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(Created page with "== TOPAS == TOPAS (Tool for Particle Simulation) is a program that uses the Geant4 Monte Carlo toolkit to build 3D models of medical physics systems and simulate particle transport through treatment heads, patients, and detectors *Useful Links: ** [https://opentopas.readthedocs.io/en/latest/index.html OpenTOPAS Website] ** [https://opentopas.readthedocs.io/en/latest/getting-started/install.html OpenTOPAS Installation Guide] This is a tutorial about installing and using...")
 
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This sets up all the required EasyBuild modules and environment variables. The version of BDSIM that is used within this script is not the latest build (v1.1.0 instead of v1.2.+) but should be stable. If a newer version is required then contact James Chappell and he will compile a newer version for you to use.
This sets up all the required EasyBuild modules and environment variables. The version of BDSIM that is used within this script is not the latest build (v1.1.0 instead of v1.2.+) but should be stable. If a newer version is required then contact James Chappell and he will compile a newer version for you to use.
Now your system is ready to use <code>BDSIM</code>. To check that it is working correctly, test the built-in help function:
<pre>
$ bdsim --help
</pre>
This should produce an output explaining all the possible options that can be used within <code>BDSIM</code>.
=== Running on the UCL HEP Linux Cluster (Old) ===
'''These instructions are now out of date and it is not recommended that you use this version of BDSIM unless you have experience with the pain of compiling BDSIM, Geant4 and all their dependencies. Whenever possible, use the EasyBuild version. Contact Simon Jolly or James Chappell if any required functionality is missing.'''
In order to run <code>BDSIM</code> simulations on the UCL HEP Cluster, you must first source the development version of the PBT environment from a system within the cluster that is running either CentOS7 or Scientific Linux V6. This can be done using the following command:
<pre>
$ source /unix/pbt/software/scripts/pbt.sh -vd
</pre>
'''Note:''' the '-d' flag is essential as this sources the script that links the latest development software available on the PBT section of the cluster.


Now your system is ready to use <code>BDSIM</code>. To check that it is working correctly, test the built-in help function:  
Now your system is ready to use <code>BDSIM</code>. To check that it is working correctly, test the built-in help function:  

Revision as of 13:43, 20 June 2025

TOPAS

TOPAS (Tool for Particle Simulation) is a program that uses the Geant4 Monte Carlo toolkit to build 3D models of medical physics systems and simulate particle transport through treatment heads, patients, and detectors

This is a tutorial about installing and using TOPAS. TOPAS is installed on the HEP Linux cluster at UCL. You will need an account on that cluster to be able to use this software, run example tutorials and create your own simulations.

Running TOPAS Simulations

In order to run TOPAS simulations, you will either need to download and install the software yourself or make use of the existing installation on the UCL HEP Linux cluster.

In order to use the UCL HEP Linux cluster, you will need a HEP account: please contact Prof. Simon Jolly for more details.

Running on the UCL HEP Linux Cluster (via CVMFS)

In order to run TOPAS simulations on the UCL HEP Cluster, you must source the TOPAS PBT environment from a system within the cluster. This can be done using the following command: 

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

This sets up all the required EasyBuild modules and environment variables. The version of BDSIM that is used within this script is not the latest build (v1.1.0 instead of v1.2.+) but should be stable. If a newer version is required then contact James Chappell and he will compile a newer version for you to use.

Now your system is ready to use BDSIM. To check that it is working correctly, test the built-in help function: 

$ bdsim --help

This should produce an output explaining all the possible options that can be used within BDSIM.

Required Software

BDSIM requires the following software to be installed:

  • Recent compiler with full C++11 support - proven compiler versions are GCC v4.9 or higher, or Clang 6 or higher.
  • CMake v2.8.12 or higher
  • CLHEP v2.1.3.1 or higher
  • ROOT v6.x or higher
  • Geant4 v4.10 or higher
  • Flex v2.5.37 or higher
  • Bison v2.3 or higher

These are all installed on the UCL HEP cluster.

Details

Website
https://twiki.ph.rhul.ac.uk/twiki/bin/view/PP/JAI/BdSim
Latest Version
0.9.9.2 (19th October 2017)

Installation Instructions

The installation process follows the general process described on the UCL HEP Linux Cluster page. The basic method used is as follows:

  1. Check that all the prerequisites for building BDSIM are installed (see above);
  2. Download the latest version of the source code;
  3. Create a build folder;
  4. Configure, build and install BDSIM from within the build folder.

Download BDSIM from its central repository

The BDSIM source code can be downloaded from its git repository using: 

 $ git clone --recursive https://bitbucket.org/jairhul/bdsim

This creates a /bdsim folder within your current folder. This folder contains all the code, examples, documentation and associated Python packages.

Configure, build and install BDSIM

Retrieved from "https://www.hep.ucl.ac.uk/pbt/pbtWiki/index.php?title=Software/TOPAS&oldid=5888"