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howtodocker.html

@@ -89,22 +89,22 @@ <h3>Contents</h3>
                     <li><a href="#linux">On linux with GUI (graphical interface without paraview):</a></li>
                   </ul>
                 </li>
-                <li><a href="#start">Start a container (if existing and not running) :</a></li>
+                <li><a href="#start">Start a container (if existing and not running):</a></li>
                 <li><a href="#attach">Attach to a running container (if existing and running):</a></li>
               </ul>
             </li>
           </ul>
         </nav>
-<p>Here is a How To about using the sedFoam docker.</p><p>The prerequisites is to install Docker : <a href="https://docs.docker.com/engine/install/">https:/<wbr />/<wbr />docs.docker.com/<wbr />engine/<wbr />install/<wbr /></a></p><p>This page is organised in two sections:</p><ul><li><a href="howtodocker.html#configuration" class="m-doc">Configuration of the sedFoam docker</a></li><li><a href="howtodocker.html#howtouse" class="m-doc">How to use/launch sedFoam docker ?</a></li></ul><section id="configuration"><h2><a href="#configuration">Configuration of the sedFoam docker</a></h2><p>Operating System : Ubuntu focal</p><p>Openfoam version : 2312 (openfoam.com) with all tutorials and source files</p><p>sedFoam version : the latest of the develop branch</p><p>user : sudofoam (with sudo)</p><p>Installed packages : swak4foam, python3-numpy, python3-matplotlib, fluidfoam, vim...</p><p>Official link : <a href="https://hub.docker.com/r/cbonamy/sedfoam_2312_ubuntu">https://hub.docker.com/r/cbonamy/sedfoam_<wbr />2312_<wbr />ubuntu</a></p><p>Dockerfile : <a href="https://github.com/SedFoam/sedfoam/blob/develop/docker/Dockerfile">https:/<wbr />/<wbr />github.com/<wbr />SedFoam/<wbr />sedfoam/<wbr />blob/<wbr />develop/<wbr />docker/<wbr />Dockerfile</a></p><p>Extended docker (supporting notebook) : <a href="https://hub.docker.com/r/cbonamy/sedfoam_2312_notebook">https://hub.docker.com/r/cbonamy/sedfoam_<wbr />2312_<wbr />notebook</a></p><p>Please note that Paraview is not included in the sedFoam docker. The users are encouraged to install and use Paraview on the host machine.</p></section><section id="howtouse"><h2><a href="#howtouse">How to use/launch sedFoam docker ?</a></h2><section id="launch"><h3><a href="#launch">launch/initiate docker:</a></h3><ul><li><a href="howtodocker.html#notebook" class="m-doc">In jupyter notebook using your web browser (macOS, linux, windows):</a></li><li><a href="howtodocker.html#macOS" class="m-doc">On macOS with GUI (graphical interface without paraview):</a></li><li><a href="howtodocker.html#windows" class="m-doc">On Windows with GUI (graphical interface without paraview):</a></li><li><a href="howtodocker.html#linux" class="m-doc">On linux with GUI (graphical interface without paraview):</a></li></ul><section id="notebook"><h4><a href="#notebook">In jupyter notebook using your web browser (macOS, linux, windows):</a></h4><p>On host :</p><ul><li><p>initiate docker :</p><pre>    docker run -p 8888:8888 --name &quot;sedfoam_2312_notebook&quot; -v=&quot;/Users/toto&quot;:/home/sudofoam/workingDir &quot;cbonamy/sedfoam_2312_notebook&quot;
-</pre></li><li>use your web browser :<ul><li>The previous command will give you a url like <a href="http://127.0.0.1:8888/?token=ae5f299fc77312f079793a9ca818d5973ed4df5a5a85b9fa">http:/<wbr />/<wbr />127.0.0.1:8888/<wbr />?token=ae5f299fc77312f079793a9ca818d5973ed4df5a5a85b9fa</a></li><li>Just copy and paste the link into your web browser</li></ul></li></ul><p>The -v=&quot;/Users/toto&quot;:/home/sudofoam/workingDir option is not mmandatory. It is used to mmount a shared space between host and jupyter notebook. If you use this option, please adapt the directories to your configuration. In this example, &quot;/Users/toto&quot; will be mounted on the vm in /home/sudofoam/workingDir.</p></section><section id="macOS"><h4><a href="#macOS">On macOS with GUI (graphical interface without paraview):</a></h4><p>On host :</p><ul><li>configure xquartz<ul><li>install xquartz to allow network connection</li><li>in Xquartz : Go to Preferences &gt; Security</li><li>and Check &quot;allow connections from network clients&quot;</li><li><p>in a terminal :</p><pre>    IP=$(ifconfig en0 | grep inet | awk &#x27;$1==&quot;inet&quot; {print $2}&#x27;)
+<p>Here is a How To about using the sedFoam docker.</p><p>The prerequisites is to install Docker: <a href="https://docs.docker.com/engine/install/">https:/<wbr />/<wbr />docs.docker.com/<wbr />engine/<wbr />install/<wbr /></a></p><p>This page is organised in two sections:</p><ul><li><a href="howtodocker.html#configuration" class="m-doc">Configuration of the sedFoam docker</a></li><li><a href="howtodocker.html#howtouse" class="m-doc">How to use/launch sedFoam docker ?</a></li></ul><section id="configuration"><h2><a href="#configuration">Configuration of the sedFoam docker</a></h2><p>Operating System: Ubuntu focal</p><p>Openfoam version: 2406 (openfoam.com) with all tutorials and source files</p><p>sedFoam version: the latest of the develop branch</p><p>user: sudofoam (with sudo)</p><p>Installed packages: swak4foam, python3-numpy, python3-matplotlib, fluidfoam, vim...</p><p>Official link: <a href="https://hub.docker.com/r/cbonamy/sedfoam_2406_ubuntu">https://hub.docker.com/r/cbonamy/sedfoam_<wbr />2406_<wbr />ubuntu</a></p><p>Dockerfile: <a href="https://github.com/SedFoam/sedfoam/blob/develop/docker/Dockerfile">https:/<wbr />/<wbr />github.com/<wbr />SedFoam/<wbr />sedfoam/<wbr />blob/<wbr />develop/<wbr />docker/<wbr />Dockerfile</a></p><p>Extended docker (supporting notebook): <a href="https://hub.docker.com/r/cbonamy/sedfoam_2406_notebook">https://hub.docker.com/r/cbonamy/sedfoam_<wbr />2406_<wbr />notebook</a></p><p>Please note that Paraview is not included in the sedFoam docker. The users are encouraged to install and use Paraview on the host machine.</p></section><section id="howtouse"><h2><a href="#howtouse">How to use/launch sedFoam docker ?</a></h2><section id="launch"><h3><a href="#launch">launch/initiate docker:</a></h3><ul><li><a href="howtodocker.html#notebook" class="m-doc">In jupyter notebook using your web browser (macOS, linux, windows):</a></li><li><a href="howtodocker.html#macOS" class="m-doc">On macOS with GUI (graphical interface without paraview):</a></li><li><a href="howtodocker.html#windows" class="m-doc">On Windows with GUI (graphical interface without paraview):</a></li><li><a href="howtodocker.html#linux" class="m-doc">On linux with GUI (graphical interface without paraview):</a></li></ul><section id="notebook"><h4><a href="#notebook">In jupyter notebook using your web browser (macOS, linux, windows):</a></h4><p>On host:</p><ul><li><p>initiate docker:</p><pre>    docker run -p 8888:8888 --name &quot;sedfoam_2406_notebook&quot; -v=&quot;/Users/toto&quot;:/home/sudofoam/workingDir &quot;cbonamy/sedfoam_2406_notebook&quot;
+</pre></li><li>use your web browser:<ul><li>The previous command will give you a url like <a href="http://127.0.0.1:8888/?token=ae5f299fc77312f079793a9ca818d5973ed4df5a5a85b9fa">http:/<wbr />/<wbr />127.0.0.1:8888/<wbr />?token=ae5f299fc77312f079793a9ca818d5973ed4df5a5a85b9fa</a></li><li>Just copy and paste the link into your web browser</li></ul></li></ul><p>The -v=&quot;/Users/toto&quot;:/home/sudofoam/workingDir option is not mmandatory. It is used to mmount a shared space between host and jupyter notebook. If you use this option, please adapt the directories to your configuration. In this example, &quot;/Users/toto&quot; will be mounted on the vm in /home/sudofoam/workingDir.</p></section><section id="macOS"><h4><a href="#macOS">On macOS with GUI (graphical interface without paraview):</a></h4><p>On host:</p><ul><li>configure xquartz<ul><li>install xquartz to allow network connection</li><li>in Xquartz: Go to Preferences &gt; Security</li><li>and Check &quot;allow connections from network clients&quot;</li><li><p>in a terminal:</p><pre>    IP=$(ifconfig en0 | grep inet | awk &#x27;$1==&quot;inet&quot; {print $2}&#x27;)
     xhost + $IP
-</pre></li></ul></li><li><p>initiate docker :</p><pre>    docker run -it --net=host -e DISPLAY=$IP:0 -v /tmp/.X11-unix:/tmp/.X11-unix --name &quot;sedfoam_2312&quot; --workdir=&quot;/home/sudofoam&quot; -v=&quot;/Users/toto&quot;:/home/sudofoam/workingDir &quot;cbonamy/sedfoam_2312_ubuntu&quot; /bin/bash
-</pre><p>Please adapt the directories to your configuration. In this example, &quot;/Users/toto&quot; will be mounted on the vm in /home/sudofoam/workingDir. If you change IP, for example when returning from work to home, change the Display variable (in the Docker) accordingly.</p></li></ul></section><section id="windows"><h4><a href="#windows">On Windows with GUI (graphical interface without paraview):</a></h4><ul><li>configure Docker Engine for windows (with all system requirements : WSL2, step 1-5 from <a href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">https:/<wbr />/<wbr />docs.microsoft.com/<wbr />en-us/<wbr />windows/<wbr />wsl/<wbr />install-win10</a>)</li><li>configure vcxsrv : <a href="https://sourceforge.net/projects/vcxsrv/">https:/<wbr />/<wbr />sourceforge.net/<wbr />projects/<wbr />vcxsrv/<wbr /></a> (disable access control in extra settings)</li><li><p>Get your IP and set DISPLAY variable :</p><pre>    set-variable -name DISPLAY -value YOUR-IP:0.0
-</pre></li><li><p>initiate docker :</p><pre>    docker run -it --net=host --env DISPLAY=$DISPLAY --name &quot;sedfoam_2312&quot; --workdir=&quot;/home/sudofoam&quot; -v=&quot;c:/mydataspace&quot;:/home/sudofoam/workingDir &quot;cbonamy/sedfoam_2312_ubuntu&quot; /bin/bash
-</pre><p>Please adapt the directories to your configuration. In this example, &quot;c:/mydataspace&quot; will be mounted on the vm in /home/sudofoam/workingDir. If you change IP, for example when returning from work to home, change the Display variable (in the Docker) accordingly.</p></li></ul></section><section id="linux"><h4><a href="#linux">On linux with GUI (graphical interface without paraview):</a></h4><pre>    docker run -it --net=host --env DISPLAY=$DISPLAY --volume $XAUTH:/root/.Xauthority --name &quot;sedfoam_2312&quot; --workdir=&quot;/home/sudofoam&quot; -v=&quot;/home/users/toto&quot;:/home/sudofoam/workingDir &quot;cbonamy/sedfoam_2312_ubuntu&quot; /bin/bash
-</pre><p>Please adapt the directories to your configuration. In this example, &quot;/home/users/toto&quot; will be mounted on the vm in /home/sudofoam/workingDir. If you change IP, for example when returning from work to home, change the Display variable (in the Docker) accordingly.</p></section></section><section id="start"><h3><a href="#start">Start a container (if existing and not running) :</a></h3><pre>    docker container start sedfoam_2312
-</pre></section><section id="attach"><h3><a href="#attach">Attach to a running container (if existing and running):</a></h3><pre>    docker container attach sedfoam_2312
-</pre><p>Now hack and enjoy! The sedFoam files will be in /home/sudofoam and the solver is already compiled. Note that the bashrc file from openfoam is here : /openfoam/bash.rc</p></section></section>
+</pre></li></ul></li><li><p>initiate docker:</p><pre>    docker run -it --net=host -e DISPLAY=$IP:0 -v /tmp/.X11-unix:/tmp/.X11-unix --name &quot;sedfoam_2406&quot; --workdir=&quot;/home/sudofoam&quot; -v=&quot;/Users/toto&quot;:/home/sudofoam/workingDir &quot;cbonamy/sedfoam_2406_ubuntu&quot; /bin/bash
+</pre><p>Please adapt the directories to your configuration. In this example, &quot;/Users/toto&quot; will be mounted on the vm in /home/sudofoam/workingDir. If you change IP, for example when returning from work to home, change the Display variable (in the Docker) accordingly.</p></li></ul></section><section id="windows"><h4><a href="#windows">On Windows with GUI (graphical interface without paraview):</a></h4><ul><li>configure Docker Engine for windows (with all system requirements: WSL2, step 1-5 from <a href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">https:/<wbr />/<wbr />docs.microsoft.com/<wbr />en-us/<wbr />windows/<wbr />wsl/<wbr />install-win10</a>)</li><li>configure vcxsrv: <a href="https://sourceforge.net/projects/vcxsrv/">https:/<wbr />/<wbr />sourceforge.net/<wbr />projects/<wbr />vcxsrv/<wbr /></a> (disable access control in extra settings)</li><li><p>Get your IP and set DISPLAY variable:</p><pre>    set-variable -name DISPLAY -value YOUR-IP:0.0
+</pre></li><li><p>initiate docker:</p><pre>    docker run -it --net=host --env DISPLAY=$DISPLAY --name &quot;sedfoam_2406&quot; --workdir=&quot;/home/sudofoam&quot; -v=&quot;c:/mydataspace&quot;:/home/sudofoam/workingDir &quot;cbonamy/sedfoam_2406_ubuntu&quot; /bin/bash
+</pre><p>Please adapt the directories to your configuration. In this example, &quot;c:/mydataspace&quot; will be mounted on the vm in /home/sudofoam/workingDir. If you change IP, for example when returning from work to home, change the Display variable (in the Docker) accordingly.</p></li></ul></section><section id="linux"><h4><a href="#linux">On linux with GUI (graphical interface without paraview):</a></h4><pre>    docker run -it --net=host --env DISPLAY=$DISPLAY --volume $XAUTH:/root/.Xauthority --name &quot;sedfoam_2406&quot; --workdir=&quot;/home/sudofoam&quot; -v=&quot;/home/users/toto&quot;:/home/sudofoam/workingDir &quot;cbonamy/sedfoam_2406_ubuntu&quot; /bin/bash
+</pre><p>Please adapt the directories to your configuration. In this example, &quot;/home/users/toto&quot; will be mounted on the vm in /home/sudofoam/workingDir. If you change IP, for example when returning from work to home, change the Display variable (in the Docker) accordingly.</p></section></section><section id="start"><h3><a href="#start">Start a container (if existing and not running):</a></h3><pre>    docker container start sedfoam_2406
+</pre></section><section id="attach"><h3><a href="#attach">Attach to a running container (if existing and running):</a></h3><pre>    docker container attach sedfoam_2406
+</pre><p>Now hack and enjoy!\ The sedFoam files will be in /home/sudofoam and the solver is already compiled. Note that the bashrc file from openfoam is here: /openfoam/bash.rc and the python environment here: /home/sudofoam/pyenv\</p></section></section>
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install.html

@@ -80,7 +80,7 @@ <h3>Contents</h3>
             <li><a href="#use_docker">Don&#x27;t install sedFoam and use the latest sedFoam docker</a></li>
           </ul>
         </nav>
-<section id="install_src_unix"><h2><a href="#install_src_unix">Compiling from source with supported OpenFOAM (last ESI version)</a></h2><p>You need OpenFOAM-v2312 to build the executable. SedFoam versions released after SedFoam-3.3 will be named accordingly to OpenFOAM ESI versions. Currently the latest version is SedFoam-2312.</p><ul><li>First go to the <a href="https://www.openfoam.com/download">download</a> page of the software</li><li><a href="https://www.openfoam.com/download/installation.php">Install OpenFOAM</a>.</li></ul><p>To take full advantage of SedFoam the following additional tools should be installed.</p><ul><li><a href="https://openfoamwiki.net/index.php/Contrib/swak4Foam">swak4Foam</a> extension combines many fonctionalities and is needed for the tutorials</li><li><p>Python usually comes pre-installed in Linux. However, if not installed or if you need a specific version, you can install Python with the following command:</p><pre>sudo apt install python3
+<section id="install_src_unix"><h2><a href="#install_src_unix">Compiling from source with supported OpenFOAM (last ESI version)</a></h2><p>You need OpenFOAM-v2406 to build the executable. SedFoam versions released after SedFoam-3.3 will be named accordingly to OpenFOAM ESI versions. Currently the latest version is SedFoam-2406.</p><ul><li>First go to the <a href="https://www.openfoam.com/download">download</a> page of the software</li><li><a href="https://www.openfoam.com/download/installation.php">Install OpenFOAM</a>.</li></ul><p>To take full advantage of SedFoam the following additional tools should be installed.</p><ul><li><a href="https://openfoamwiki.net/index.php/Contrib/swak4Foam">swak4Foam</a> extension combines many fonctionalities and is needed for the tutorials</li><li><p>Python usually comes pre-installed in Linux. However, if not installed or if you need a specific version, you can install Python with the following command:</p><pre>sudo apt install python3
 </pre></li><li>the python package <a href="https://github.com/fluiddyn/fluidfoam">fluidfoam</a> is needed for postprocessing of the tutorials.</li></ul><p>Compilation is now done by performing the following steps:</p><ol><li><p>Download the official SedFoam package:</p><pre>git clone --recurse-submodules http://github.com/sedfoam/sedfoam
 </pre></li><li><p>Compile the program by running Allwmake:</p><pre>cd sedfoam
 source $FOAM_ETC/bashrc # load the openfoam environment