ELogs/OhieMayenin

To Do

High Priority

• Expand on the troubleshooting log with more detail.
• Find the Clatterbridge simulations for BDSIM which Laurie has referred to.
• Obtain and implement correct dimensions for new dose monitor enclosures.
• Clatterbridge visit to be scheduled for 28th February.

Low Priority

• Rerun Geant4 Clatterbridge simulation in full.
• Update python analysis scripts.

Completed

• Literature review.
• CAD model packaging.
• Progress report.
• Geant4 pencil beam example simulations.
• Understand how to setup Geant4, BDSIM and Python environments on HEP Cluster.
• Fixed x11 forwarding issues.
• Project interview.
• Setup Python 2.7 environment.
• Fixed plot view issues and reported pybdsim bug.
• Fixed BDSIM OpenGL visualiser issues.
• Ran atf2 example in full.
• Created troubleshooting log.
• Verified new dose monitor version and scheduled Clatterbridge visit.

Troubleshooting Log

• Initially ran the following setup script:

$ source /unix/pbt/software/scripts/bdsim.sh

which partially works but crashes when running pybdsim, giving a runtime error every time a pybdsim function is executed. The error I received was as follows:

h = _ROOT.Header() RuntimeError:Header::Header() could not resolve ::()

I fixed this issue by instead running the following setup script:

$ source /unix/pbt/software/scripts/bdsim_setup_jc.sh

which fixes the pybdsim runtime error issues.

• When using SSH to connect to Linux cluster from a Windows machine, X11 forwarding was not enabled. This meant that any graphical windows like ROOT TBrowser and BDSIM GUI could not be accessed. To get around this I use the Exceed client with X11-enabled client PuTTY.

PuTTY for Windows was easily installed from the web. Exceed was installable from the UCL Software Database.

The Exceed client must be opened before starting an ssh session via PuTTY. Once Exceed is open, open PuTTY and go to the SSH tab. Then, under the Auth tab, click on X11, and check the box "Enable X11 forwarding." Then, navigate back to the session tab and connect to plus1 by writing plus1.hep.ucl.ac.uk. A PuTTY terminal window will then open allowing you to input username and password as usual.

• Even after fixing this X11 issues, the BDSIM visualiser which renders the geometry in the BDSIM GUI was not working correctly, showing a static black screen. To fix this, I installed the Exceed extension Exceed 3D, also available from the UCL Software Database, which enables the OpenGL visualiser. Once Exceed 3D is installed, one must open Xconfig from the Exceed terminal and go to the OpenGL tab. Check that 'Enable OpenGL' is enabled, as well as the checkbox 'Direct Rendering'. For my setup, all boxes are checked except for 'Overlay Support'.

• Pybdsim plots did not pop up in a graphical window when generated, even with X11 forwarding enabled. To force these plots to open, one must type the following:

>>> import matplotlib.pyplot as plt

>>> plt.show(block=False)

Once can also use pyplot.savefig() to save these figures, as some pybdsim plot functions do not have any outputsavefile arguments.