021 at 1:11 PM Karthikeyan Chockalingam - STFC UKRI <
karthikeyan.chockalingam at stfc.ac.uk> wrote:

> Thank you that worked. I have attached the output of the run
>
>
>
> ./ex56 -cells 2,2,1 -max_conv_its 2 -lx 1. -alpha .01 -petscspace_degree 1
> -ksp_type cg -ksp_monitor -ksp_rtol 1.e-8 -pc_type asm -snes_monitor
> -use_mat_nearnullspace true -snes_rtol 1.e-10 -ex56_dm_view
>
>
>
> Below is the mesh information I get before the solve.
>
> Not sure how to interpret them – is ‘18’ say number of elements in certain
> direction?
>

0-cells are vertices, 1-cells are edges, etc, so this has 4 cubes. That is
why it has 18 vertices, 9 on top and 9 on the bottom. A
bunch of stuff is labeled on this mesh, but you don't have to worry about
it I think.


> How does ‘18’ come about – given cells 2,2,1 as input?
>
> Sorry, bit lost what markers and other labels represent.
>
>
>
> Mesh in 3 dimensions:
>
>   0-cells: 18
>
>   1-cells: 33
>
>   2-cells: 20
>
>   3-cells: 4
>
> Labels:
>
>   marker: 1 strata with value/size (1 (48))
>
>   Face Sets: 6 strata with value/size (6 (2), 5 (2), 3 (2), 4 (2), 1 (4),
> 2 (4))
>
>   depth: 4 strata with value/size (0 (18), 1 (33), 2 (20), 3 (4))
>
>   boundary: 1 strata with value/size (1 (66))
>
>   celltype: 4 strata with value/size (7 (4), 0 (18), 4 (20), 1 (33))
>
>
>
> I am more puzzled as the mesh information changes after the solve?
>

Mark refined it once regularly, so each hexahedron is split into 8, giving
32 cubes.

  Thanks,

    Matt


> Mesh in 3 dimensions:
>
>   0-cells: 75
>
>   1-cells: 170
>
>   2-cells: 128
>
>   3-cells: 32
>
> 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 (18), 3 (18), 4 (18), 1
> (36), 2 (36))
>
>   boundary: 1 strata with value/size (1 (258))
>
>
>
> Best,
>
> Karthik.
>
>
>
>
>
>
>
>
>
> *From: *Matthew Knepley <knepley at gmail.com>
> *Date: *Friday, 10 December 2021 at 16:17
> *To: *"Chockalingam, Karthikeyan (STFC,DL,HC)" <
> karthikeyan.chockalingam at stfc.ac.uk>
> *Cc: *"petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Unstructured mesh
>
>
>
> On Fri, Dec 10, 2021 at 10:49 AM Karthikeyan Chockalingam - STFC UKRI <
> karthikeyan.chockalingam at stfc.ac.uk> wrote:
>
> Thank you for your response.
>
> I tried using the flag -dm_view to get mesh information.
>
> I was hoping it might create a output file with mesh information but it
> didn’t create any.
>
> What should I expect with -dm_view?
>
>
>
> -dm_view prints the Plex information to the screen (by default), but it
> responds to the normal viewer options.
>
> However, it looks like Mark changes the prefix on the mesh, so I think you
> need
>
>
>
>   -ex56_dm_view
>
>
>
>   Thanks,
>
>
>
>     Matt
>
>
>
> Best,
>
> Karthik.
>
>
>
> *From: *Matthew Knepley <knepley at gmail.com>
> *Date: *Friday, 10 December 2021 at 13:04
> *To: *"Chockalingam, Karthikeyan (STFC,DL,HC)" <
> karthikeyan.chockalingam at stfc.ac.uk>
> *Cc: *"petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Unstructured mesh
>
>
>
> On Fri, Dec 10, 2021 at 7:42 AM Karthikeyan Chockalingam - STFC UKRI <
> karthikeyan.chockalingam at stfc.ac.uk> wrote:
>
> Hi Matt,
>
>
>
> I intend to perform a scaling study – I have a few more questions from ex56
>
> *3D, tri-quadratic hexahedra (Q1), displacement finite element
> formulation.*
>
> i)                    What makes the problem non-linear? I believe SNES
> are used to solve non-linear problems.
>
> It is a linear problem. We use SNES because it is easier to use it for
> everything.
>
> ii)                   2,2,1 does it present the number of elements used
> in each direction?
>
> You can use -dm_view to show the mesh information actually used in the run.
>
> iii)                 What makes the problem unstructured? I believe the
> geometry is a cube or cuboid – is it because it uses DMPlex?
>
> Yes.
>
> iv)                 Do any external FEM package with an unstructured
> problem domain has to use DMPlex mat type?
>
> DMPlex is not a Mat type, but rather a DM type. I do not understand the
> question. For example, LibMesh uses PETSc solvers but has
>
> its own mesh types.
>
> v)                   What about -mat_type (not _dm_mat_type) ajicusparse
> – will it work with unstructured FEM discretised domains?
>
> dm_mat_type is just a way of setting the MatType that the DM creates. You
> can set it to whatever type you want. Since it uses MatSetValues()
>
> there may be overhead in converting to that matrix type, but it should
> work.
>
>
>
> I tried to run two problems of ex56 with two different domain size ( -
> attached you find the log_view outputs of both on *gpus*) using _pc_type
> asm:
>
>
>
> ./ex56 -cells 2,2,1 -max_conv_its 2 -lx 1. -alpha .01 -petscspace_degree 1
> -ksp_type cg -ksp_monitor -ksp_rtol 1.e-8 -pc_type asm -snes_monitor
> -use_mat_nearnullspace true  -snes_rtol 1.e-10 > output_221.txt
>
>
>
>
>
> ./ex56 -cells 10,10,5 -max_conv_its 2 -lx 1. -alpha .01 -petscspace_degree
> 1 -ksp_type cg -ksp_monitor -ksp_rtol 1.e-8 -pc_type asm -snes_monitor
> -use_mat_nearnullspace true  -snes_rtol 1.e-10 > output_221.txt
>
>
>
> Below is the SNES iteration for problem with 2,2,1 cells which converges
> after two non-linear iterations:
>
>
>
> 0 SNES Function norm 0.000000000000e+00
>
>   0 SNES Function norm 7.529825940191e+01
>
>   1 SNES Function norm 4.734810707002e-08
>
>   2 SNES Function norm 1.382827243108e-14
>
>
>
> Your KSP tolerance is too high, so it takes another iterate. Use -ksp_rtol
> 1e-10.
>
>
>
> Below is the SNES iteration for problem with 10,10,5 cells– why does it
> first decrease and then increase to *0 SNES Function norm
> 1.085975028558e+01* and finally converge?
>
>
>
>   0 SNES Function norm 2.892801019593e+01
>
>   1 SNES Function norm 5.361683383932e-07
>
>   2 SNES Function norm 1.726814199132e-14
>
>   0 SNES Function norm 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.
>
>
>
> *From: *Matthew Knepley <knepley at gmail.com>
> *Date: *Thursday, 2 December 2021 at 10:57
> *To: *"Chockalingam, Karthikeyan (STFC,DL,HC)" <
> karthikeyan.chockalingam at stfc.ac.uk>
> *Cc: *"petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Unstructured mesh
>
>
>
> On Thu, Dec 2, 2021 at 3:33 AM Karthikeyan Chockalingam - STFC UKRI <
> karthikeyan.chockalingam at 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
> solver can run on the GPU, but the vector/matrix
>
> FEM assembly does not. I am working on that now.
>
>
>
>   Thanks,
>
>
>
>      Matt
>
>
>
> Kind regards,
>
> Karthik.
>
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>
> --
>
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
>
>
>
> --
>
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
>
>
>
> --
>
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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