AliRoot installation instructions for Ubuntu

AliRoot installation instructions for Ubuntu

There are many people who have been doing this longer than me, but this is what worked for me and there have been a few updates to various components recently. I got many useful Ubuntu tips from this page. Please feel free to email me with questions, but I don't promise to be able to answer them. These instructions are derived substantially from instructions for installation of AliRoot on SL by Ken Read. Things which are not actually needed for a base working system are denoted with a *. I am assuming that you start with a valid grid certificate and that you'll be using bash.

System: 64 bit running Ubuntu 12.04, AliRoot 5.04.03.AN, gcc 4.6.3
Notes on what needs to be done for a mac in green - these notes are not complete.

Install additional programs you may need, either through the synaptic package manager or apt-get or whatever your favorite method is. This can include:
build-essential gfortran subversion xorg-dev libxml2-dev libmysqlclient-dev libfftw3-dev libssl-dev libglu1-mesa-dev curl libboost1.40-dev libboost1.40-all-dev libpng12-dev libimlib2-dev
This may not be a complete list and let me know if there's something I need to add.
Set up scripts aliceme.sh and setup_AliROOT.sh
These are scripts which set up the environmental variables. I tried to add comments so that it's clear how you should change them for your system. Once you've adjusted them properly:
source aliceme.sh && source setup_AliROOT.sh
(If you take a break somewhere in the process and shut down, you'll need to redo this step before continuing on your next step.)
Installation of AliEn
Make sure your installation alien and .alien directories are clean. Not a bad idea to wipe out ~/.alien too.
If this machine will be used by more than one person (or may be used by more than one person in the future):

ln -s /bin/sh
If this points to dash:
rm /bin/sh
ln -s /bin/bash /bin/sh

This solves an Ubuntu-specific problem with alien
wget http://alien.cern.ch/alien-installer
chmod u+x alien-installer
(note if you already have an alien installer in this directory, the new one will be named alien-installer.1 - be sure you run the latest version!)
./alien-installer -install-dir $ALIEN
After you reach this step you should be able to test your alien installation by setting up your grid environmental variables and then getting a token. This can be done by "setstorageelementALICEDISK" if you've used the aliases in the setup file. You may be prompted to recompile parts of alien - this is fine. But you should successfully get a token. If you can't get a token, you will likely have problems connecting to the grid and may have to recompile parts of ROOT and/or AliRoot.

Note: Recompilation will fail if you do not have curl installed, and you will get the error
chmod: cannot access `/tmp/xgapi': No such file or directory
because there are lines in alien-token-init
                rm -rf /tmp/xgapi
                curl -s http://project-arda-dev.web.cern.ch/project-arda-dev/alice/xalienfs/xgapi -o /tmp/xgapi >& /dev/null
                chmod u+x /tmp/xgapi
Notice how it redirects the output to /dev/null so you don't know it failed because you don't have curl.
As of 13 July, 2010, for Ubuntu, you should not recompile alien when it prompts you to when you get a token. It tells you you can't make links to other libraries because you used a different version of gcc, but you can. Compiling alien fails in a weird obscure way that is not yet sorted out. This is not a good long term solution, but it's a temporary function work around.

Installation of ROOT
Check the compatibility of the version of AliRoot you're trying to install here and install the necessary version of ROOT. This page lists the packages currently available on the grid. This configuration file should work. (But if you have a 32 bit system you need to change the line ./configure linuxx8664gcc \" to "./configure \".) Note that if your fortran compiler is wrong (not gfortran) you can actually compile ROOT but you will get stuck later and have to recompile ROOT.
mkdir root5.26.00
ln -s root5.26.00 root
cd root
svn co https://root.cern.ch/svn/root/tags/v5-26-00 root (for trunk - not recommended unless you NEED it - https://root.cern.ch/svn/root/trunk root)
mv root/* .
mv root/.svn .
ls -a root (move anything in there to .)
rmdir root
cd $ROOTSYS
pwd (make sure you're in the right directory and have loaded your environmental variables. Compiling over a good installation of root will make your life uncomfortable.)
./configureroot
make
(If you need to recompile, make clean && make.)
If you see no errors, try
root -b -q
check the version number and make sure the right version of root got loaded if you have multiple versions on your computer.
You can test root:
cd test
make
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:.
./stress
./stressHepix
(This has never failed for me when there were no compilation problems and my environmental variables were set properly. However, when I didn't set my environmental variables properly and I did have another version of root, it doesn't compile.)
cd $ALICE

Now you can test that alien and root compiled well together. Download this macro and this collection file. Get an alien token (alien-token-init username) and run 'root -b -q TestAlien.C'. If this does not work, you have a problem in your alien installation or root installation.

*Installation of FLUKA
Unless you know what you're doing and really need fluka, skip this step for now!
This isn't needed for everyone. If you need FLUKA, you need to get a Fluka ID and agree to the license to download Fluka and you need permission from Peter Hristov to get access to the AliRoot interface to FLUKA. Then...
cd $FLUPRO ($ALICE/fluka) (mkdir $ALICE/fluka if does not exist)
Download the latest FLUKA version from http://www.fluka.org
mv fluka.tar.gz $FLUPRO
tar -xvzf fluka.tar.gz
#export FLUPRO=/somePath/myFlukaArea (done in setup)

cd $ALICE
svn co https://alisoft.cern.ch/fluka_vmc/trunk fluka_vmc
(now requires a password)
cd fluka_vmc/source
make
#export FLUKALIB=$ALICE/fluka_vmc/lib/tgt_$ALICE_TARGET (done in setup)
#export LD_LIBRARY_PATH=$FLUKALIB/\:$LD_LIBRARY_PATH (done in setup)
cd $ALICE
GEANT
cd $ALICE
svn co https://root.cern.ch/svn/geant3/tags/v1-11 geant3
cd $ALICE/geant3
make
*Installation of FastJet
This is not needed for everyone. I would strongly recommend that you not do this if you don't need fastjet because there are many potential hiccups. The versions of CGAL and FastJet are important because not all versions work with each other.

Installation of BOOST
Install the package libboost1.40-dev, libboost1.40-all-dev (recommended)
For Mac: sudo port install boost
or
cd $ALICE/boost
download boost_1_40_0.tar.gz from http://www.boost.org/ (may use later version)
gunzip boost_1_40_0.tar.gz
tar -xvf boost_1_40_0.tar
./bootstrap.sh
./bjam
Installation of CGAL
download CGAL-4.0.tar.gz from http://www.cgal.org/
[yes it does matter which CGAL version is installed. Not all versions are compatible with FastJet.]
tar -xzvf CGAL-4.0.tar.gz
cd CGAL-4.0
cmake-gui .
This pops up a window and you can check configuration choices. You will need to set the following things by hand:
1. It doesn't find MPFR by default so you'll have to input its location. If you don't have mpfr by default, install it. Use 'locate libmpfr' to find the location of the location of mpfr. For me MPFR_INCLUDE_DIR=/usr/include, MPFR_LIBRARIES=usr/lib/x86_64-linux-gnu/libmpfr.so, MPFR_LIBRARIES_DIR=usr/lib/x86_64-linux-gnu/
2. Uncheck WITH_GMP and WITH_GMPXX [Currently the version of GMP installed by default on Ubuntu is too old to work with CGAL. This means you would need to install a new version of GMP to get it to compile properly with CGAL. Unfortunately the compiler still finds the old GMP when compiling FastJet. But you can't remove GMP because gfortran is cross-compiled with the old GMP. And at that point you'd just have to cross compile too much stuff.]
3. Set your CGAL install directory - be sure this matches your configuration script.
4. Set your cxx flags as "-lgmp -frounding-math" (not sure this is necessary without GMP but it works at least.)
Then
make
make install
Installation of FastJet
Download fastjet-2.4.0.tar.gz from http://fastjet.fr (Other versions may work but I know this one does.)
./configure --enable-cgal --prefix=`pwd`/../fastjet-install
./configure --prefix=`pwd`/../fastjet-install
make
make check
make install
cd ..
bash fixfastjet.sh

FastJet 3.0.3 currently doesn't work with AliRoot but thes instructions are kept for future use
Download fastjet-3.0.3.tar.gz from http://fastjet.fr (Other versions may work but I know this one does.)
./configure --prefix=`pwd`/../fastjet-3.0.3-install --enable-cgal --with-cgaldir=$CGAL
make
make check
make install

Now you can check fastjet. Copy this file and this macro to your computer and run 'aliroot -b -q testFastJet.C'. It should run ok. (The macro is from $ALICE_ROOT/JETAN/, with one minor modification.)

AliRoot
cd $ALICE
svn co http://svn.cern.ch/guest/AliRoot/tags/v5-04-08-AN/ AliRoot (http://svn.cern.ch/guest/AliRoot/trunk https://svn.cern.ch/reps/AliRoot/trunk or for trunk. The latter is the version you need to log in to - you probably want that for trunk if you will be checking code in)
mkdir $ALICE_ROOT/objdir [name of object directory, cannot be same as $ALICE_ROOT]
cd $ALICE_ROOT/objdir [name of object directory, cannot be same as $ALICE_ROOT]
cmake $ALICE_ROOT
make -j4
make install

*If you installed FLUKA
cd $ALICE_ROOT/TFluka/scripts
./runflukageo.sh
Note: If your gcc version changed because things were updated on your system, you will need to re-install CGAL, update the path to the CGAL library, reinstall FASTJET (starting with the tarball because the fix for AliRoot prevents the FASTJET compilation from working) and recompile JETAN AND HLT. It may be necessary to recompile other parts of AliRoot, too - I'm not sure.

Differences between Ubuntu and SL5
Differences which are definitely related to Ubuntu

ROOT configuration file needs extra options:
--with-f77=gfortran --build=debug --disable-xrootd

Note I was not able to get alien-token-init to work in csh. I did not spend a lot of time debugging this.

Time protocol issues
You won't be able to connect to AliEN unless you have your time server working. To set the time server on Ubuntu, go to System->Administration->Time and Date. Click to make changes and enter your password. Select "Keep synchronized with internet servers." I have found ntp.cesnet.cz works quite well.