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installGateRTion.md

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~/rtion/# VM setup

Installed XUbuntu v18.04 LTS

uname: gate
psswd: virtual

Install VirtualBox guest packages to enable things like copy-paste

Start the Virtual Machine
From the menus at the top of the virtual machine container window
Select Devices -> Install Guest Additions
This will mount the Guest Additions CD
Open a terminal, navigate to the CD, then run
sudo apt-get install virtualbox-guest-additions-iso
`sudo ./VBoxLinuxAdditions.run

Also remember to set things like clipboard to bidirectional in you VBox manager.

VBox setup is frozen after initialisation - all updates turned off!!!

Using instructions from
https://github.com/OpenGATE/Gate/wiki/Gate-RTion-project

Configuration

  • GEANT4-10.3
  • ROOTv6.08.06
  • Physics: GBBC_EMZ or QGSP_BIC_EMZ

Basic preparation

making an install directory

cd ~/
mkdir rtion

Required basic packages for installation

sudo apt-get install gcc g++ cmake make

GEANT4.10.03.p03

following instructions from:
https://scicomex.com/how-to-install-geant4-on-linux

additional dependencies for geant4 - produce error messages:

sudo apt-get install libexpat-dev qt5-default libx11-dev libxmu-dev

These are included due to the following error messages received when installing without:

missing: EXPAT_LIBRARY EXPAT_INCLUDE_DIR

Qt version "" from NOTFOUND, this code requires Qt 4.x
X11 Xmu library and/or headers

obtain geant4.10.03 with patch-03 from:
https://geant4.web.cern.ch/support/download_archive

cd ~/rtion/
mkdir geant4
cd geant4/
wget -c http://cern.ch/geant4-data/releases/geant4.10.03.p03.tar.gz
tar -zxf geant4.10.03.p03.tar.gz
mkdir geant4.10.03.p03-build
mkdir geant4.10.03.p03-install
mkdir geant4.10.03.p03-data
cd geant4.10.03.p03-build/

generate install files with cmake and following options

cmake \
-DCMAKE_INSTALL_PREFIX=~/rtion/geant4/geant4.10.03.p03-install/ \
-DGEANT4_BUILD_MULTITHREADED=OFF \
-DGEANT4_INSTALL_DATA=ON \
-DCMAKE_INSTALL_DATADIR=cdata/ \
-DGEANT4_USE_OPENGL_X11=ON \
-DGEANT4_USE_QT=ON \
-DGEANT4_USE_RAYTRACER_X11=ON \
~/rtion/geant4/geant4.10.03.p03/

if cmake successful

make (-j<nCPU>)

make install

activate by sourcing the appropriate .sh file

source ~/rtion/geant4/geant4.10.03.p03-install/bin/geant4.sh

also add into .bash_aliases for future useres

ROOTv6.08.06

install required dependencies as listed at:
https://root.cern/install/dependencies

sudo apt-get install git dpkg-dev cmake g++ gcc \
binutils libx11-dev libxpm-dev libxext-dev libxft-dev

libxft-dev may not install properly, if so this is because it requires a specific version of libfreetype6. In this case:

sudo apt-get install libfreetype6=2.10.1-2
sudo apt-get install libxft-dev

install required version of ROOT from:
https://root.cern/install/all_releases/
https://root.cern/releases/release-60806/

Building from source to ensure compatible gcc and other compilers.

cd ~/rtion/
mkdir root/
cd root/

wget -c https://root.cern/download/root_v6.08.06.source.tar.gz
tar -xzf root_v6.08.06.source.tar.gz
mv root_v6.08.06.source.tar.gz root-6.08.06/
mkdir root-6.08.06-build/ root-6.08.06-install/
cd root-6.08.06-build/
cmake \
-DCMAKE_INSTALL_PREFIX=~/rtion/root/root-6.08.06-install/ \
~/rtion/root/root-6.08.06/

As long as cmake is successful,

make [-- -j<nCPU>]

make install

The compilation instructions on the website which included make and install simultaneously failed repeatedly so separated to allow completion.

<make install requires sudo permissions to write to location.
May be able to avoid this requirement by specifying an install directory.>

activate by sourcing the appropriate .sh file

source ~/rtion/root/root-6.08.06/bin/thisroot.sh

also add into .bash_aliases for future useres

GATE 8.1 RT-ion

Following instructions from these sources:
http://www.opengatecollaboration.org/GateRTion
https://github.com/OpenGATE/Gate/tree/GateRTion

cd ~/rtion/
mkdir gate
cd gate/
wget -c https://github.com/OpenGATE/Gate/archive/GateRTion.zip
unzip GateRTion.zip

then following the instructions from:
https://opengate.readthedocs.io/en/latest/compilation_instructions.html

mkdir gate-build
mkdir gate-install
cd gate-build/

generate install files with cmake and following options

cmake \
-DCMAKE_INSTALL_PREFIX=~/rtion/gate/gate-install/ \
~/rtion/gate/Gate-GateRTion/

if cmake successful

make (-j<nCPU>)

make install

finally add the location of the gate executable to the system path

export PATH=$PATH:~/rtion/gate/gate-install/bin/

also add into .bash_aliases for future useres

Issues

Currently no known issues but only very minimal testing has been performed.

START HERE.txt

Paste the following into a text file on the desktop of the device

Welcome to the GATE RT-ion virtual machine

Created by Andrew Gosling on YYYY-MM-DD
For details contact [email protected]

This VM should meet the requirements of the GATE RT-ion project.
Setup is according to the instructions found here:
https://github.com/OpenGATE/Gate/wiki/Gate-RTion-project

This VM is supplied under GNU GPL-3.0
###   USE IS ENTIRELY AT YOUR OWN RISK   ###



uname:  gate
pword:  virtual



The installation was performed in line with the documentation found here:
https://github.com/UCLHp/how-to/blob/master/installGateRTion.md


 - The keyboard is currently set for UK standard but can be changed in settings
 - Ensure copy and paste are set to biderectional in your VM manager
 - Networking is set to NAT which should work on most systems
 - Processors and memory allocation should also be adjusted in your VM manager
 - All automatic updates have been disabled where possible
   - Take care when performing updates that they do not affect the underlying function of GATE