FSI installation instructions - Revision history

NikLebedenko: /* Install preCICE on Ubuntu */ formatting

2022-02-05T10:10:18Z

Install preCICE on Ubuntu: formatting

← Older revision		Revision as of 10:10, 5 February 2022
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	</syntaxhighlight>		</syntaxhighlight>
	~~Now either install the Ubuntu~~ package directly ~~with the instructions below (which~~ did not work for me~~)..~~.<syntaxhighlight lang="bash">
			==== Option 1: Install package directly ====
			Note that this did not work for me, but is apparently a method that is possible for some users.<syntaxhighlight lang="bash">
	wget https://github.com/precice/precice/releases/download/v2.3.0/libprecice2_2.3.0_focal.deb		wget https://github.com/precice/precice/releases/download/v2.3.0/libprecice2_2.3.0_focal.deb
	sudo apt install ./libprecice2_2.3.0_focal.deb		sudo apt install ./libprecice2_2.3.0_focal.deb
	</syntaxhighlight>		</syntaxhighlight>
	~~... or~~ install from source:<syntaxhighlight lang="bash">
			==== Option 2: Install from source ====
			If installing the package directly did not work (like in my case), then install from source:<syntaxhighlight lang="bash">
	tar -xzf v2.3.0.tar.gz		tar -xzf v2.3.0.tar.gz
	cd precice-2.3.0		cd precice-2.3.0
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	make -j 4		make -j 4
	</syntaxhighlight>		</syntaxhighlight>
	Test that the cmake ~~command~~ worked as expected:<syntaxhighlight lang="bash">		Test that the <code>cmake</code> and <code>make</code> commands worked as expected:<syntaxhighlight lang="bash">
	cd ~/FSI/precice-2.3.0/build		cd ~/FSI/precice-2.3.0/build
	ctest --output-on-failure		ctest --output-on-failure

NikLebedenko: /* Install FEniCS on Ubuntu */

2022-02-05T10:06:18Z

Install FEniCS on Ubuntu

← Older revision		Revision as of 10:06, 5 February 2022
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	===Install FEniCS on Ubuntu===		===Install FEniCS on Ubuntu===
	''Update 05/02/2022 - These instructions are for FEniCS, which is now legacy. Ideally FEniCSx should be used instead (todo). Note that around 50% of the documentation online is for FEniCS, which adds to confusion.''		''Update 05/02/2022 - These instructions are for FEniCS, which is now considered legacy. Ideally FEniCSx should be used instead (todo), but the FEniCSx-preCICE adapter is in its infancy, so FEniCS is still the best option. Note that around 50% of the documentation online is for FEniCS, 50% for FEniCSx, which adds to confusion.''

	FEniCS is an open-source Finite Element Method (FEM) library. We will use it to simulate how a solid bends as a result of applied forces.		FEniCS is an open-source Finite Element Method (FEM) library. We will use it to simulate how a solid bends as a result of applied forces.

NikLebedenko: /* Install preCICE on Ubuntu */ formatting

2022-02-05T10:01:26Z

Install preCICE on Ubuntu: formatting

← Older revision		Revision as of 10:01, 5 February 2022
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	mkdir build		mkdir build
	cd build		cd build
	cmake -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/FSI/precice-2.3.0 -DPRECICE_MPICommunication=ON .. ### IMPORTANT! INCLUDE THE TWO DOTS!		cmake -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/FSI/precice-2.3.0 -DPRECICE_MPICommunication=ON .. ### IMPORTANT! INCLUDE THE TWO DOTS!
	make -j 4		make -j 4
	</syntaxhighlight>		</syntaxhighlight>

NikLebedenko: /* Step-by-step instructions */ added update note for FEniCS

2022-02-05T09:59:03Z

Step-by-step instructions: added update note for FEniCS

← Older revision		Revision as of 09:59, 5 February 2022
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	===Install FEniCS on Ubuntu===		===Install FEniCS on Ubuntu===
			''Update 05/02/2022 - These instructions are for FEniCS, which is now legacy. Ideally FEniCSx should be used instead (todo). Note that around 50% of the documentation online is for FEniCS, which adds to confusion.''

	FEniCS is an open-source Finite Element Method (FEM) library. We will use it to simulate how a solid bends as a result of applied forces.		FEniCS is an open-source Finite Element Method (FEM) library. We will use it to simulate how a solid bends as a result of applied forces.

NikLebedenko: reworded slightly

2022-01-25T20:29:08Z

reworded slightly

← Older revision		Revision as of 20:29, 25 January 2022
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	'''''Important:''''' Although I include the links to the official websites for installation instructions, I recommend you <u>follow these instructions for installation</u> (unless they no longer work), since the official instructions contain some mistakes and omissions.		'''''Important:''''' Although I include the links to the official websites for installation instructions, I recommend you <u>follow these instructions for installation</u> (unless they no longer work), since the official instructions contain some mistakes and omissions.

	These instructions only work for Ubuntu or Windows 10 ~~with WSL~~.		These instructions only work for Ubuntu or Windows 10.

	===Install OpenFOAM===		===Install OpenFOAM===

NikLebedenko: reworded slightly

2022-01-25T20:26:44Z

reworded slightly

← Older revision		Revision as of 20:26, 25 January 2022
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	'''''Important:''''' Although I include the links to the official websites for installation instructions, I recommend you <u>follow these instructions for installation</u> (unless they no longer work), since the official instructions contain some mistakes and omissions.		'''''Important:''''' Although I include the links to the official websites for installation instructions, I recommend you <u>follow these instructions for installation</u> (unless they no longer work), since the official instructions contain some mistakes and omissions.

	These instructions only work for Ubuntu ~~(whether native, via~~ WSL~~, or via a virtual machine)~~		These instructions only work for Ubuntu or Windows 10 with WSL.

	===Install OpenFOAM===		===Install OpenFOAM===

NikLebedenko: Moved OpenFOAM installation instructions to a separate page

2022-01-25T20:25:22Z

Moved OpenFOAM installation instructions to a separate page

← Older revision		Revision as of 20:25, 25 January 2022
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			Fluid-structure interaction (FSI) simulations model the interactions between a moving structure and a fluid flowing around it. Below are instructions of how to run FSI with free open-source software.

	== Step-by-step instructions==		== Step-by-step instructions==
	'''''~~IMPORTANT~~:''''' Although I include the links to the official websites for installation instructions, I recommend you <u>follow my instructions for installation</u> (unless ~~my instructions~~ no longer work~~, or you are a masochist~~), since the official instructions contain some mistakes and omissions.		'''''Important:''''' Although I include the links to the official websites for installation instructions, I recommend you <u>follow these instructions for installation</u> (unless they no longer work), since the official instructions contain some mistakes and omissions.

	~~These instructions only work for Ubuntu or Windows 10 and above.~~

	MacOS: I recommend installing everything on an Ubuntu virtual machine, since installing OpenFOAM on MacOS is possible (using a Docker image), but the steps after that are only possible with Ubuntu (or similar Linux distro).

	~~=== Optional: Install ParaView ===~~
	~~If you wish to view the results of the simulations, the best way to do this is with ParaView.~~

	~~Simply download the executable for your operating system from [https://www.paraview.org/download/ this website].~~

	~~The same website also hosts excellent tutorials and documentation PDFs - these should be your first resource when learning how to use ParaView.~~

	~~Windows 10: In order to run ParaView from the command line, you must add <code>paraview.exe</code> to Path:~~

	* Find the folder containing your <code>paraview.exe</code> executable, and copy the folder's location (not the file's location) to your clipboard with <code>CTRL+C</code>.
	* In the search bar, type "Edit the system environment variables" and click the first option.
	* Click the box labelled "Environment Variables..." in the lower right corner.
	* A dialogue box appears. In the lower half labelled "System Variables", scroll to the variable "Path"
	* Double click on the "Path" variable.
	* Click "New"
	* Paste the folder path you copied earlier into the text box that is now selected.
	* Click "OK" on all the dialogue boxes.

	~~You can now open files in ParaView from the command line with <code>paraview.exe <file></code>, replacing <code><file></code> the file you wish to open~~.

	~~===Windows 10 and above: Install~~ Ubuntu~~===~~		These instructions only work for Ubuntu (whether native, via WSL, or via a virtual machine)
	~~I recommend installing [https://docs.microsoft.com/en-us/windows/wsl/install-manual Windows Subsystem for Linux] instead of setting up a dual-boot partition~~ (~~use WSL1~~, ~~discussion of WSL2 below~~).
	*''WSL1 Pros: fairly fast read/write in both Ubuntu and Windows file systems. Cons: much slower at read/write in Ubuntu file system than WSL2.''
	*''WSL2 Pros: lightning fast read/write in Ubuntu. Cons: very slow read/write when moving data between Ubuntu and Windows.''
	*''Summary: Use WSL1 if you have a Windows-based ParaView or another app that will read lots of data between file systems.''
	**''If you want to use WSL2 anyway, I recommend you install ParaView on Ubuntu to avoid reading between file systems. You must also install XMing to view the GUI. See [https://stackoverflow.com/questions/61110603/how-to-set-up-working-x11-forwarding-on-wsl2 this page] and [https://newbedev.com/how-to-set-up-working-x11-forwarding-on-wsl2 this page] for further information.''

	===Install OpenFOAM ~~on Ubuntu~~===		===Install OpenFOAM===
	OpenFOAM ~~is an open-source Computational Fluid Dynamics~~ (~~CFD~~) ~~package. We will use it to simulate the fluid (air) flow.~~		Ensure you have installed OpenFOAM (v1812 or later) - [[OpenFOAM installation instructions\|installation instructions here]].

	~~The Ubuntu~~ installation instructions ~~as of 31/12/2021 are summarised below (adapted from [https://develop.openfoam.com/Development/openfoam/-/wikis/precompiled/debian this website]):<syntaxhighlight lang="bash">~~
	~~curl -s https://dl.openfoam.com/add-debian-repo.sh~~ \| ~~sudo bash~~
	~~sudo apt-get install openfoam2112-default~~
	~~</syntaxhighlight>~~
	~~Append the following line to your <code>~/.bashrc</code> file, if not already present:<syntaxhighlight lang="bash">~~
	~~source /usr/lib/openfoam/openfoam2112/etc/bashrc~~
	~~</syntaxhighlight>~~
	~~Restart Ubuntu. Now check the~~ installation ~~completed correctly by running a tutorial case:<syntaxhighlight lang="bash">~~
	~~cd ~~~
	~~mkdir -p OpenFOAM-sims/tutorials~~
	~~cp -r $FOAM_TUTORIALS/incompressible OpenFOAM-sims/tutorials~~
	~~cd OpenFOAM-sims/tutorials/incompressible/icoFoam/cavity/cavity/~~
	~~blockMesh > log.blockMesh~~
	~~icoFoam > log.icoFoam~~
	~~</syntaxhighlight>~~
	~~Note: this used OpenFOAMv2112, but versions >= v1812 should work~~.

	===Install FEniCS on Ubuntu===		===Install FEniCS on Ubuntu===
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	./run.sh		./run.sh
	</syntaxhighlight>		</syntaxhighlight>
	Both terminals should now have log outputs flying. After around 1 minute of computation, both terminals should finish at (roughly) the same time. ~~You can view the results with the following commands, assuming~~ you have installed ParaView on Windows and added the folder containing its .exe file to the Windows PATH environment variable:<syntaxhighlight lang="bash">		Both terminals should now have log outputs flying. After around 1 minute of computation, both terminals should finish at (roughly) the same time.

			If you have installed ParaView on Windows and added the folder containing its .exe file to the Windows PATH environment variable, then you can run these commands to visualise the results:<syntaxhighlight lang="bash">
	cd ~/FSI/tutorials/perpendicular-flap/fluid-openfoam		cd ~/FSI/tutorials/perpendicular-flap/fluid-openfoam
	paraview.exe fluid-openfoam.foam		paraview.exe fluid-openfoam.foam

NikLebedenko: /* Install the FEniCS-preCICE adapter */ formatting

2022-01-24T18:29:42Z

Install the FEniCS-preCICE adapter: formatting

← Older revision		Revision as of 18:29, 24 January 2022
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	===Install the FEniCS-preCICE adapter===		===Install the FEniCS-preCICE adapter===
	This adapter allows FEniCS to talk to preCICE.		This adapter allows FEniCS to talk to preCICE.


	The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://precice.org/adapter-fenics.html this website]). This requires Python3, which should already be installed if you followed my previous instructions: <syntaxhighlight lang="bash">		The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://precice.org/adapter-fenics.html this website]). This requires Python3, which should already be installed if you followed my previous instructions: <syntaxhighlight lang="bash">
	(optional, should not need this line) python3 -m pip install scipy		(optional, should not need this line) python3 -m pip install scipy

NikLebedenko: Added descriptions of what each package does, and how the combination of all the packages works

2022-01-24T18:28:41Z

Added descriptions of what each package does, and how the combination of all the packages works

← Older revision		Revision as of 18:28, 24 January 2022
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	===Install OpenFOAM on Ubuntu===		===Install OpenFOAM on Ubuntu===
			OpenFOAM is an open-source Computational Fluid Dynamics (CFD) package. We will use it to simulate the fluid (air) flow.

	The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://develop.openfoam.com/Development/openfoam/-/wikis/precompiled/debian this website]):<syntaxhighlight lang="bash">		The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://develop.openfoam.com/Development/openfoam/-/wikis/precompiled/debian this website]):<syntaxhighlight lang="bash">
	curl -s https://dl.openfoam.com/add-debian-repo.sh \| sudo bash		curl -s https://dl.openfoam.com/add-debian-repo.sh \| sudo bash
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	===Install FEniCS on Ubuntu===		===Install FEniCS on Ubuntu===
			FEniCS is an open-source Finite Element Method (FEM) library. We will use it to simulate how a solid bends as a result of applied forces.

	The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://fenicsproject.org/download/ this website]):<syntaxhighlight lang="bash">		The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://fenicsproject.org/download/ this website]):<syntaxhighlight lang="bash">
	sudo apt-get install software-properties-common		sudo apt-get install software-properties-common
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	===Install preCICE on Ubuntu===		===Install preCICE on Ubuntu===
			preCICE is an open-source library for coupling simulations together. We will use it to allow OpenFOAM and FEniCS to communicate with each other.

	The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://precice.org/quickstart.html this website]): <syntaxhighlight lang="bash">		The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://precice.org/quickstart.html this website]): <syntaxhighlight lang="bash">
	sudo apt update		sudo apt update
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	===Install the OpenFOAM-preCICE adapter===		===Install the OpenFOAM-preCICE adapter===
			This adapter allows OpenFOAM to talk to preCICE.

	The Ubuntu installation instructions as of 23/01/2021 are summarised below (adapted from [https://precice.org/adapter-openfoam-get.html this website]):<syntaxhighlight lang="bash">		The Ubuntu installation instructions as of 23/01/2021 are summarised below (adapted from [https://precice.org/adapter-openfoam-get.html this website]):<syntaxhighlight lang="bash">
	cd ~/FSI		cd ~/FSI
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	</syntaxhighlight>		</syntaxhighlight>
	===Install the FEniCS-preCICE adapter===		===Install the FEniCS-preCICE adapter===
			This adapter allows FEniCS to talk to preCICE.


	The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://precice.org/adapter-fenics.html this website]). This requires Python3, which should already be installed if you followed my previous instructions: <syntaxhighlight lang="bash">		The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from [https://precice.org/adapter-fenics.html this website]). This requires Python3, which should already be installed if you followed my previous instructions: <syntaxhighlight lang="bash">
	(optional, should not need this line) python3 -m pip install scipy		(optional, should not need this line) python3 -m pip install scipy
	python3 -m pip install --user fenicsprecice		python3 -m pip install --user fenicsprecice
	</syntaxhighlight>		</syntaxhighlight>

			=== Summary of how the software works ===
			The following four steps are run in a loop:

			# OpenFOAM sends the aerodynamic forces at each point on the solid to preCICE.
			# FEniCS reads the aerodynamic forces from preCICE, and calculates the displacement of the solid at each point.
			# FEniCS sends the displacement of the solid to preCICE.
			# OpenFOAM reads the displacement from preCICE, and calculates the new aerodynamic forces.

			This is a simplification of the process (called a ''serial explicit coupling''). In reality, a better method is to have all four steps occur simultaneously until the residual is low enough (called ''parallel implicit coupling''). This is faster and more accurate.

			Further information about coupling is [https://precice.org/couple-your-code-overview.html available here].

	===Test the installation ran correctly===		===Test the installation ran correctly===

NikLebedenko: Added link to 3D upgrade page

2022-01-24T08:48:54Z

Added link to 3D upgrade page

← Older revision		Revision as of 08:48, 24 January 2022
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	Congratulations! You should now have a functional FSI installation.		Congratulations! You should now have a functional FSI installation.

	Note that as of 31/12/2021, the unmodified FEniCS-preCICE adapter only works in 2D, so you will have to edit the adapter ~~(or download my edited version, TODO add link here)~~ in order to add 3D FSI functionality~~. Or just wait a few months until I get around~~ to ~~submitting a pull request for my version~~.		Note that as of 31/12/2021, the unmodified FEniCS-preCICE adapter only works in 2D, so you will have to edit the adapter in order to add 3D FSI functionality, instructions [[FSI 3D Upgrade\|here]]

			== Upgrade to 3D ==
			Please see [[FSI 3D Upgrade\|this page]].