For the project you will need an envinronment that allows you to compile and run different types of software. In the student room there are linux machines that you can use. If you prefer to use your windows computer, you will need to run linux on a virtual machine or use docker (more modern).
First you have to install docker on your laptop. For windows you can download it here: https://docs.docker.com/docker-for-windows/
Once you have installed docker you will have to install some libraries. Follow these instructions that have you can type into the terminal:
docker pull ubuntu:23.04 #this gets long-term support ubuntu version 23.04
docker run -i -t ubuntu /bin/bash # add --platform linux/amd64 when using apple M chip
apt update -y
apt install -y vim wget curl libcurl4-gnutls-dev build-essential gfortran cmake libmysqlclient-dev xorg-dev libglu1-mesa-dev libfftw3-dev libssl-dev libxml2-dev git unzip python3-pip autoconf automake autopoint texinfo gettext libtool libtool-bin pkg-config bison flex libperl-dev libbz2-dev libboost-all-dev swig liblzma-dev libnanomsg-dev libyaml-cpp-dev rsync lsb-release unzip environment-modules
apt-get install xutils-dev libgsl-dev libtbb-dev
apt-get install apt-utils
pip install matplotlib numpy certifi ipython==7.28.0 ipywidgets ipykernel notebook metakernel pyyamlIf you prefer to use a virtual machine running ubuntu, use google to find one that you like. Afterwards you will have to install the same libraries as listed above for docker. Note that you will have to put sudo in front of all the apt commands.
On a mac there is no need for a virtual machine or docker. But you will need a C++ compiler that you can get by installing xcode to be found in the AppStore.
On this webpage you find useful information about connecting to the Nikhef server and setting up VSCode: https://codimd.web.cern.ch/bt5CCq7JQlCsDk5xT-EHrw#Setting-up-your-Visual-Studio-Code-remote
Start with creating a directory in which you want to install the software that you will use for this project. For example:
mkdir softNow go into the created directory:
cd softThe easiest is to just grep a precompiled version from the root website https://root.cern/install/all_releases/ (take ROOT6). You can do this directly from the terminal:
wget https://root.cern/download/root_v6.30.02.Linux-ubuntu23.04-x86_64-gcc12.3.tar.gz #adjust this line with the appropriate version for you OS (see link above)
tar xvfz root_v6.30.02.Linux-ubuntu23.04-x86_64-gcc12.3.tar.gz
rootsetup=$PWD/root/bin/thisroot.sh
cd root
source $rootsetup
echo 'cd '${PWD}'' >> ~/.bashrc
echo 'source '${rootsetup}'' >> ~/.bashrc
cd ..
echo 'cd '${PWD}'' >> ~/.bashrcIf you are working on a system with cvmfs you can also grep it from there. For example
source /cvmfs/sft.cern.ch/lcg/views/setupViews.sh LCG_105 x86_64-centos7-gcc12-optwget https://pythia.org/download/pythia83/pythia8310.tgz
tar xvfz pythia8310.tgz
cd pythia8310
./configure
make
PYTHIA=$PWD
cd ..curl -O http://fastjet.fr/repo/fastjet-3.4.3.tar.gz
tar zxvf fastjet-3.4.3.tar.gz
cd fastjet-3.4.3/
./configure --prefix=$PWD/../fastjet343-install
make
make check
make install
FASTJET=$PWD/../fastjet343-install
cd ..
export FJ_CONTRIB_VER=1.053
curl -Lo source.tar.gz http://fastjet.hepforge.org/contrib/downloads/fjcontrib-"$FJ_CONTRIB_VER".tar.gz
tar xzf source.tar.gz
cd fjcontrib-"$FJ_CONTRIB_VER"
./configure --fastjet-config=$FASTJET/bin/fastjet-config --prefix=`$FASTJET/bin/fastjet-config --prefix`
make
make install
make fragile-shared #make shared library
make fragile-shared-install
cd ..git clone https://github.com/mverwe/JetToyHI.git
cd JetToyHI
git pull --rebase origin master
echo `$FASTJET/bin/fastjet-config --prefix` > .fastjet
echo $PYTHIA > .pythia8cd PU14
echo `$FASTJET/bin/fastjet-config --prefix` > .fastjet
./mkmk
make
cd ..
scripts/mkcxx.pl -f -s -1 -r -8 '-IPU14' -l '-LPU14 -lPU14 -lz'
makeNow you are done installing software. Let's generate 10 pythia events and run a simple jet analysis.
./runCreatePythiaEvents -nev 10 -pthat 120 -tune 14
./runSimpleJetAnalysis -hard PythiaEventsTune14PtHat120.pu14 -nev 10You will have produced a root file with a tree. In this tree properties of jets are stored in std::vector format. To check what is inside do:
root JetToyHIResultSimpleJetAnalysis.root -l
TBrowser b
Click on jetTree and play around.
- If you want to contribute to this code you need to have a github account. Go here to do so: https://github.com/join.
- Fork the original repository. Go to: https://github.com/mverwe/JetToyHI and click 'Fork' in the upper right corner.
- Instead of cloning the original repository as shown above, clone your own.
- After committing your changes to your own branch, push them to your own fork. Don't know how to do this, ask your colleages or use google which might bring you here https://services.github.com/on-demand/downloads/github-git-cheat-sheet/
- Do a pull request once you have finished your developments.
ssh -Y [solisID]@gemini.uu.nl
ssh -Y quark.science.uu.nl
Now you are remotely logged in.
We will use the centrally installed software for ROOT, pythia and fastjet:
module load python/2.7
export PATH=/cm/local/apps/environment-modules/3.2.10/Modules/3.2.10/bin/:$PATH
export ALIBUILD_WORK_DIR=/data1/software/alisoft
alienv enter --shellrc VO_ALICE@pythia::v8243-3,VO_ALICE@ROOT::v6-18-04-alice1-2,VO_ALICE@fastjet::latest-v3.3.3-release,VO_ALICE@GSL::v1.16-4
Last step is to install JetToyHI. (note that a new branch was created to make it compatible with the fastjet version that is available on the quark cluster)
git clone https://github.com/mverwe/JetToyHI.git
cd JetToyHI
git pull --rebase origin forbsc2
pythia8-config --prefix > .pythia8
fastjet-config --prefix > .fastjet
cd PU14
cp ../.fastjet .
./mkmk
make
cd ..
scripts/mkcxx.pl -f -s -1 -r -8 '-IPU14' -l '-LPU14 -lPU14 -lz'
make
A handy way is to make a submit script. Here I list an example and I name this file runJob.sh:
#!/bin/bash
mkdir gqoexjburg
cd gqoexjburg
cp /nethome/verwe121/soft2/JetToyHI/runCreatePythiaEvents .
./runCreatePythiaEvents -nev 10 -tune 14 -pthat 120
ls
To submit this job to the quark cluster you type:
qsub -V -cwd -N job1 runJob.sh
More info on the quark cluster can be found here: https://uugrasp.github.io/UUComputingDocs/quarkCluster.html
Event samples can be found in the jet quenching CERNBOX:
- From lxplus (CERN account required): /eos/project/j/jetquenching/www
- Webbrowser CERNBOX (CERN account required): https://cernbox.cern.ch/index.php/s/kRy9M7NC9iilE9Z
- Webbrowser (publicly accessible): https://jetquenchingtools.web.cern.ch/JetQuenchingTools/ (You can use wget and curl on this)
- Mount eos on a laptop or local desktop (CERN account required): https://cern.service-now.com/service-portal/article.do?n=KB0003493
You will find samples from various event generators. For underlying event we have: 'thermal' which is independent particle production using a Boltzmann distribution with a fixed multiplicity and mean pT (indicated in the file names). For the hard signal we have PYTHIA8 and JEWEL events with various pT,hat settings.
More details about the available samples can be found here: https://jetquenchingtools.github.io/ (public) (old twiki at cern: https://twiki.cern.ch/twiki/bin/view/JetQuenchingTools/PU14Samples)