subject:"\[petsc\-users\] dm_view of high\-order geometry\/solution"

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Jed Brown

CGNS supports fourth order and it's coded in PETSc, but Paraview hasn't 
implemented reading it yet. I think it would not be much work for someone 
(maybe you) to add it to Paraview. I have lots of applications on cubics, but 
not much beyond that so it hasn't risen to top priority for me.

There is an accepted extension, but the CGNS implementation is still in a 
branch.

https://cgns.github.io/ProposedExtensions/CPEX0045_HighOrder_v2.pdf
https://github.com/CGNS/CGNS/tree/CPEX45_high_order

There have been recent (announced in a blog post, yet still undocumented) 
extensions to the VTU format that would support this, but the format is so bad 
for parallel IO and time series that I haven't been motivated to extend the 
PETSc writer. Of course we would welcome contributions.

Duan Junming  writes:

> Dear Jed,
>
>
> Thank you for your help!
>
> Now I moved the line using "DMViewFromOptions" after the function 
> "PetscDSSetObjective",
>
> and it works for "-dm_coord_petscspace_degree 3 -petscspace_degree 3".
>
>
> But when I tried degree 4:
>
> ./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
> -dm_coord_space 0 -dm_coord_petscspace_degree 4 -petscspace_degree 4 
> -dm_refine 1 -dm_view cgns:test.cgns
>
> Paraview gives an empty render.
>
>
> Using degree 5:
>
> ./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
> -dm_coord_space 0 -dm_coord_petscspace_degree 5 -petscspace_degree 5 
> -dm_refine 1 -dm_view cgns:test.cgns
>
> it reports:
>
>
> [0]PETSC ERROR: - Error Message 
> --
> [0]PETSC ERROR: No support for this operation for this object type
> [0]PETSC ERROR: Cell type quadrilateral with closure size 36
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.19.2, unknown
> [0]PETSC ERROR: ./ex33 on a arch-darwin-c-debug named 
> JunmingMacBook-Pro.local by Junming Mon Jun 12 20:23:04 2023
> [0]PETSC ERROR: Configure options --download-cgns --download-hdf5 
> --download-openmpi --download-triangle --with-fc=0 
> PETSC_ARCH=arch-darwin-c-debug --download-cgns
> [0]PETSC ERROR: #1 DMPlexCGNSGetPermutation_Internal() at 
> /Users/Junming/Packages/petsc/src/dm/impls/plex/cgns/plexcgns2.c:533
> [0]PETSC ERROR: #2 DMView_PlexCGNS() at 
> /Users/Junming/Packages/petsc/src/dm/impls/plex/cgns/plexcgns2.c:769
> [0]PETSC ERROR: #3 DMView_Plex() at 
> /Users/Junming/Packages/petsc/src/dm/impls/plex/plex.c:1801
> [0]PETSC ERROR: #4 DMView() at 
> /Users/Junming/Packages/petsc/src/dm/interface/dm.c:996
> [0]PETSC ERROR: #5 PetscObjectView() at 
> /Users/Junming/Packages/petsc/src/sys/objects/destroy.c:78
> [0]PETSC ERROR: #6 PetscObjectViewFromOptions() at 
> /Users/Junming/Packages/petsc/src/sys/objects/destroy.c:128
> [0]PETSC ERROR: #7 DMViewFromOptions() at 
> /Users/Junming/Packages/petsc/src/dm/interface/dm.c:940
> [0]PETSC ERROR: #8 CreateDiscretization() at ex33.c:232
> [0]PETSC ERROR: #9 main() at ex33.c:263
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: -dm_coord_petscspace_degree 5 (source: command line)
> [0]PETSC ERROR: -dm_coord_space 0 (source: command line)
> [0]PETSC ERROR: -dm_plex_box_faces 1,1 (source: command line)
> [0]PETSC ERROR: -dm_plex_simplex 0 (source: command line)
> [0]PETSC ERROR: -dm_refine 1 (source: command line)
> [0]PETSC ERROR: -dm_view cgns:test.cgns (source: command line)
> [0]PETSC ERROR: -mesh_transform annulus (source: command line)
> [0]PETSC ERROR: -petscspace_degree 5 (source: command line)
> [0]PETSC ERROR: End of Error Message ---send entire error 
> message to petsc-ma...@mcs.anl.gov--
> --
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
> with errorcode 56.
>
>
> Does cgns work for degree >= 4?
>
>
> Junming
>
>
> 
> From: Jed Brown 
> Sent: Monday, June 12, 2023 19:07
> To: Duan Junming; Matthew Knepley
> Cc: petsc-users@mcs.anl.gov
> Subject: Re: [petsc-users] dm_view of high-order geometry/solution
>
> And here's an MR to do what you want without any code/arg changes.
>
> https://gitlab.com/petsc/petsc/-/merge_requests/6588
>
> Jed Brown  writes:
>
>> Duan Junming  writes:
>>
>>> Dear Jed,
>>>
>>>
>>> Thank you for the suggestion.
>>>
>>> When I run tests/ex33.c with
>>>
>>> ./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
>>> -dm_coord_space 0 -dm_coord_petscspace_degree 3 -dm_refine 1 -dm_

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Duan Junming via petsc-users

Dear Jed,


Thank you for your help!

Now I moved the line using "DMViewFromOptions" after the function 
"PetscDSSetObjective",

and it works for "-dm_coord_petscspace_degree 3 -petscspace_degree 3".


But when I tried degree 4:

./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
-dm_coord_space 0 -dm_coord_petscspace_degree 4 -petscspace_degree 4 -dm_refine 
1 -dm_view cgns:test.cgns

Paraview gives an empty render.


Using degree 5:

./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
-dm_coord_space 0 -dm_coord_petscspace_degree 5 -petscspace_degree 5 -dm_refine 
1 -dm_view cgns:test.cgns

it reports:


[0]PETSC ERROR: - Error Message 
--
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Cell type quadrilateral with closure size 36
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.19.2, unknown
[0]PETSC ERROR: ./ex33 on a arch-darwin-c-debug named JunmingMacBook-Pro.local 
by Junming Mon Jun 12 20:23:04 2023
[0]PETSC ERROR: Configure options --download-cgns --download-hdf5 
--download-openmpi --download-triangle --with-fc=0 
PETSC_ARCH=arch-darwin-c-debug --download-cgns
[0]PETSC ERROR: #1 DMPlexCGNSGetPermutation_Internal() at 
/Users/Junming/Packages/petsc/src/dm/impls/plex/cgns/plexcgns2.c:533
[0]PETSC ERROR: #2 DMView_PlexCGNS() at 
/Users/Junming/Packages/petsc/src/dm/impls/plex/cgns/plexcgns2.c:769
[0]PETSC ERROR: #3 DMView_Plex() at 
/Users/Junming/Packages/petsc/src/dm/impls/plex/plex.c:1801
[0]PETSC ERROR: #4 DMView() at 
/Users/Junming/Packages/petsc/src/dm/interface/dm.c:996
[0]PETSC ERROR: #5 PetscObjectView() at 
/Users/Junming/Packages/petsc/src/sys/objects/destroy.c:78
[0]PETSC ERROR: #6 PetscObjectViewFromOptions() at 
/Users/Junming/Packages/petsc/src/sys/objects/destroy.c:128
[0]PETSC ERROR: #7 DMViewFromOptions() at 
/Users/Junming/Packages/petsc/src/dm/interface/dm.c:940
[0]PETSC ERROR: #8 CreateDiscretization() at ex33.c:232
[0]PETSC ERROR: #9 main() at ex33.c:263
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -dm_coord_petscspace_degree 5 (source: command line)
[0]PETSC ERROR: -dm_coord_space 0 (source: command line)
[0]PETSC ERROR: -dm_plex_box_faces 1,1 (source: command line)
[0]PETSC ERROR: -dm_plex_simplex 0 (source: command line)
[0]PETSC ERROR: -dm_refine 1 (source: command line)
[0]PETSC ERROR: -dm_view cgns:test.cgns (source: command line)
[0]PETSC ERROR: -mesh_transform annulus (source: command line)
[0]PETSC ERROR: -petscspace_degree 5 (source: command line)
[0]PETSC ERROR: End of Error Message ---send entire error 
message to petsc-ma...@mcs.anl.gov--
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
with errorcode 56.


Does cgns work for degree >= 4?


Junming



From: Jed Brown 
Sent: Monday, June 12, 2023 19:07
To: Duan Junming; Matthew Knepley
Cc: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] dm_view of high-order geometry/solution

And here's an MR to do what you want without any code/arg changes.

https://gitlab.com/petsc/petsc/-/merge_requests/6588

Jed Brown  writes:

> Duan Junming  writes:
>
>> Dear Jed,
>>
>>
>> Thank you for the suggestion.
>>
>> When I run tests/ex33.c with
>>
>> ./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
>> -dm_coord_space 0 -dm_coord_petscspace_degree 3 -dm_refine 1 -dm_view 
>> cgns:test.cgns
>>
>> and load it using Paraview,
>>
>> the mesh is still with straight lines.
>
> Ah, the viewer is keyed on the field (since the CGNS as supported by Paraview 
> specifies coordinates and fields in the same space). That doesn't exist in 
> your case. If you apply this patch and add `-petscspace_degre 3` to your 
> command, you'll see that high order information is present. Paraview doesn't 
> render as curves in all views, but it has the data.
>
> diff --git i/src/dm/impls/plex/tests/ex33.c w/src/dm/impls/plex/tests/ex33.c
> index 803095bc082..590facfa4f4 100644
> --- i/src/dm/impls/plex/tests/ex33.c
> +++ w/src/dm/impls/plex/tests/ex33.c
> @@ -198,7 +198,6 @@ PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *ctx, DM 
> *dm)
>default:
>  SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Unknown mesh transform %d", 
> ctx->meshTransform);
>}
> -  PetscCall(DMViewFromOptions(*dm, NULL, "-dm_view"));
>PetscFunctionReturn(PETSC_SUCCESS);
>  }
>
> @@ -227,6 +226,7 @@ static PetscErrorCode CreateDiscretization(DM dm, AppCtx 
> *ctx)
>PetscCall(DMCreateDS(dm));
>PetscCall(DMGetDS(dm, ));
>PetscCall(Petsc

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Jed Brown

And here's an MR to do what you want without any code/arg changes.

https://gitlab.com/petsc/petsc/-/merge_requests/6588

Jed Brown  writes:

> Duan Junming  writes:
>
>> Dear Jed,
>>
>>
>> Thank you for the suggestion.
>>
>> When I run tests/ex33.c with
>>
>> ./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
>> -dm_coord_space 0 -dm_coord_petscspace_degree 3 -dm_refine 1 -dm_view 
>> cgns:test.cgns
>>
>> and load it using Paraview,
>>
>> the mesh is still with straight lines.
>
> Ah, the viewer is keyed on the field (since the CGNS as supported by Paraview 
> specifies coordinates and fields in the same space). That doesn't exist in 
> your case. If you apply this patch and add `-petscspace_degre 3` to your 
> command, you'll see that high order information is present. Paraview doesn't 
> render as curves in all views, but it has the data.
>
> diff --git i/src/dm/impls/plex/tests/ex33.c w/src/dm/impls/plex/tests/ex33.c
> index 803095bc082..590facfa4f4 100644
> --- i/src/dm/impls/plex/tests/ex33.c
> +++ w/src/dm/impls/plex/tests/ex33.c
> @@ -198,7 +198,6 @@ PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *ctx, DM 
> *dm)
>default:
>  SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Unknown mesh transform %d", 
> ctx->meshTransform);
>}
> -  PetscCall(DMViewFromOptions(*dm, NULL, "-dm_view"));
>PetscFunctionReturn(PETSC_SUCCESS);
>  }
>  
> @@ -227,6 +226,7 @@ static PetscErrorCode CreateDiscretization(DM dm, AppCtx 
> *ctx)
>PetscCall(DMCreateDS(dm));
>PetscCall(DMGetDS(dm, ));
>PetscCall(PetscDSSetObjective(ds, 0, volume));
> +  PetscCall(DMViewFromOptions(dm, NULL, "-dm_view"));
>PetscFunctionReturn(PETSC_SUCCESS);
>  }
>  
>
> I can update the viewer to handle the degenerate case of no field (all my 
> models have fields).

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Jed Brown

Duan Junming  writes:

> Dear Jed,
>
>
> Thank you for the suggestion.
>
> When I run tests/ex33.c with
>
> ./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
> -dm_coord_space 0 -dm_coord_petscspace_degree 3 -dm_refine 1 -dm_view 
> cgns:test.cgns
>
> and load it using Paraview,
>
> the mesh is still with straight lines.

Ah, the viewer is keyed on the field (since the CGNS as supported by Paraview 
specifies coordinates and fields in the same space). That doesn't exist in your 
case. If you apply this patch and add `-petscspace_degre 3` to your command, 
you'll see that high order information is present. Paraview doesn't render as 
curves in all views, but it has the data.

diff --git i/src/dm/impls/plex/tests/ex33.c w/src/dm/impls/plex/tests/ex33.c
index 803095bc082..590facfa4f4 100644
--- i/src/dm/impls/plex/tests/ex33.c
+++ w/src/dm/impls/plex/tests/ex33.c
@@ -198,7 +198,6 @@ PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *ctx, DM 
*dm)
   default:
 SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Unknown mesh transform %d", 
ctx->meshTransform);
   }
-  PetscCall(DMViewFromOptions(*dm, NULL, "-dm_view"));
   PetscFunctionReturn(PETSC_SUCCESS);
 }

@@ -227,6 +226,7 @@ static PetscErrorCode CreateDiscretization(DM dm, AppCtx 
*ctx)
   PetscCall(DMCreateDS(dm));
   PetscCall(DMGetDS(dm, ));
   PetscCall(PetscDSSetObjective(ds, 0, volume));
+  PetscCall(DMViewFromOptions(dm, NULL, "-dm_view"));
   PetscFunctionReturn(PETSC_SUCCESS);
 }

I can update the viewer to handle the degenerate case of no field (all my 
models have fields).

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Duan Junming via petsc-users

Dear Jed,

Thank you for the suggestion.

When I run tests/ex33.c with

./ex33 -dm_plex_simplex 0 -dm_plex_box_faces 1,1 -mesh_transform annulus 
-dm_coord_space 0 -dm_coord_petscspace_degree 3 -dm_refine 1 -dm_view 
cgns:test.cgns

and load it using Paraview,

the mesh is still with straight lines.

Should I modify the code to make cgns work? Or any other examples for me to 
start?

Thanks!

Junming

From: Jed Brown 
Sent: Monday, June 12, 2023 2:52:48 PM
To: Matthew Knepley; Duan Junming
Cc: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] dm_view of high-order geometry/solution

Matthew Knepley  writes:

> On Mon, Jun 12, 2023 at 6:01 AM Duan Junming  wrote:
>
>> Dear Matt,
>>
>> Thank you for the reply. I have a more specific question about the
>> spectral element example. Do you have any suggestions that how to write
>> all the nodes in each cell to .vtu?
>>
> It is the same procedure. VTU is not a great format for this. It wants
> everything at first order.

I would recommend configuring with --download-cgns and running with -dm_view 
cgns:output.cgns. This format has efficient parallel IO and curved elements 
work for moderate order in Paraview.

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Jed Brown

Matthew Knepley  writes:

> On Mon, Jun 12, 2023 at 6:01 AM Duan Junming  wrote:
>
>> Dear Matt,
>>
>> Thank you for the reply. I have a more specific question about the
>> spectral element example. Do you have any suggestions that how to write
>> all the nodes in each cell to .vtu?
>>
> It is the same procedure. VTU is not a great format for this. It wants
> everything at first order.

I would recommend configuring with --download-cgns and running with -dm_view 
cgns:output.cgns. This format has efficient parallel IO and curved elements 
work for moderate order in Paraview.

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Matthew Knepley

On Mon, Jun 12, 2023 at 6:01 AM Duan Junming  wrote:

> Dear Matt,
>
> Thank you for the reply. I have a more specific question about the
> spectral element example. Do you have any suggestions that how to write
> all the nodes in each cell to .vtu?
>
It is the same procedure. VTU is not a great format for this. It wants
everything at first order.

  Thanks,

Matt

> Thanks!
>
> Junming
> --
> *From:* knep...@gmail.com 
> *Sent:* Monday, June 12, 2023 1:34:24 PM
> *To:* Duan Junming
> *Cc:* petsc-users@mcs.anl.gov
> *Subject:* Re: [petsc-users] dm_view of high-order geometry/solution
>
> On Mon, Jun 12, 2023 at 4:13 AM Duan Junming via petsc-users <
> petsc-users@mcs.anl.gov> wrote:
>
>> Dear all,
>>
>>
>> I am playing with dm/impls/plex/tests/ex33.c and know how to set
>> high-order geometry.
>>
>> Is it possible to output the final mesh to vtu, e.g. annulus example?
>>
>
> The problem is that VTK has no nice, standard way to talk about higher
> order polynomials. Thus, the
> best way to do this is to call DMRefine() once or twice and output that
> mesh.
>
>   Thanks,
>
> Matt
>
>
>> Thanks!
>>
>> Junming
>>
>>
>
> --
> 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/>

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Duan Junming via petsc-users

Dear Matt,


Thank you for the reply. I have a more specific question about the spectral 
element example. Do you have any suggestions that how to write all the nodes in 
each cell to .vtu?


Thanks!

Junming


From: knep...@gmail.com 
Sent: Monday, June 12, 2023 1:34:24 PM
To: Duan Junming
Cc: petsc-users@mcs.anl.gov
Subject: Re: [petsc-users] dm_view of high-order geometry/solution

On Mon, Jun 12, 2023 at 4:13 AM Duan Junming via petsc-users 
mailto:petsc-users@mcs.anl.gov>> wrote:

Dear all,


I am playing with dm/impls/plex/tests/ex33.c and know how to set high-order 
geometry.

Is it possible to output the final mesh to vtu, e.g. annulus example?

The problem is that VTK has no nice, standard way to talk about higher order 
polynomials. Thus, the
best way to do this is to call DMRefine() once or twice and output that mesh.

  Thanks,

Matt


Thanks!

Junming


--
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/>

Re: [petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Matthew Knepley

On Mon, Jun 12, 2023 at 4:13 AM Duan Junming via petsc-users <
petsc-users@mcs.anl.gov> wrote:

> Dear all,
>
>
> I am playing with dm/impls/plex/tests/ex33.c and know how to set
> high-order geometry.
>
> Is it possible to output the final mesh to vtu, e.g. annulus example?
>

The problem is that VTK has no nice, standard way to talk about higher
order polynomials. Thus, the
best way to do this is to call DMRefine() once or twice and output that
mesh.

  Thanks,

Matt

> Thanks!
>
> Junming
>
>

-- 
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/

[petsc-users] dm_view of high-order geometry/solution

2023-06-12 Thread Duan Junming via petsc-users

Dear all,


I am playing with dm/impls/plex/tests/ex33.c and know how to set high-order 
geometry.

Is it possible to output the final mesh to vtu, e.g. annulus example?


Thanks!

Junming

Re: [petsc-users] dm_view of high-order geometry/solution

Re: [petsc-users] dm_view of high-order geometry/solution

Re: [petsc-users] dm_view of high-order geometry/solution

Re: [petsc-users] dm_view of high-order geometry/solution

Re: [petsc-users] dm_view of high-order geometry/solution

Re: [petsc-users] dm_view of high-order geometry/solution

Re: [petsc-users] dm_view of high-order geometry/solution

Re: [petsc-users] dm_view of high-order geometry/solution

Re: [petsc-users] dm_view of high-order geometry/solution

[petsc-users] dm_view of high-order geometry/solution

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