Overview#

tomwer

Tomwer is offering tools to automate acquisition and reconstruction processes for Tomography. It contains:

  • A library to access each acquisition process individually.

  • GUI and applications to control main processes (reconstruction, data transfer, etc.) and execute them as standalone applications.

  • An Orange add-on to help users define their own workflow (http://orange.biolab.si)

Be aware that some demo/tutorial videos are available on https://www.youtube.com/@tomotools This notebook focuses on how to run things with Tomwer 1.x versions.

It is available from the cluster by:

  1. Allocating a node with a GPU like:

salloc --partition gpu --gres=gpu:1 --mem=256G srun --pty bash -l

  1. Load the ‘tomotools’ module:

module load tomotools  # or module load tomotools/{version==dev|stable|1.x} for a specific version

Version can be dev, stable, 1.0, for example.

  1. Launch Tomwer:

tomwer {command} {options}

For example, to launch the canvas with a workflow file as a parameter:

tomwer canvas my_file.ows

Be aware that on beamline computers, you can have your own (editable / dedicated) Python virtual environment with Tomotools installed. They are usually on the /nobackup partition. Furthermore, some aliases to those virtual environments can exist, like:

tomwer-1.0 {command} {options}

Documentation can be found at https://tomotools.gitlab-pages.esrf.fr/tomwer/

Troubleshooting - X Forwarding#

If you encounter the following error:

qt.qpa.xcb: could not connect to display
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb.

Aborted (core dumped)

It most probably means that you have trouble with X Forwarding.

As a reminder, usually to connect to the cluster, users must use:

ssh -XC {user}@cluster-access

Then on some OS, you might need to add X Forwarding (--x11 option) like:

salloc --partition gpu --x11 --gres=gpu:1 --mem=256G srun --pty bash -l