From 253ef13637ab6cce132e532f1a17718927037abd Mon Sep 17 00:00:00 2001 From: Umar <83470599+UmarAbubacar@users.noreply.github.com> Date: Fri, 10 Nov 2023 16:55:37 +0000 Subject: [PATCH] Update Singularity.md --- doc/user_guide/Singularity.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/doc/user_guide/Singularity.md b/doc/user_guide/Singularity.md index e7f132970..ca3350275 100644 --- a/doc/user_guide/Singularity.md +++ b/doc/user_guide/Singularity.md @@ -92,16 +92,20 @@ complex use cases. ## Exporting visualisations on HPC's -Some HPC systems may not allow users to export visualisations using the paraview exporter. To bypass this issue there are two options. - +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 -Start a virtual frame buffer with: +```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 by the arguments ```start```|```stop```|```restart``` +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