libmesh-users — General information for libmesh users

Re: [Libmesh-users] Defining hanging nodes in the XDA format

[Paul T. B. <ptb...@gm...>]

I'm not sure I'm following (a picture is worth a thousand words here), but
it sounds like you're trying to create a child of a quad by only splitting
in one direction and not both?

On Tue, Jan 23, 2018 at 7:22 PM, Salazar De Troya, Miguel <
sal...@ll...> wrote:

> Hello,
>
> I have the mesh attached below. It is the result of having three
> quadrangular elements in line, refine the left and right ones, then on
> their leftmost and rightmost children, do another refinement. After this, I
> flattened out the mesh and removed the leftmost and rightmost layer of
> elements. The issue is that I’ve got hanging nodes that libmesh does not
> recognize. Is there any way to find them or tell libMesh which ones they
> are?
>
> Is there an alternative way to generate a similar mesh? I was not able to
> remove the leftmost and rightmost children without flattening the mesh
> first. It seems as if each parent element must have four elements.
>
> Thanks
> Miguel
>
> libMesh-1.3.0
> 13           # number of elements
> 26           # number of nodes
> n/a         # boundary condition specification file
> .               # subdomain id specification file
> n/a         # processor id specification file
> n/a         # p-level specification file
> 8              # type size
> 0              # uid size
> 0              # pid size
> 8              # sid size
> 0              # p-level size
> 0              # eid size
> 0              # side size
> 0              # bid size
> 0              # subdomain id to name map
> 13           # n_elem at level 0, [ type sid (n0 ... nN-1) ]
> 5 0 0 1 2 3
> 5 0 4 0 5 6
> 5 0 6 5 3 7
> 5 0 1 8 9 10
> 5 0 10 9 11 2
> 5 0 12 4 13 14
> 5 0 14 13 6 15
> 5 0 15 6 16 17
> 5 0 17 16 7 18
> 5 0 8 19 20 21
> 5 0 21 20 22 9
> 5 0 9 22 23 24
> 5 0 24 23 25 11
> 5.0000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
> 1.0000000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
> 1.0000000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
> 5.0000000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
> 2.5000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
> 5.0000000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
> 2.5000000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
> 2.5000000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
> 1.2500000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
> 1.0000000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
> 2.5000000000000000e+01 1.2500000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+01 1.2500000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
> 2.5000000000000000e+01 3.7500000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+01 3.7500000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
> 1.3750000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
> 1.3750000000000000e+02 1.2500000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+02 1.2500000000000000e+01 0.0000000000000000e+00
> 1.3750000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
> 1.3750000000000000e+02 3.7500000000000000e+01 0.0000000000000000e+00
> 1.2500000000000000e+02 3.7500000000000000e+01 0.0000000000000000e+00
> 1.3750000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
> 0              # presence of unique ids
> 0              # sideset id to name map
> 0              # number of side boundary conditions
> 0              # nodeset id to name map
> 0              # number of nodesets
> 0              # sideset id to name map
> 0              # number of edge boundary conditions
> 0              # sideset id to name map
> 0              # number of shellface boundary conditions
>
>
> --
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

Re: [Libmesh-users] question about the numeric vector

[Paul T. B. <ptb...@gm...>]

Sorry for slow response. I have nothing better to offer other than 3
vectors, but maybe others will.

On Mon, Jan 22, 2018 at 12:40 PM, Michael Povolotskyi <mpo...@pu...>
wrote:

> Dear Libmesh developers and users,
>
> I need to compute a field on mesh based on a solution.
>
> To do so I usually add a vector to a system and fill it with data.
>
> This works perfectly for a scalar field.
>
> What would you recommend to do for a vector field.
>
> Of course, I can add 3 vectors, one for each component of the field. Is
> there a better way?
>
> Thank you,
>
> Michael.
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

Re: [Libmesh-users] Best mesh format for writing and reading in parallel

[Paul T. B. <ptb...@gm...>]

Others can and should chime in, but I believe CheckpointIO will allow this.
My only uncertainty is on whether is supports AMR meshes or not, but I
think it does. Beware we're not guaranteeing backward compatibility with it
yet, so please watch for potential changes in the future if you do use it.

HTH,

Paul

On Wed, Jan 24, 2018 at 6:03 PM, Salazar De Troya, Miguel <
sal...@ll...> wrote:

> Hi,
>
> Basically, the question in the title. XDA/XDR do not work for distributed
> meshes in parallel. What is the best alternative? I have a big mesh result
> of an AMR, I want to write it to file and then read it again to use it in a
> posterior simulation.
>
> Thanks
> Miguel
>
> --
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

[Libmesh-users] Best mesh format for writing and reading in parallel

[Salazar De T. M. <sal...@ll...>]

Hi,

Basically, the question in the title. XDA/XDR do not work for distributed meshes in parallel. What is the best alternative? I have a big mesh result of an AMR, I want to write it to file and then read it again to use it in a posterior simulation.

Thanks
Miguel

--

[Libmesh-users] Defining hanging nodes in the XDA format

[Salazar De T. M. <sal...@ll...>]

Hello,

I have the mesh attached below. It is the result of having three quadrangular elements in line, refine the left and right ones, then on their leftmost and rightmost children, do another refinement. After this, I flattened out the mesh and removed the leftmost and rightmost layer of elements. The issue is that I’ve got hanging nodes that libmesh does not recognize. Is there any way to find them or tell libMesh which ones they are?

Is there an alternative way to generate a similar mesh? I was not able to remove the leftmost and rightmost children without flattening the mesh first. It seems as if each parent element must have four elements.

Thanks
Miguel

libMesh-1.3.0
13           # number of elements
26           # number of nodes
n/a         # boundary condition specification file
.               # subdomain id specification file
n/a         # processor id specification file
n/a         # p-level specification file
8              # type size
0              # uid size
0              # pid size
8              # sid size
0              # p-level size
0              # eid size
0              # side size
0              # bid size
0              # subdomain id to name map
13           # n_elem at level 0, [ type sid (n0 ... nN-1) ]
5 0 0 1 2 3
5 0 4 0 5 6
5 0 6 5 3 7
5 0 1 8 9 10
5 0 10 9 11 2
5 0 12 4 13 14
5 0 14 13 6 15
5 0 15 6 16 17
5 0 17 16 7 18
5 0 8 19 20 21
5 0 21 20 22 9
5 0 9 22 23 24
5 0 24 23 25 11
5.0000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
1.0000000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.0000000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
5.0000000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
2.5000000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
5.0000000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
2.5000000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
2.5000000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.2500000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
1.0000000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 0.0000000000000000e+00 0.0000000000000000e+00
2.5000000000000000e+01 1.2500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 1.2500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 2.5000000000000000e+01 0.0000000000000000e+00
2.5000000000000000e+01 3.7500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 3.7500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+01 5.0000000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 0.0000000000000000e+00 0.0000000000000000e+00
1.3750000000000000e+02 1.2500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 1.2500000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 2.5000000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 3.7500000000000000e+01 0.0000000000000000e+00
1.2500000000000000e+02 3.7500000000000000e+01 0.0000000000000000e+00
1.3750000000000000e+02 5.0000000000000000e+01 0.0000000000000000e+00
0              # presence of unique ids
0              # sideset id to name map
0              # number of side boundary conditions
0              # nodeset id to name map
0              # number of nodesets
0              # sideset id to name map
0              # number of edge boundary conditions
0              # sideset id to name map
0              # number of shellface boundary conditions


--

Re: [Libmesh-users] [Libmesh-devel] Example fem_system_ex2 failing to run

[Paul T. B. <ptb...@gm...>]

OK, I'll try and push a PR before the end of today.

On Mon, Jan 22, 2018 at 2:54 PM, Roy Stogner <roy...@ic...>
wrote:

>
> On Mon, 22 Jan 2018, Paul T. Bauman wrote:
>
> John: Should I go ahead and change that one to XFAIL? I'm not sure
>> it will cause less confusion for users, but it would permit a
>> blanket `make check`. Downside is it won't show up as a failure on
>> CIVET testing.
>>
>
> That's an extremely good idea.
>
> We can change it back to PASS/FAIL after an actual fix is in.
>
> Sorry about the delay.
> ---
> Roy
>

Re: [Libmesh-users] [Libmesh-devel] Example fem_system_ex2 failing to run

[Roy S. <roy...@ic...>]

On Mon, 22 Jan 2018, Paul T. Bauman wrote:

> John: Should I go ahead and change that one to XFAIL? I'm not sure
> it will cause less confusion for users, but it would permit a
> blanket `make check`. Downside is it won't show up as a failure on
> CIVET testing.

That's an extremely good idea.

We can change it back to PASS/FAIL after an actual fix is in.

Sorry about the delay.
---
Roy

Re: [Libmesh-users] Example fem_system_ex2 failing to run

[Paul T. B. <ptb...@gm...>]

Two strategies:

1. Don't configure with VTK (that test depends on VTK and won't run if you
haven't configured with VTK)
2. You can run make check in the subdirectories directly and bypass that
example, using a shell script, for example.

John: Should I go ahead and change that one to XFAIL? I'm not sure it will
cause less confusion for users, but it would permit a blanket `make check`.
Downside is it won't show up as a failure on CIVET testing.

On Mon, Jan 22, 2018 at 12:42 PM, Daniel Vasconcelos <
dan...@ou...> wrote:

> Thank you for the quick reply, I appreciate it.
>
> Is there a way to run the make check command and skip this example?
>
> Regards,
>
> Daniel F. M. Vasconcelos.
>
>
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
> From: John Peterson<mailto:jwp...@gm...>
> Sent: Monday, January 22, 2018 15:38
> To: Daniel Vasconcelos<mailto:dan...@ou...>
> Cc: libmesh-users<mailto:lib...@li...>;
> libmesh-devel<mailto:lib...@li...>
> Subject: Re: [Libmesh-users] Example fem_system_ex2 failing to run
>
>
>
> On Mon, Jan 22, 2018 at 10:35 AM, Daniel Vasconcelos <
> dan...@ou...<mailto:dan...@ou...>> wrote:
> Sorry, I have forgotten to include the actual libMesh configuration log.
>
> Once again. thanks in advance.
>
> Daniel F. M. Vasconcelos.
>
> 2018-01-22 15:28 GMT-02:00 Daniel Vasconcelos <dan...@ou...<
> mailto:dan...@ou...><mailto:dan...@ou...<mailto:
> dan...@ou...>>>:
> Dear libMesh users,
>
> Currently I am with problems when running example fem_system_ex2.
> MPI_ABORT is invoked in step 1 right after assembling the system (see
> attached file).
>
> Below is the setup I am using:
>
>   *   CPU: Intel i7
>   *   Oracle Virtual Box 5.2.6 r120293
>   *   Host system: Windows 10
>   *   Guest system: Linux Mint 18.3 Mate
>      *   Cloned libMesh master branch as per 01-21-2018
>      *   All libMesh optional libraries installed using apt-get (VTK,
> openMPI, PETSc, HDF5, …)
>
> I have also attached the libMesh configuration log and the fem_system_ex2
> traceout file.
>
> Thanks, we are aware of the issue, but not sure what the right fix is yet.
>
> (https://github.com/libMesh/libmesh/issues/1559<https://
> nam01.safelinks.protection.outlook.com/?url=https%3A%2F%
> 2Fgithub.com%2FlibMesh%2Flibmesh%2Fissues%2F1559&data=02%7C01%7C%
> 7C4f2c2890c38d4b31d54c08d561bf00ce%7C84df9e7fe9f640afb435aaaaaaaa
> aaaa%7C1%7C0%7C636522395328398299&sdata=eTEd2aYe3xE23iCBlf%
> 2FVhUAuZh9wIxYyFwOtLUPXF7s%3D&reserved=0>)
>
> --
> John
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

Re: [Libmesh-users] Example fem_system_ex2 failing to run

[Daniel V. <dan...@ou...>]

Thank you for the quick reply, I appreciate it.

Is there a way to run the make check command and skip this example?

Regards,

Daniel F. M. Vasconcelos.



Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: John Peterson<mailto:jwp...@gm...>
Sent: Monday, January 22, 2018 15:38
To: Daniel Vasconcelos<mailto:dan...@ou...>
Cc: libmesh-users<mailto:lib...@li...>; libmesh-devel<mailto:lib...@li...>
Subject: Re: [Libmesh-users] Example fem_system_ex2 failing to run



On Mon, Jan 22, 2018 at 10:35 AM, Daniel Vasconcelos <dan...@ou...<mailto:dan...@ou...>> wrote:
Sorry, I have forgotten to include the actual libMesh configuration log.

Once again. thanks in advance.

Daniel F. M. Vasconcelos.

2018-01-22 15:28 GMT-02:00 Daniel Vasconcelos <dan...@ou...<mailto:dan...@ou...><mailto:dan...@ou...<mailto:dan...@ou...>>>:
Dear libMesh users,

Currently I am with problems when running example fem_system_ex2. MPI_ABORT is invoked in step 1 right after assembling the system (see attached file).

Below is the setup I am using:

  *   CPU: Intel i7
  *   Oracle Virtual Box 5.2.6 r120293
  *   Host system: Windows 10
  *   Guest system: Linux Mint 18.3 Mate
     *   Cloned libMesh master branch as per 01-21-2018
     *   All libMesh optional libraries installed using apt-get (VTK, openMPI, PETSc, HDF5, …)

I have also attached the libMesh configuration log and the fem_system_ex2 traceout file.

Thanks, we are aware of the issue, but not sure what the right fix is yet.

(https://github.com/libMesh/libmesh/issues/1559<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FlibMesh%2Flibmesh%2Fissues%2F1559&data=02%7C01%7C%7C4f2c2890c38d4b31d54c08d561bf00ce%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636522395328398299&sdata=eTEd2aYe3xE23iCBlf%2FVhUAuZh9wIxYyFwOtLUPXF7s%3D&reserved=0>)

--
John

[Libmesh-users] question about the numeric vector

[Michael P. <mpo...@pu...>]

Dear Libmesh developers and users,

I need to compute a field on mesh based on a solution.

To do so I usually add a vector to a system and fill it with data.

This works perfectly for a scalar field.

What would you recommend to do for a vector field.

Of course, I can add 3 vectors, one for each component of the field. Is 
there a better way?

Thank you,

Michael.

Re: [Libmesh-users] Example fem_system_ex2 failing to run

[John P. <jwp...@gm...>]

On Mon, Jan 22, 2018 at 10:35 AM, Daniel Vasconcelos <
dan...@ou...> wrote:

> Sorry, I have forgotten to include the actual libMesh configuration log.
>
> Once again. thanks in advance.
>
> Daniel F. M. Vasconcelos.
>
> 2018-01-22 15:28 GMT-02:00 Daniel Vasconcelos <dan...@ou...<
> mailto:dan...@ou...>>:
> Dear libMesh users,
>
> Currently I am with problems when running example fem_system_ex2.
> MPI_ABORT is invoked in step 1 right after assembling the system (see
> attached file).
>
> Below is the setup I am using:
>
>   *   CPU: Intel i7
>   *   Oracle Virtual Box 5.2.6 r120293
>   *   Host system: Windows 10
>   *   Guest system: Linux Mint 18.3 Mate
>      *   Cloned libMesh master branch as per 01-21-2018
>      *   All libMesh optional libraries installed using apt-get (VTK,
> openMPI, PETSc, HDF5, …)
>
> I have also attached the libMesh configuration log and the fem_system_ex2
> traceout file.
>

Thanks, we are aware of the issue, but not sure what the right fix is yet.

(https://github.com/libMesh/libmesh/issues/1559)

-- 
John

Re: [Libmesh-users] Example fem_system_ex2 failing to run

[Paul T. B. <ptb...@gm...>]

Unfortunately, this is a known problem. Discussion here:
https://github.com/libMesh/libmesh/issues/1559

TL; DR: Has to do with doing reinit on a single System (as opposed to all
Systems as once). If you're not doing that, then you should be OK.

HTH,

Paul

On Mon, Jan 22, 2018 at 12:35 PM, Daniel Vasconcelos <
dan...@ou...> wrote:

> Sorry, I have forgotten to include the actual libMesh configuration log.
>
> Once again. thanks in advance.
>
> Daniel F. M. Vasconcelos.
>
> 2018-01-22 15:28 GMT-02:00 Daniel Vasconcelos <dan...@ou...<
> mailto:dan...@ou...>>:
> Dear libMesh users,
>
> Currently I am with problems when running example fem_system_ex2.
> MPI_ABORT is invoked in step 1 right after assembling the system (see
> attached file).
>
> Below is the setup I am using:
>
>   *   CPU: Intel i7
>   *   Oracle Virtual Box 5.2.6 r120293
>   *   Host system: Windows 10
>   *   Guest system: Linux Mint 18.3 Mate
>      *   Cloned libMesh master branch as per 01-21-2018
>      *   All libMesh optional libraries installed using apt-get (VTK,
> openMPI, PETSc, HDF5, …)
>
> I have also attached the libMesh configuration log and the fem_system_ex2
> traceout file.
>
> Thanks in advance
>
> Daniel F. M. Vasconcelos.
>
>
> Sent from Mail<https://eur02.safelinks.protection.outlook.com/?url=
> https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%
> 3D550986&data=02%7C01%7C%7C0e43d093590a4547252308d561bd8630%
> 7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636522388979942063&sdata=
> EhkdQ8CgY0oLi0wcajY4MIyWyXVv3dp4jetbpOUlwGg%3D&reserved=0> for Windows 10
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

Re: [Libmesh-users] Example fem_system_ex2 failing to run

[Daniel V. <dan...@ou...>]

Sorry, I have forgotten to include the actual libMesh configuration log.

Once again. thanks in advance.

Daniel F. M. Vasconcelos.

2018-01-22 15:28 GMT-02:00 Daniel Vasconcelos <dan...@ou...<mailto:dan...@ou...>>:
Dear libMesh users,

Currently I am with problems when running example fem_system_ex2. MPI_ABORT is invoked in step 1 right after assembling the system (see attached file).

Below is the setup I am using:

  *   CPU: Intel i7
  *   Oracle Virtual Box 5.2.6 r120293
  *   Host system: Windows 10
  *   Guest system: Linux Mint 18.3 Mate
     *   Cloned libMesh master branch as per 01-21-2018
     *   All libMesh optional libraries installed using apt-get (VTK, openMPI, PETSc, HDF5, …)

I have also attached the libMesh configuration log and the fem_system_ex2 traceout file.

Thanks in advance

Daniel F. M. Vasconcelos.


Sent from Mail<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986&data=02%7C01%7C%7C0e43d093590a4547252308d561bd8630%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636522388979942063&sdata=EhkdQ8CgY0oLi0wcajY4MIyWyXVv3dp4jetbpOUlwGg%3D&reserved=0> for Windows 10

[Libmesh-users] Example fem_system_ex2 failing to run

[Daniel V. <dan...@ou...>]

Dear libMesh users,

Currently I am with problems when running example fem_system_ex2. MPI_ABORT is invoked in step 1 right after assembling the system (see attached file).

Below is the setup I am using:

  *   CPU: Intel i7
  *   Oracle Virtual Box 5.2.6 r120293
  *   Host system: Windows 10
  *   Guest system: Linux Mint 18.3 Mate
     *   Cloned libMesh master branch as per 01-21-2018
     *   All libMesh optional libraries installed using apt-get (VTK, openMPI, PETSc, HDF5, …)

I have also attached the libMesh configuration log and the fem_system_ex2 traceout file.

Thanks in advance

Daniel F. M. Vasconcelos.


Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

Re: [Libmesh-users] Using gzstream from an app

[David K. <dav...@ak...>]

On Thu, Jan 18, 2018 at 8:53 PM, John Peterson <jwp...@gm...> wrote:

> I think you’ll need to run bootstrap at the top level and also commit
> those changes. Or you can wait for one of us to do it...
>

OK, I just did that.

David



>
> On Jan 18, 2018, at 6:07 PM, David Knezevic <dav...@ak...>
> wrote:
>
> On Thu, Jan 18, 2018 at 5:58 PM, John Peterson <jwp...@gm...>
> wrote:
>
>>
>>
>> On Thu, Jan 18, 2018 at 3:52 PM, Roy Stogner <roy...@ic...>
>> wrote:
>>
>>>
>>> On Thu, 18 Jan 2018, John Peterson wrote:
>>>
>>> On Thu, Jan 18, 2018 at 2:07 PM, David Knezevic <
>>>> dav...@ak...>
>>>> wrote:
>>>>
>>>> I configured with gzstream support, and I'd like to use this from an
>>>>> app.
>>>>> To do that I've copied gzstream.h to the app directory, and then it
>>>>> works,
>>>>> but I was wondering if it's possible to use libMesh's copy of
>>>>> gzstream.h
>>>>> directly? I guess not since it's not copied into the installed
>>>>> directory,
>>>>> is that right?
>>>>>
>>>>> Anyway, any suggestions on the cleanest way to handle this would be
>>>>> appreciated.
>>>>>
>>>>>
>>>> It looks like it would be as simple as adding the gzstream.h header to
>>>> the
>>>> list of files that get installed by the build system?
>>>>
>>>> I think this can be done by adding
>>>>
>>>> nobase_include_HEADERS = gzstream.h
>>>>
>>>> (see also the boost and Eigen Makefile.am files in contrib) to the
>>>> Makefile.am in contrib/gzstream and rebootstrapping, but I'm not an
>>>> automake expert by any means :-)
>>>>
>>>
>>> That's about it.
>>>
>>> Did we avoid installing it because we were worried about collisions
>>> for users with a system gzstream.h installed, though?
>>>
>>
>> I don't think it was actively avoided for any reason. As a rule we
>> generally didn't install contrib headers that weren't included by our
>> headers...
>>
>
>
> The change you suggested works for me, thanks! I just made a PR with this
> one line change.
>
> David
>
>
>

Re: [Libmesh-users] Using gzstream from an app

[John P. <jwp...@gm...>]

I think you’ll need to run bootstrap at the top level and also commit those changes. Or you can wait for one of us to do it...

> On Jan 18, 2018, at 6:07 PM, David Knezevic <dav...@ak...> wrote:
> 
>> On Thu, Jan 18, 2018 at 5:58 PM, John Peterson <jwp...@gm...> wrote:
>> 
>> 
>>> On Thu, Jan 18, 2018 at 3:52 PM, Roy Stogner <roy...@ic...> wrote:
>>> 
>>> On Thu, 18 Jan 2018, John Peterson wrote:
>>> 
>>>> On Thu, Jan 18, 2018 at 2:07 PM, David Knezevic <dav...@ak...>
>>>> wrote:
>>>> 
>>>>> I configured with gzstream support, and I'd like to use this from an app.
>>>>> To do that I've copied gzstream.h to the app directory, and then it works,
>>>>> but I was wondering if it's possible to use libMesh's copy of gzstream.h
>>>>> directly? I guess not since it's not copied into the installed directory,
>>>>> is that right?
>>>>> 
>>>>> Anyway, any suggestions on the cleanest way to handle this would be
>>>>> appreciated.
>>>>> 
>>>> 
>>>> It looks like it would be as simple as adding the gzstream.h header to the
>>>> list of files that get installed by the build system?
>>>> 
>>>> I think this can be done by adding
>>>> 
>>>> nobase_include_HEADERS = gzstream.h
>>>> 
>>>> (see also the boost and Eigen Makefile.am files in contrib) to the
>>>> Makefile.am in contrib/gzstream and rebootstrapping, but I'm not an
>>>> automake expert by any means :-)
>>> 
>>> That's about it.
>>> 
>>> Did we avoid installing it because we were worried about collisions
>>> for users with a system gzstream.h installed, though?
>> 
>> I don't think it was actively avoided for any reason. As a rule we generally didn't install contrib headers that weren't included by our headers...
> 
> 
> The change you suggested works for me, thanks! I just made a PR with this one line change.
> 
> David
> 
> 

Re: [Libmesh-users] Using gzstream from an app

[David K. <dav...@ak...>]

On Thu, Jan 18, 2018 at 5:58 PM, John Peterson <jwp...@gm...> wrote:

>
>
> On Thu, Jan 18, 2018 at 3:52 PM, Roy Stogner <roy...@ic...>
> wrote:
>
>>
>> On Thu, 18 Jan 2018, John Peterson wrote:
>>
>> On Thu, Jan 18, 2018 at 2:07 PM, David Knezevic <
>>> dav...@ak...>
>>> wrote:
>>>
>>> I configured with gzstream support, and I'd like to use this from an app.
>>>> To do that I've copied gzstream.h to the app directory, and then it
>>>> works,
>>>> but I was wondering if it's possible to use libMesh's copy of gzstream.h
>>>> directly? I guess not since it's not copied into the installed
>>>> directory,
>>>> is that right?
>>>>
>>>> Anyway, any suggestions on the cleanest way to handle this would be
>>>> appreciated.
>>>>
>>>>
>>> It looks like it would be as simple as adding the gzstream.h header to
>>> the
>>> list of files that get installed by the build system?
>>>
>>> I think this can be done by adding
>>>
>>> nobase_include_HEADERS = gzstream.h
>>>
>>> (see also the boost and Eigen Makefile.am files in contrib) to the
>>> Makefile.am in contrib/gzstream and rebootstrapping, but I'm not an
>>> automake expert by any means :-)
>>>
>>
>> That's about it.
>>
>> Did we avoid installing it because we were worried about collisions
>> for users with a system gzstream.h installed, though?
>>
>
> I don't think it was actively avoided for any reason. As a rule we
> generally didn't install contrib headers that weren't included by our
> headers...
>


The change you suggested works for me, thanks! I just made a PR with this
one line change.

David

Re: [Libmesh-users] Using gzstream from an app

[John P. <jwp...@gm...>]

On Thu, Jan 18, 2018 at 3:52 PM, Roy Stogner <roy...@ic...>
wrote:

>
> On Thu, 18 Jan 2018, John Peterson wrote:
>
> On Thu, Jan 18, 2018 at 2:07 PM, David Knezevic <
>> dav...@ak...>
>> wrote:
>>
>> I configured with gzstream support, and I'd like to use this from an app.
>>> To do that I've copied gzstream.h to the app directory, and then it
>>> works,
>>> but I was wondering if it's possible to use libMesh's copy of gzstream.h
>>> directly? I guess not since it's not copied into the installed directory,
>>> is that right?
>>>
>>> Anyway, any suggestions on the cleanest way to handle this would be
>>> appreciated.
>>>
>>>
>> It looks like it would be as simple as adding the gzstream.h header to the
>> list of files that get installed by the build system?
>>
>> I think this can be done by adding
>>
>> nobase_include_HEADERS = gzstream.h
>>
>> (see also the boost and Eigen Makefile.am files in contrib) to the
>> Makefile.am in contrib/gzstream and rebootstrapping, but I'm not an
>> automake expert by any means :-)
>>
>
> That's about it.
>
> Did we avoid installing it because we were worried about collisions
> for users with a system gzstream.h installed, though?
>

I don't think it was actively avoided for any reason. As a rule we
generally didn't install contrib headers that weren't included by our
headers...

-- 
John

Re: [Libmesh-users] Using gzstream from an app

[Roy S. <roy...@ic...>]

On Thu, 18 Jan 2018, John Peterson wrote:

> On Thu, Jan 18, 2018 at 2:07 PM, David Knezevic <dav...@ak...>
> wrote:
>
>> I configured with gzstream support, and I'd like to use this from an app.
>> To do that I've copied gzstream.h to the app directory, and then it works,
>> but I was wondering if it's possible to use libMesh's copy of gzstream.h
>> directly? I guess not since it's not copied into the installed directory,
>> is that right?
>>
>> Anyway, any suggestions on the cleanest way to handle this would be
>> appreciated.
>>
>
> It looks like it would be as simple as adding the gzstream.h header to the
> list of files that get installed by the build system?
>
> I think this can be done by adding
>
> nobase_include_HEADERS = gzstream.h
>
> (see also the boost and Eigen Makefile.am files in contrib) to the
> Makefile.am in contrib/gzstream and rebootstrapping, but I'm not an
> automake expert by any means :-)

That's about it.

Did we avoid installing it because we were worried about collisions
for users with a system gzstream.h installed, though?
---
Roy

Re: [Libmesh-users] Using gzstream from an app

[John P. <jwp...@gm...>]

On Thu, Jan 18, 2018 at 2:07 PM, David Knezevic <dav...@ak...>
wrote:

> I configured with gzstream support, and I'd like to use this from an app.
> To do that I've copied gzstream.h to the app directory, and then it works,
> but I was wondering if it's possible to use libMesh's copy of gzstream.h
> directly? I guess not since it's not copied into the installed directory,
> is that right?
>
> Anyway, any suggestions on the cleanest way to handle this would be
> appreciated.
>

It looks like it would be as simple as adding the gzstream.h header to the
list of files that get installed by the build system?

I think this can be done by adding

nobase_include_HEADERS = gzstream.h

(see also the boost and Eigen Makefile.am files in contrib) to the
Makefile.am in contrib/gzstream and rebootstrapping, but I'm not an
automake expert by any means :-)

-- 
John

[Libmesh-users] Using gzstream from an app

[David K. <dav...@ak...>]

I configured with gzstream support, and I'd like to use this from an app.
To do that I've copied gzstream.h to the app directory, and then it works,
but I was wondering if it's possible to use libMesh's copy of gzstream.h
directly? I guess not since it's not copied into the installed directory,
is that right?

Anyway, any suggestions on the cleanest way to handle this would be
appreciated.

Thanks,
David

Re: [Libmesh-users] Question regarding imposition of non-zero Dirichlet conditions in RB

[David K. <dav...@ak...>]

Hello,

The key point here is that if you check the literature on reduced basis
methods you'll see that you should not impose non-zero Dirichlet conditions
directly. If you do that then the RB basis functions would have non-zero
boundary values on the Dirichlet boundary and that would impose a
constraint on how the basis functions can be summed up in order to satisfy
the specified boundary values, and this would strongly limit the RB
convergence.

What you should do instead is use a "lifting function", i.e. let u denote
the desired solution with non-zero boundary values, and introduce \hat u =
u - g, where g is the lifting function that you specify yourself which
satisfies the boundary conditions as well. Substitute u = \hat u + g into
your PDE, and you'll get a PDE for \hat u that you can solve, where g ends
up on the right-hand side. You can then solve for \hat u, which has zero
Dirichlet boundary conditions, and reconstruct u at the end via u = \hat u
+ g.

Hope that helps,
David



On Thu, Jan 18, 2018 at 12:22 PM, <cau...@gm...> wrote:

> Hello,
>
>
>
> I am now trying to solve the thermoelasticity problem using libmesh. I
> modified ex3 of reduced_basis  by adding the temperature as a variable and
> by adjusting the matrixes. I started from a simple steady case of a cuboid.
> Its left side is clamped and the temperature there is fixed at 0 degree
> while there is a heat flux entering on the right side. The heat flux is set
> as the only parameter. It works well but I encountered problems when
> imposing a non-zero temperature on the left.
>
>
>
> At the beginning, I tried penalty method and intended to set the boundary
> temperature as a parameter. Therefore, I add a new matrix and a new vector
> in assembly.c. These two objects are defined as boundary_assembly  and the
> terms are calculated like in ex3 of introduction. However, a convergence
> error occurs:
>
>
>
> ============================================================
> ================
> ====================================
>
> Assembling affine operator 1 of 2
>
> Assembling affine operator 2 of 2
>
> Assembling affine vector 1 of 2
>
> Assembling affine vector 2 of 2
>
> Convergence error. Error id: -3
>
> Stack frames: 8
>
> 0: libMesh::print_trace(std::ostream&)
>
> 1: libMesh::MacroFunctions::report_error(char const*, int, char const*,
> char
> const*)
>
> 2:
> libMesh::RBConstruction::check_convergence(libMesh::LinearSolver<double>&)
>
> 3: libMesh::RBConstruction::compute_Fq_representor_innerprods(bool)
>
> 4: libMesh::RBConstruction::train_reduced_basis(bool)
>
> 5: ./Thermoelasticity-opt() [0x41df39]
>
> 6: __libc_start_main
>
> 7: ./Thermoelasticity-opt() [0x41e77d]
>
> [0] src/reduced_basis/rb_construction.C, line 2124, compiled Jan  6 2018
> at
> 16:42:44
>
>
>
>
>
> Then I turned to another method. I created a DirichletBoundary object and
> add it to the map just like ex4 of introduction except that I defined a
> function that returns a constant instead of the "exact_solution":
>
>
>
> ============================================================
> ================
> ============================================================
> ================
> ===========================
>
> std::set<boundary_id_type> boundary_ids;
>   boundary_ids.insert(BOUNDARY_ID_MIN_X);
>
>   // Create a vector storing the variable numbers which the BC applies to
>   std::vector<unsigned int> variables(4);
>   variables[0] = T_var;
>
>   std::vector<unsigned int> variables_displacement(3);
>   variables_displacement[0] = u_var;  variables_displacement[1] = v_var;
> variables_displacement[2] = w_var;
>
>   ZeroFunction<> zf;
>   AnalyticFunction<> fun_object(fun_wrapper);
>
>   DirichletBoundary dirichlet_bc(boundary_ids, variables, fun_object);
>
>   DirichletBoundary dirichlet_bc_displacment(boundary_ids,
> variables_displacement, zf);
>
>   get_dof_map().add_dirichlet_boundary(dirichlet_bc);
>
>    get_dof_map().add_dirichlet_boundary(dirichlet_bc_displacement);
>
> ============================================================
> ================
> =====================================
>
>
>
> in rb_classes.h. The code runs well but when I check the output, I find
> that
> the temperature on the left remains 0 instead of the value I set in the
> constant function.
>
>
>
> I would like to know whether my methods are right or not. If not, could you
> please tell me where the error is and show me other possible solution?
> Thanks a lot for your kindness.
>
>
>
> Best regards,
>
>
>
> Gauvain
>
>
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

[Libmesh-users] Question regarding imposition of non-zero Dirichlet conditions in RB

[<cau...@gm...>]

Hello,

 

I am now trying to solve the thermoelasticity problem using libmesh. I
modified ex3 of reduced_basis  by adding the temperature as a variable and
by adjusting the matrixes. I started from a simple steady case of a cuboid.
Its left side is clamped and the temperature there is fixed at 0 degree
while there is a heat flux entering on the right side. The heat flux is set
as the only parameter. It works well but I encountered problems when
imposing a non-zero temperature on the left. 

 

At the beginning, I tried penalty method and intended to set the boundary
temperature as a parameter. Therefore, I add a new matrix and a new vector
in assembly.c. These two objects are defined as boundary_assembly  and the
terms are calculated like in ex3 of introduction. However, a convergence
error occurs:

 

============================================================================
====================================

Assembling affine operator 1 of 2

Assembling affine operator 2 of 2

Assembling affine vector 1 of 2

Assembling affine vector 2 of 2

Convergence error. Error id: -3

Stack frames: 8

0: libMesh::print_trace(std::ostream&)

1: libMesh::MacroFunctions::report_error(char const*, int, char const*, char
const*)

2:
libMesh::RBConstruction::check_convergence(libMesh::LinearSolver<double>&)

3: libMesh::RBConstruction::compute_Fq_representor_innerprods(bool)

4: libMesh::RBConstruction::train_reduced_basis(bool)

5: ./Thermoelasticity-opt() [0x41df39]

6: __libc_start_main

7: ./Thermoelasticity-opt() [0x41e77d]

[0] src/reduced_basis/rb_construction.C, line 2124, compiled Jan  6 2018 at
16:42:44

 

 

Then I turned to another method. I created a DirichletBoundary object and
add it to the map just like ex4 of introduction except that I defined a
function that returns a constant instead of the "exact_solution":

 

============================================================================
============================================================================
===========================

std::set<boundary_id_type> boundary_ids;
  boundary_ids.insert(BOUNDARY_ID_MIN_X);

  // Create a vector storing the variable numbers which the BC applies to
  std::vector<unsigned int> variables(4);
  variables[0] = T_var; 

  std::vector<unsigned int> variables_displacement(3);
  variables_displacement[0] = u_var;  variables_displacement[1] = v_var;
variables_displacement[2] = w_var;

  ZeroFunction<> zf;
  AnalyticFunction<> fun_object(fun_wrapper);

  DirichletBoundary dirichlet_bc(boundary_ids, variables, fun_object);

  DirichletBoundary dirichlet_bc_displacment(boundary_ids,
variables_displacement, zf);

  get_dof_map().add_dirichlet_boundary(dirichlet_bc);

   get_dof_map().add_dirichlet_boundary(dirichlet_bc_displacement);

============================================================================
=====================================

 

in rb_classes.h. The code runs well but when I check the output, I find that
the temperature on the left remains 0 instead of the value I set in the
constant function. 

 

I would like to know whether my methods are right or not. If not, could you
please tell me where the error is and show me other possible solution?
Thanks a lot for your kindness. 

 

Best regards,

 

Gauvain

 

 

Re: [Libmesh-users] intel compilers and libmesh

[John P. <jwp...@gm...>]

On Wed, Jan 17, 2018 at 1:06 PM, Salazar De Troya, Miguel <
sal...@ll...> wrote:

> Hello
>
> What’s your experience with intel compilers and libMesh? Which compiler
> versions and flags seem to work more optimally?
>

You can look in m4/compiler.m4 to see what flags we use for different
versions of the Intel compiler.

This has not been updated recently, however, so if you find some flags you
think we can add or remove let us know.

-- 
John

[Libmesh-users] intel compilers and libmesh

[Salazar De T. M. <sal...@ll...>]

Hello

What’s your experience with intel compilers and libMesh? Which compiler versions and flags seem to work more optimally?

Thanks
Miguel

--