ELogs/OhieMayenin

To Do

High Priority

• Learn CAD conversion/import method, which is currently understood to be STEP to GDML conversion using python script.
• Run the BDSIM simulations with varying quadropole strength
• Obtain and implement correct dimensions for new dose monitor enclosures.
• Confirm Clatterbridge visit which is to be scheduled for 28th February.

Low Priority

• Update CAD model with Jacinta's measurements (cannot be finalised until Clatterbridge trip in order to measure dose monitor enclosures so set to low priority).
• Rerun Geant4 Clatterbridge simulation in full.
• Update python analysis scripts.

Completed

Term 1

• Background theory reading.
• Literature review.
• CAD model packaging.
• Progress report.
• Geant4 pencil beam example simulations.
• Understand how to setup Geant4, BDSIM and Python environments on HEP Cluster.
• Partially ran Geant4 simulation of CCC by Matthieu.
• Fixed x11 forwarding issues.

Term 2

• 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 and added more detail on fixing issues.
• Verified new dose monitor version and scheduled Clatterbridge visit.
• Modified CAD model to include updated physical measurements sent by Jacinta.
• Obtained and visualised CCC BDSIM gmad files sent by Jacinta.

Troubleshooting Log

Setting up BDSIM envrionment

• 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.

X11 Forwarding via SSH

• 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.

BDSIM Visualiser using OpenGL

• 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'.

Plotting with Pybdsim

• 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.