This article gives a step-by-step instruction on how to set up a Ubuntu 64 Bit machine to be a development machine for high energy physics

Set up Geant and Root Development Environment On 64 bits
Ubuntu 8.0.4 AMD 64 bits machine

 

0.1) Install Ubuntu 8.0.4

Install Ubuntu 8.0.4 and complete basic setup such as networking.

0.2) Install Necessary Package

Installed the following packages using "apt-get install" command.

 

libX11-dev g++ libxft-dev libxpm-dev libxt-dev freeglut3 freeglut3-dev libglut3 libglut3-dev libmotif3 libmotif-dev x11proto-print-dev libxaw7-dev libmudflap0 libmudflap0-dev po-debconf intltool-debian subversion libusb-dev libboost-dev libmysql++-dev autoconf automake libtool libc6-dev-i386 graphviz and graphviz-dev for GraphViz software libcxx libxerces28 libxerces28-dev cppunit-dev

 

1) Set up Root

 

Obtain the latest Root from http://root.cern.ch. I used Root version 5.18.

 

Unzip the Root package to the location of choice, say ~/mt-sys. After unzipping, there will be a “root” directory in ~/dev. We will come back in the later step to set up root configuration.

 

To build Root from source, download the source ball, unzip it, then change to the source directory

#cd ~/SetUpZip #tar -zxvpf <root_src>.tar.gz #cd <root_src> #./configure –-prefix=~/install/root --enable-mysql --enable-opengl --enable-python # make # make install

 

Notes on tar options used above

• -z : unzip the file first

• -x : extract the files from the tarball

• -v : "verbose" (i.e tar tells you what files it's extracting)

• -p : preserves dates, permissions of the original files

• -f : use the file in question (if you don't specify this, tar just sort of sits around doing nothing)

 

Add the following lines to your ~/.bashrc file

 

CURCWD=`pwd` cd ~/dev/root source bin/thisroot.sh cd $CURCWD export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib/root export PATH=$ROOTSYS/bin:$PATH

 

2) Set up CLHEP

 

To build CLHEP, you need gcc-3.2.3 or higher.

 

Obtain CLHEP source package from http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/clhep.html.

 

I used version 2.0.3.1 (

http://proj-clhep.web.cern.ch/projclhep/DISTRIBUTION/distributions/clhep-2.0.3.1.tgz)

 

Save the tar ball in a directory of choice, say ~/install. Then unzip and then do configure, make, and make install in the unzipped directory. Note that by default, the CLHEP is installed in /usr/local. I set the installation path to /home/username/dev/CLHEP by doing “./configure –-prefix=/home/username/dev/CLHEP”.

 

cd ~/SetUpZip tar -zxvpf clhep-<version>.tar cd <version>/CLHEP ./configure –-prefix=/home/username/dev/CLHEP make make install

 

Add the following lines to /home/jessica/.bashrc file

 

export CLHEP_BASE_DIR=/home/username/dev/CLHEP export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CLHEP_BASE_DIR/lib

 

3) Set up Geant4

 

Obtain the source package from Geant4 site http://geant4.web.cern.ch/geant4/. I used Geant4.8.2.p01 (http://geant4.web.cern.ch/geant4/support/source/geant4.8.2.p01.tar.gz).

 

Unzip the tar ball to your directory of choice, say ~/geant4. Unzip and then change directory to ~/geant4/geant4.8.2.p01 to run the “Configure” script.

 

cd ~/SetUpZip tar -zxvpf geant<version>.tar.gz cd geant<version> mkdir data ./Configure -build

 

 

 

Extra actions:

Add /home/jessica/SetUpZip/geant4.8.2.p01/data

 

Entered the CLHEP_BASE_DIR

CLHEP_BASE_DIR: /home/jessica/mt-sys/CLHEP

 

You will be asked a series of question and most of them can be answered with a default answer. The questions you need to answer carefully are

 

• the path to your CLHEP install (from step 2)

• whether to install certain libraries

  NOT  

  OPTION NAME	VALUE
  G4UI_NONE	NO
  G4UI_BUILD_XAW	YES
  G4UI_USE_XM	YES
  G4UI_BUILD_QT	NO
  G4VIS_NONE	NO
  G4VIS_USE_OPENGLX	YES
  G4VIS_USE_OPENGLXM	YES
  G4VIS_USE_DAWN	NO
  G4VIS_USE_OIX	NO
  G4VIS_USE_RAYTRACERX	YES
  G4VIS_USE_VRML	NO
  G4VIS_BUILD_OPENGLQT	NO
  G4LIB_BUILD_GDML	NO
  G4LIB_BUILD_G3TOG4	NO
  G4LIB_BUILD_ZLIB	YES
  G4ANALYSIS_USE (NO)	NO

   

 

 

NOTE: Instead of libX11-devel, use libX11-dev

 

Once geant4 has been installed, you need to create a script named “env.sh” to set the Geant4 environment variables. To create “env.sh” automatically:

 

cd ~/SetUpZip/geant4.8.2.p01 ./Configure cp: overwrite `./env.csh` (enter y) cp: overwrite `./env.sh`

 

Two files will be created: “env.sh” and “env.csh”. Next step is to modify the .bashrc script so that this environment variables for CLHEP, Root, and Geant4 will all be set up correctly. I added the following line to ~/.bashrc:

 

source ~/SetUpZip/geant4.8.2.p01/env.sh export G4WORKDIR=~/g4work

 

Log out and log back in to your account, then a slew of log messages from running "env.sh" should be printed to the screen.

 

 

4) Install MySQL Databaser Server

 

 

sudo apt-get install mysql-server

 

Optionally, for remote access, install PHPMYADMIN, a web-based MySQL query browser, as followed:

 

sudo apt-get install apache2 sudo apt-get install php5 libapache2-mod-php5 sudo apt-get install phpmyadmin

 

You wi

phpmyadmin is installed under /var/www, and we need to set phpmyadmin as the default document root in Apache2. To do so

 

sudo cp /etc/apache2/sites-available/default /etc/apache2/sites-available/phpmyadmin sudo vi /etc/apache2/sites-available/phpmyadmin

 

Then search for "DocumentRoot" in "/etc/apache2/sites/available/phpmyadmin", when found, change that line from

... DocumentRoot /var/www ... <Directory /var/www/> ...

 

to be consistent with the phpmyadmin site path:

... DocumentRoot /usr/share/phpmyadmin Ser... <Directory /usr/share/phpmyadmin/> ... ...

 

 

Then disable default site and enable phpmyadmin site as followed:

 

sudo a2dissite default sudo a2ensite phpmyadmin sudo /etc/init.d/apache2 restart

 

Now you should be able to browse phpmyadmin site by opening http://<ip-of-this-server>.

 

 

Also, to have Apache2 recognize a host name, instead of just IP,

 

sudo vi /etc/apache2/apache2.conf

 

Then add the following line at the top of apache2.conf.

ServerName server-name

 

Restart Apache2 HTTP server

 

sudo /etc/init.d/apache2 restart

 

Now you should be able to browse phpmyadmin site by opening http://server-name.

5) Install VTKViewer (Optional)

First we need to install VTK (The Visualization Toolkit) from source.

Install cmake if not already installed:

 

sudo apt-get install cmake

 

 

Go to VTK site (http://www.vtk.org/index.php) and download

 

VTK source tar ball, vtk-<version>.tar.gz,

VTK data tar ball, vtkdata-<version>.tar.gz,

VTK MPeg encoder, vtkmpeg2encode.tar.gz.

 

Extract the all three tar ball:

 

cd ~/SetUpZip tar xvf vtk-<version>.tar.gz tar xvf vtkdata-<version>.tar.gz tar xvf vtkmpeg2encode.tar.gz cd ~/mt-sys

First build and install vtkmpeg2encode. NOTE: Please build vtkmpeg2encode BEFORE building VTK, so that the VTK's configure script can detect vtkmpeg2encode, which is required for a successful VTK source build.

cd vtkmpeg2encode ccmake .

 

You would see the selection as followed:

CMAKE_BACKWARDS_COMPATIBILITY 2.4

 

Leave it unchanged and enter [c] to configure. Then you would see:

 

CMAKE_BUILD_TYPE * CMAKE_INSTAL_PREFIX */usr/local EXECUTABLE_OUTPUT_PATH /home/jessica/mt-sys/vtk/bin LIBRARY_OUTPUT_PATH /home/jessica/mt-sys/vtk/lib CMAKE_BACKWARDS_COMPATIBILITY 2.4

 

Toggle 't' to turn on the Advanced mode and add "-fPIC" at both CMAKE_CXX_FLAGS and CMAKE_C_FLAGS flags

 

... CMAKE_CXX_FLAGS -fPIC ... CMAKE_C_FLAGS -fPIC

 

 

 

 

 

Then press 'c' to configure, then 'g' to generate make file. After makefile is generated, make vtkmpeg2encode.

 

make

 

 

To build Visual Tool Kit SDK from source,

 

cd ~/SetUpZip cd VTK ccmake .

 

 

BUILD_EXAMPLES ON BUILD_SHARED_LIBS ON vtkMPEG2Encode_INCLUDE_PATH /home/jessica/SetUpZip/vtkmpeg2encode vtkMPEG2Encode_LIBRARIES /home/jessica/SetUpZip/vtkmpeg2encode/libvtkMPEG2Encode.a

 

 

Press [c] to configure and then [g] to generate makefile.

 

make

 

 

Press 'g' to generate and exit. Then "make" to compile. I've added a VOXViewer folder under VTK/Examples, modified VTK/Examples/CMakeLists.txt to include VOXViewer in the build. Therefore, when the build completes, there should be a "voxview" binary in VTK/bin. The voxview needs to read from a vox file, which is located in VTK/Examples/VOXViewer. To run voxviewer and read from a vox file:

 

 

#bin/voxview Examples/VOXViewer/mutom_vansim_Wobj_medreg_1m.vox

 

 

 

 

 

 

 

 

 

 

 

cd ${TRUNK}/vtkviewer ccmake .

 

Move blinking box to the VTK_DIR line, then hit enter. Enter the path to the VTK directory. Then hit enter, and click 'g' to regenerate the build script.

 

make

 

 

7) Set up Python Development Environment

The list of python modules to install (use apt-get)

python2.5 python2.5-dev python-glade2 python-gtk2 python-gtkmvc python-imaging python-mysqldb python-paramiko python-reportlab python-vtk python-vte

 

I am using Netbean6.5 and for most of my back-end python development and Glade Interface Designer for front-end development. I also like IDLE because it provides python session and can easily indent and dedent but occasionally it crashes.

 

 

 

 

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