Jessica Chiang

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.

To enabled remote access to the MySQL Database server, read this nixCraft page.

But the essence is to add a line to my.cnf (in Ubuntu, /etc/mysql/my.cnf), and make sure "skip-
networking" line is commented out.

#skip-networking
ServerName server-name or IP

Also, to set the firewall so the server can accept remote connections, follow this Ubuntu doc.

5) Set up G-MT Specific Components

First create a local sandbox and check out the trunk from the svn repository as followed:
cd
mkdir sandbox
cd sandbox
svn co svn+ssh://subversion.dsccorp.com/home/svn/repository/g-mt g-mt

5.1) Schema and Data in MySQL Database

cd ~/sandbox/trunk/DataService/db
svn update
./init-db.sh
./resetdb.sh
5.2) Build and Install smDAQ

cd ~/sandbox/g-mt/trunk/smDAQ/src/main/c++
svn update
build/bucket.sh
make install

The content of build/release.sh is as followed:

#!/bin/sh
CPPFLAGS="-O0 -Wall -fPIC" ./configure --prefix=${HOME} --enable-mtbucket &&
make && echo "Type \"make install\" to install"

The build script specifies that smDAQ will be installed in ${HOME} or ~/. The smDAQ
installation will install "bin" and "lib" in ${HOME} according to the release.sh script content
shown above. To change the installation location, change the "--prefix=${HOME}" to desirable
location such as "--prefix=${HOME}/smdaq-test".

If initiating from the flat file, set the SMDAQ_TUBE_FILE envrionment variable to the flat file
path, or make sure that there is ${HOME}/lib/sm0-tube-positions.dat.

5) Set up Analysis Engine (mtbucket)

Set SM0_TUBE_DATA_FILE point to ~/mt-sys/smDAQ/data/sm0-tube-info.dat and

SM1_TUBE_DATA_FILE to ~/mt-sys/smDAQ/data/sm1-tube-info.dat

1. Set environment variables

For smDAQ:
export SMDAQ_TUBE_FILE=/home/jessica/sandbox/lmt-trunk/smDAQ/data/sm0-tube-info-scint.dat

For mtbucket:
export SM0_TUBE_DATA_FILE=/home/jessica/sandbox/lmt-trunk/smDAQ/data/
sm0-tube-info-scint-sm-positions.dat
export SM1_TUBE_DATA_FILE=/home/jessica/sandbox/lmt-trunk/smDAQ/data/
 sm1-tube-info-scint-sm-positions.dat
export SM2_TUBE_DATA_FILE=/home/jessica/sandbox/lmt-trunk/smDAQ/data/
sm2-tube-info-scint-sm-positions.dat
export SM3_TUBE_DATA_FILE=/home/jessica/sandbox/lmt-trunk/smDAQ/data/
sm3-tube-info-scint-sm-positions.dat

For showing tubes

export MTB_SHOW_TUBES=1

2. Build analysis engine

cd ~/mt-sys
svn --username USERNAME co svn+ssh://<muon_ip>/scratch/svn/mt/mtbucket mtbucket
cd mtbucket

./build.sh

6) 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.