Difference between revisions of "FSI installation instructions"

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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.
These instructions only work for Ubuntu or Windows 10.


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).
===Install OpenFOAM===
Ensure you have installed OpenFOAM (v1812 or later) - [[OpenFOAM installation instructions|installation instructions here]].


=== Optional: Install ParaView ===
===Install FEniCS on Ubuntu===
If you wish to view the results of the simulations, the best way to do this is with ParaView.
''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.''
 
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:
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.
 
* 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===
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===
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===
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
Line 60: Line 22:


===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
Line 69: Line 33:


</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
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>
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
Line 92: Line 60:


===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
Line 100: Line 70:
</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===
Line 120: Line 103:
./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
Line 126: Line 111:
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]].

Latest revision as of 10:10, 5 February 2022

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

Important: Although I include the links to the official websites for installation instructions, I recommend you follow these instructions for installation (unless they no longer work), since the official instructions contain some mistakes and omissions.

These instructions only work for Ubuntu or Windows 10.

Install OpenFOAM

Ensure you have installed OpenFOAM (v1812 or later) - installation instructions here.

Install FEniCS on Ubuntu

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.

The Ubuntu installation instructions as of 31/12/2021 are summarised below (adapted from this website):

sudo apt-get install software-properties-common
sudo add-apt-repository ppa:fenics-packages/fenics
sudo apt-get update
sudo apt-get install fenics

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 this website):

sudo apt update
sudo apt install build-essential cmake libeigen3-dev libxml2-dev libboost-all-dev petsc-dev python3-dev python3-numpy
cd ~
mkdir FSI
cd FSI

Option 1: Install package directly

Note that this did not work for me, but is apparently a method that is possible for some users.

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

Option 2: Install from source

If installing the package directly did not work (like in my case), then install from source:

tar -xzf v2.3.0.tar.gz
cd precice-2.3.0
mkdir 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!
make -j 4

Test that the cmake and make commands worked as expected:

cd ~/FSI/precice-2.3.0/build
ctest --output-on-failure

If no errors were shown, install the software and test it worked:

make install
make test_install

Note: I used preCICE v2.3.0, but later versions should also work.

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 this website):

cd ~/FSI
git clone https://github.com/precice/openfoam-adapter
cd openfoam-adapter
export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH   ### You might need this line, it depends.
./Allwmake

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 this website). This requires Python3, which should already be installed if you followed my previous instructions:

(optional, should not need this line) python3 -m pip install scipy
python3 -m pip install --user fenicsprecice

Summary of how the software works

The following four steps are run in a loop:

  1. OpenFOAM sends the aerodynamic forces at each point on the solid to preCICE.
  2. FEniCS reads the aerodynamic forces from preCICE, and calculates the displacement of the solid at each point.
  3. FEniCS sends the displacement of the solid to preCICE.
  4. 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 available here.

Test the installation ran correctly

... by running this tutorial case:

cd ~/FSI
git clone --branch=master --depth 1 https://github.com/precice/tutorials.git
cd ~/FSI/tutorials/perpendicular-flap/fluid-openfoam
./run.sh

The command line output should have paused after this output. If it did not pause, something went wrong.

---[precice]  I am participant "Fluid"
---[precice]  Setting up master communication to coupling partner/s

Now open another Ubuntu terminal, and run these commands:

cd ~/FSI/tutorials/perpendicular-flap/solid-fenics
./run.sh

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:

cd ~/FSI/tutorials/perpendicular-flap/fluid-openfoam
paraview.exe fluid-openfoam.foam

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 in order to add 3D FSI functionality, instructions here

Upgrade to 3D

Please see this page.