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Improve Singularity.md documentation (#349)
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UmarAbubacar authored Nov 10, 2023
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Expand Up @@ -90,3 +90,22 @@ If you wish to read further about Singularity, you can find a substantial amount
singularity home website: https://sylabs.io/guides/3.5/user-guide/introduction.html. Including many tutorials and more
complex use cases.


## Exporting visualisations on HPC's
By default, BioDynaMo uses ParaView for visualization, which needs an X-display server to function. Since the Singularity image does not provide a graphical desktop environment and hence no X-server, there are two workarounds.

### Option 1: Using xvfb
```xvfb``` stands for X virtual frame buffer and emulates the required display server. Start a virtual frame buffer with:
```
/biodynamo/util/xvfb-initd.sh start
```
The buffer can be managed with the arguments ```start```|```stop```|```restart```

Note: Some systems may require display forwarding **before** starting the frame buffer. This can be achived through ```export DISPLAY=0```.

### Option 2: Setting Paraview to work in a headless mode using the CMAKE flag
Paraview with the osmesa or EGL backend does not require an X-server. To change the backend, you have to edit the cmake options in [1], build paraview, and replace the ParaView version that BioDynaMo installs. See also [2].

[1] https://github.com/BioDynaMo/biodynamo/blob/HPC-documentation/util/build-third-party/paraview/build.sh

[2] https://discourse.paraview.org/t/pvpython-offscreen-rendering-segfault/246/3

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