WIP: aste Replay Mode tutorial on elastic flap case #73

richahert · 2020-03-09T12:05:55Z

This PR adds an tutorial for aste. From the OpenFOAM-FEniCS-FSI tutorial OpenFOAM is replaced with aste that sends previously exported results to FEniCS.

# Conflicts: # FSI/cylinderFlap/OpenFOAM-FEniCS/Solid/cyl-flap.py

# Conflicts: # FSI/flap_perp/OpenFOAM-CalculiX/precice-config_serial.xml # FSI/flap_perp/OpenFOAM-FEniCS/precice-config_serial.xml

# Conflicts: # FSI/flap_perp/OpenFOAM-FEniCS/precice-config.xml

uekerman · 2020-03-10T14:43:51Z

Try to merge the develop branch into your branch https://github.com/richahert/tutorials/tree/aste. Then, the changes here should be easier to overlook.
What is your overall plan, to create a new tutorial ASTE-OpenFOAM or to explain how to generate such a tutorial from OpenFOAM-FEniCS?

BenjaminRodenberg

FSI/flap_perp/ASTE/Solid/perp-flap.py is a copy from FSI/cylinderFlap/OpenFOAM-FEniCS/Solid/perp-flap.py. We ask the user explicitly to copy this file in our README.md, therefore, we could avoid this duplicate (related #28). I also think it is a bit counter-intuitive to ask the user to copy the file even though it is already provided in the folder.

For precice-config.xml the situation is different: Changes are required and therefore, we should provide this file. The user may directly use it (quick path) or try to come up with his or her own ASTE/precice-config.xml derived from OpenFOAM-FEniCS/precice-config.xml.

The remaining changes are minor formatting / cleanup changes:

A comment on markdown formatting: Note that one backtick is enough for inline code, if you want to have code blocks, use three backticks (see here).
Don't use from fenics import *. Better use from fenics import .... This will require you to add XDMFFile, TensorFunctionSpace and LocalSolver to the from fenics import ... in perp-flap.py.

Note:

I'm currently stuck with a segmentation fault, when I try to run preciceMap -v -c precice-config.xml -p A --mesh preCICE-output/Solid-fenics --vectordata. It looks like an error that is not being treated properly within preCICE, but it might also be wrong usage on my side. Therefore, I will submit this review now and do another review as soon as I'm able to run the case.

FSI/cylinderFlap/OpenFOAM-CalculiX/Fluid/system/controlDict

CHT/flow-over-plate/buoyantPimpleFoam-nutils/README.md

FSI/cylinderFlap/OpenFOAM-FEniCS-bigdt/OpenFOAM-FEniCS/.gitignore

FSI/cylinderFlap/OpenFOAM-FEniCS/Postprocessing/plot_tip.py

FSI/flap_perp/ASTE/README.md

FSI/flap_perp/OpenFOAM-FEniCS/Solid/perp-flap.py

FSI/flap_perp/ASTE/README.md

Co-Authored-By: Benjamin Rüth <[email protected]>

BenjaminRodenberg

currently aste seems to not provide the option --vectordata. I am using precice/aste@84ebcbc. Therefore, I cannot run the replay mode.
why is FSI/cylinderFlap/OpenFOAM-FEniCS/Postprocessing/plot_tip.py deleted? Is it not needed? In any case: I am not sure whether removing this file should be done within this PR.

✔️ the instructions in the README.md are helpful and clear

Note @richahert: I can take care of applying the changes on my own. I just need some help with the --vectordata option.

BenjaminRodenberg · 2020-05-08T13:39:28Z

Note @richahert: I can take care of applying the changes on my own. I just need some help with the --vectordata option.

The option seems to have been removed in richahert/aste@94537d4. Whether we are dealing with scalar or vector data is detected automatically.

If I remove the --vectordata option, I run into a Segmentation Fault:

benjamin@benjamin-ThinkPad-X1-Yoga-2nd:~/tutorials/FSI/flap_perp/ASTE$ preciceMap -v -c precice-config.xml -p A --mesh preCICE-output/Solid-fenics
2020-05-08 15:35:47,693 VERBOSE-1 [default] Basename: preCICE-output/Solid-fenics
2020-05-08 15:35:47,693 DEBUG [default] [benjamin@unknown-host] [std::vector<std::__cxx11::basic_string<char> > getMeshes(std::__cxx11::string, int)] [/home/benjamin/aste/src/preciceMap.cpp:48] Meshes:
(0) 15:35:47 [impl::SolverInterfaceImpl]:120 in configure: This is preCICE version 2.0.2
(0) 15:35:47 [impl::SolverInterfaceImpl]:121 in configure: Revision info: v2.0.1-146-g15fb6857-dirty
(0) 15:35:47 [impl::SolverInterfaceImpl]:122 in configure: Configuring preCICE with configuration "precice-config.xml"
(0) 15:35:47 [impl::SolverInterfaceImpl]:123 in configure: I am participant "A"
[benjamin-ThinkPad-X1-Yoga-2nd:05121] *** Process received signal ***
[benjamin-ThinkPad-X1-Yoga-2nd:05121] Signal: Segmentation fault (11)
[benjamin-ThinkPad-X1-Yoga-2nd:05121] Signal code: Address not mapped (1)
[benjamin-ThinkPad-X1-Yoga-2nd:05121] Failing at address: (nil)
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7f0d25207890]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 1] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZNKSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE5c_strEv+0x0)[0x7f0d24a86470]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 2] preciceMap(_ZN2el4base14MessageBuilderlsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1c)[0x55bfb106f1bc]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 3] preciceMap(_ZN2el4base6WriterlsINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEERS1_RKT_+0x33)[0x55bfb106ffab]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 4] preciceMap(_Z12readMainFileR4MeshRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb+0x126)[0x55bfb10641b9]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 5] preciceMap(_Z8readMeshRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb+0x60)[0x55bfb1064b30]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 6] preciceMap(main+0x3dd)[0x55bfb10650b4]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f0d24378b97]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] [ 8] preciceMap(_start+0x2a)[0x55bfb106364a]
[benjamin-ThinkPad-X1-Yoga-2nd:05121] *** End of error message ***
Segmentation fault (core dumped)

I think this is an error on my side, since the data is not provided correctly. I will try to debug this now and I might comment in precice/aste#9 or open an issue in https://github.com/precice/aste. A Segmentation Fault should, of course, be avoided.

BenjaminRodenberg · 2020-05-08T14:00:26Z

I forgot converting the data using precice_to_aste.py. After doing this and removing the --vectordata option, everything worked perfectly 👍

I will report the issue with the segmentation fault upstream. This is not related to this PR. edit: see precice/aste#11

The only remaining point is whether or not (and where) FSI/cylinderFlap/OpenFOAM-FEniCS/Postprocessing/plot_tip.py should be deleted. Then this PR is ready to merge.

I would suggest to wait for precice/aste#9 before merging this PR, since without the feature being implemented in aste this tutorial does not really help.

MakisH · 2021-04-15T21:07:56Z

This now would need to be adjusted to the new tutorials structure.

* Moves files that are not conflicting from FSI/flap_perp/ASTE to perpendicular-flap * perpendicular-flap/fluid-aste/README.md describes usage of aste for replay mode. This information needs to be incorporated into the new structure or moved to preCICE.org. * FSI/flap_perp/ASTE/Solid/precice-adapter-config-fsi-s.json is moved to perpendicular-flap/solid-fenic. Here integration is still a TODO. * Overwrites perpendicular-flap/solid-fenics/solid.py with FSI/flap_perp/OpenFOAM-FEniCS/Solid/perp-flap.py. Here integration into new structure is still a TODO. * Overwrites perpendicular-flap/precice-confix.xml with FSI/flap_perp/OpenFOAM-FEniCS/precice-config.xml. Here integration into new structure is still a TODO.

BenjaminRodenberg

Todos I identified when moving to the new tutorials structure:

We might be able to remove Allclean and .gitignore. I'm not sure whether there is anything specific to the replay-mode.
fluid-aste/README.md explains how the replay mode is used. This information could me merged into perpendicular-flap/README.md or we could provide a full explanation of the replay more on the website and only provide specific information here in this tutorial.
precice-config-aste.xml has to be updated to the new naming. Ideally we could get rid of it and just use precice-config.xml for replay-mode as well.

BenjaminRodenberg · 2021-07-01T07:17:37Z

perpendicular-flap/fluid-aste/README.md

+
+#### The quick way to run 
+
+1. Copy `perp_flap.py` from `tutorials/FSI/flap_perp/OpenFOAM-FEniCS/Solid` into `tutorials/FSI/flap_perp/ASTE/Solid`.


Copying files should not be necessary anymore with the new structure.

perpendicular-flap/fluid-aste/README.md

perpendicular-flap/precice-config-aste.xml

BenjaminRodenberg · 2021-07-01T07:21:45Z

perpendicular-flap/solid-fenics/precice-adapter-config-fsi-s-aste.json

+  "config_file_name": "../precice-config.xml",
+  "interface": {
+      "coupling_mesh_name": "Solid",
+      "read_data_name": "Data"


In replay mode we only read data from ASTE with the solid solver. This is an important difference compared to the normal tutorial.

BenjaminRodenberg · 2021-07-01T07:23:59Z

I moved the files from the old structure to the new structure. This PR is currently not working. It might be helpful to go back to
a7a3dd5 to see what the expected behavior is and to find out how paths, variable names etc. have to be mapped to the new structure.

BenjaminRodenberg · 2021-07-01T15:30:28Z

perpendicular-flap/fluid-aste/README.md

+Copy the `preCICE-output` folder to the root directory of the aste tutorial `tutorials/perpendicular-flap/fluid-aste`.
+To convert the files to the correct format, open the `preCICE-output` folder and run
+
+`precice_to_aste.py Solid-fenics -n 500 -t Forces0 --datadim 3`


I'm currently getting stuck here. Where is the script precice_to_aste.py? I cannot find it in https://github.com/precice/aste/tree/develop. @fsimonis any idea?

@BenjaminRodenberg https://github.com/precice/aste/pull/9/files

BenjaminRodenberg · 2021-12-06T08:14:31Z

Since this PR is idle some time, here is a quick status update:

Currently ASTE is under a major revision, therefore this PR is waiting. Replay mode is still on the list of features that we would like to implement in the future.
We might implement replay mode by modifying this PR or by creating a new one (using a big part of this PR as a starting point). We should make sure that the contributions by @richahert also show up in the history of a new PR, if we crate one.
In the end, replay mode should work with any solid-* solver. Therefore, the only change that should be applied to the FEniCS solver, for example, is that a different configuration file should be used (not precice-config.xml but precice-config-aste.xml). I guess that the (many) code changes in solid.py (computation of stresses, removing checkpointing) were due to development. The adapter should be able to handle the correct treatment of checkpointing on its own. Computation of stresses is not required, if I understand it correctly.
@davidscn and @kursatyurt will take care of replay mode. I'm available for reviews, if needed.

richahert and others added 18 commits November 4, 2019 14:05

commit so i can pull the master from upstream

36e9aca

Merge remote-tracking branch 'upstream/master'

bcce54b

# Conflicts: # FSI/cylinderFlap/OpenFOAM-FEniCS/Solid/cyl-flap.py

add readme

c7cb07d

create first Readme

d3cd8a0

Merge remote-tracking branch 'upstream/master' into aste

91e0ea0

precice config for aste fsi

e4f848d

precice config for aste fsi

05bf42b

precice config for aste fsi

72df6ca

new precice config

d41a002

Merge remote-tracking branch 'upstream/master'

06dd4db

# Conflicts: # FSI/flap_perp/OpenFOAM-CalculiX/precice-config_serial.xml # FSI/flap_perp/OpenFOAM-FEniCS/precice-config_serial.xml

Merge branch 'master' into aste

d08175e

# Conflicts: # FSI/flap_perp/OpenFOAM-FEniCS/precice-config.xml

Add basic files for aste tutorial

7f0ceb1

add gitignore, rename forced to data

83b3199

adds in gitignore

0e687c2

Add instructions. Extended way not finished yet.

82714d7

add links and missing infos

d14b8ff

Update README.md

4252031

Merge remote-tracking branch 'upstream/develop' into aste

09f2ce5

BenjaminRodenberg self-requested a review March 11, 2020 08:27

BenjaminRodenberg requested changes Mar 24, 2020

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richahert and others added 9 commits April 15, 2020 13:46

Merge remote-tracking branch 'upstream/develop' into aste

8079715

revert changes

dcd542c

delete strange file

4664cbe

remove file that is not relevant

e322513

Update FSI/flap_perp/ASTE/README.md

9a8c315

Co-Authored-By: Benjamin Rüth <[email protected]>

Update FSI/flap_perp/ASTE/README.md formatting

af988d7

Co-Authored-By: Benjamin Rüth <[email protected]>

Apply suggestions from code review

b8db4f6

Co-Authored-By: Benjamin Rüth <[email protected]>

delete unnecessary comments

1545b58

revert changes to upstream develop

25ea047

richahert mentioned this pull request May 8, 2020

Vectors for Participant B precice/aste#10

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BenjaminRodenberg requested changes May 8, 2020

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BenjaminRodenberg added 2 commits May 8, 2020 15:48

Clearify modifications of precice-config.xml

5866b20

Remove unneeded --vectordata option

a7a3dd5

BenjaminRodenberg mentioned this pull request May 8, 2020

Segmentation fault, if --mesh folder does not exist or contains wrong data precice/aste#11

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BenjaminRodenberg mentioned this pull request Jul 21, 2020

Create Tutorial for "Replay Mode" #45

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BenjaminRodenberg added 2 commits July 1, 2021 08:47

Merge branch 'develop' into aste

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BenjaminRodenberg requested changes Jul 1, 2021

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BenjaminRodenberg added 13 commits July 1, 2021 09:27

Update obvious changes. Whitespaces etc.

2f412b0

Some more obvious changes.

c2e2437

Update configs to new naming scheme.

95be62b

Update solver.

a9f7e1a

Clean up the diff.

36a76fd

Partially update to new tutorials structure

0a71b77

More cleaning up of the diff.

330dce5

Fix md file formatting.

fdbd5f8

Fix ShellCheck.

4bf84b0

Fix dead links.

41d5e44

Fix format.

77c91fc

Remove unnecessary clean script.

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Fix link.

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BenjaminRodenberg reviewed Jul 1, 2021

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BenjaminRodenberg assigned davidscn and unassigned BenjaminRodenberg Jan 25, 2024

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WIP: aste Replay Mode tutorial on elastic flap case #73

WIP: aste Replay Mode tutorial on elastic flap case #73

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BenjaminRodenberg commented Dec 6, 2021


		#### The quick way to run

		1. Copy `perp_flap.py` from `tutorials/FSI/flap_perp/OpenFOAM-FEniCS/Solid` into `tutorials/FSI/flap_perp/ASTE/Solid`.

WIP: aste Replay Mode tutorial on elastic flap case #73

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WIP: aste Replay Mode tutorial on elastic flap case #73

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