Computational Stuffs

Shell Scripting:

• To run a shell script use:

source file.sh

• Bash doesn't have the command "rehash", instead use:

hash -r

• To obtain permission to work, copy a some file:

chmod 777 file_name

• To check the libraries that are linking to an executable (-d -r show the undefined symbols):

ldd -d -r name_of_executable

• To see libraries dependencies:

readelf -d name_of_executable

• To create a ("soft") link to a file (when the linked file is modified all the linked directories also will use the modified file, it creates a pointer to the file):

ln -s (Directory_Path) .

CMSSW:

• At the moment of start session in lxplus or cmslpc (LS5), is required to run the commmands (these can be added in the .bashr file, the second one as an alias):

source /uscmst1/prod/grid/gLite_SL5.csh
source /uscmst1/prod/sw/cms/cshrc uaf

• To obtain a CMSSW release and setup the CMS environment (LS5 machines):

cmsrel CMSSW_5_X_X
cd CMSSW_5_3_3/src
cmsenv

• In the case of using the LSC6 or LS6 as architecture the commands to set up a CMSSW release are:

source /uscmst1/prod/sw/cms/cshrc cvmfs
scram --arch slc6_amd64_gcc481 list CMSSW | grep CMSSW_7_1
scram --arch slc6_amd64_gcc481 project CMSSW_7_1_0_pre8
cd CMSSW_7_1_0_pre8/src/
cmsenv
scram b

Grid Credentials:

• To obtain Grid Credentials follow the steps in: https://twiki.cern.ch/twiki/bin/view/Main/CRABPrerequisitesGRIDCredentials

• Or alternatively the steps in: https://twiki.cern.ch/twiki/bin/view/CMSPublic/EndUsers

• For the CERN certificate: https://twiki.cern.ch/twiki/bin/view/CMSPublic/PersonalCertificate

ROOT:

• Download the ROOT source files: http://root.cern.ch/drupal/content/downloading-root
• Download the prerequisite packages to build root: http://root.cern.ch/drupal/content/build-prerequisites
• Follow the instruction on the page to install: http://root.cern.ch/drupal/content/installing-root-source
• After the installation creates in your home directory a new .bashr (of if you have one, open it) and add the next lines at the end to be able of run root in any directory:

export ROOTSYS=~/root/ 
export PATH=$PATH:$ROOTSYS/bin 
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib

• If you want to do it in a more simple way, just run:

sudo apt-get install root-system

• With the command System is possible to load external libraries to ROOT, e.g in an interactive session:

gSystem->Load("~/work/PFCal/PFCalEE/userlib/lib/libPFCalEEuserlib.so")

Emacs

• To download emacs run:

sudo apt-get install emacs

Java

• To download java in ubuntu run:

sudo apt-get update
java -version
sudo apt-get install default-jdk

Vidyo

• To download and install Vidyo, please follow the instructions in: http://information-technology.web.cern.ch/services/fe/howto/users-install-vidyo-desktop-client

FIT Cluster:

• To access the cluster and have acces to CMS setup run:

ssh -X username@uscms1.fltech-grid3.fit.edu
source $VO_CMS_SW_DIR/cmsset_default.sh

LPC Connection:

• To connect to the LPC a kerberos client is required, to obtain this run:

sudo apt-get install krb5-user

• After this please follow the instructions in: http://www.uscms.org/uscms_at_work/data_computing/facility_operations/uaf.shtml

GIT Hub

• Is important to move the files 'id_rsa' and 'id_rsa.pub' to the home directories in any server where is is planned to work. This files contain the permission to access git
• To check the ssh access in git:

ssh -T git@github.com

• To copy a repository with git is required to initialized the same:

git init
git remote add name_choosen url_address
git clone https://url  or git clone git://url

• It can be use also:

git init
git remote add name_choosen url_address
git clone git://url

• To verified the remote connections (after git add):

git remote -v

• To check the tag of a repository run:

git tag

• To download objects from another repository or update the possible changes due new tags do:

git fetch --all

• To select one specific tag to work:

git checkout -f (tag_version)

Geant4:

Prerequisites

• To be able of use this procedure is required to have cmake, that can be downloaded from: http://www.cmake.org/cmake/resources/software.html
• To build, run in the directory where the source file where extracted:

./bootstrap
make
make install

Configuration for compilation

• Obtain the Geant4 (G4) source file from: http://geant4.web.cern.ch/geant4/support/download.shtml
• Extract the file to your Desktop or a desired directory
• Run the commands:

mkdir geant4.(version)-build
cd geant4.(version)-build
sudo apt-get install expat    (in case if needed)
sudo apt-get install mesa    
sudo apt-get install mesa-utils
sudo apt-get install libXmu-dev

• To configure for compilation run (this will create the main directory for G4 in the path /usr/local, installing examples, and using openGL as visualization tool):

cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_OPENGL_X11=ON -DGEANT4_INSTALL_EXAMPLES=ON -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON  /home/..(your path)../Desktop/geant4.(version)

• Install the missing packages indicated after the previous process and repeat until there is no warnings

Compilation and Installation

• Still in the building directory run:

nproc    (or lscpu to find the number of cores of the CPU)
make -j# VERBOSE=1    (# is the number found previously)

• After this to install:

sudo make install

How to run an example

• In this case, to run example number 3 of G4, copy the folder B3 from the directory /usr/local/share/Geant_directory/examples/basic to the Desktop
• Run:

cd Desktop
mkdir B3-build
cd B3-build
source /usr/local/bin/geant4.sh
cmake -DGeant4_DIR=/usr/local/share/Geant4.9.6 /home/wukong/Desktop/B3
make -j#    (#: number of cores of the CPU)

• Finally:

./exampleB3

• For more commands check the G4 documentation