Difference between revisions of "DF JLab Software Install Instructions"
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Revision as of 21:56, 4 July 2018
These instructions are for installing the software on Ubuntu 16.04. It is assumed that you start in a directory named JLabSoftware which contains the directories CED, COATJAVA, DB, and GEMC
These instructions set up the common environment and GEMC with it. Skip if you don't intend on installing GEMC.
The CE is dependent on the following packages which can be easily installed by
sudo apt-get install <package>:
Now, assuming you're in the JLabSoftware directory:
cd GEMC mkdir 2.2 wget http://www.jlab.org/12gev_phys/packages/sources/ceInstall/ceInstall_2.2.tar.gz tar -zxpf ceInstall_2.2.tar.gz --strip-components 1 -C 2.2
Go to the home directory and open .bashrc in your preferred text editor. Add the following to the bottom of the file:
export JLAB_ROOT=/path/to/JLabSoftware/GEMC export JLAB_VERSION=2.2 source $JLAB_ROOT/$JLAB_VERSION/ce/jlab.sh
Now close the terminal and open a fresh one. You should see something like:
!! Attention: BANKS installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/banks/1.4/bin not found !! Attention: CCDB installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/ccdb/ccdb-1.06.02/lib not found !! Attention: CLHEP installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/clhep/220.127.116.11/lib not found !! Attention: EVIO installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/evio/5.1/bin not found !! Attention: GEANT4 installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/geant4/4.10.03.p02/bin not found !! Attention: GEMC installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/gemc/2.7/gemc not found !! Attention: JANA installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/jana/0.7.7p1/bin/jana not found !! Attention: MLIBRARY installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/mlibrary/1.2/lib not found !! Attention: MYSQL installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/mysql/lib not found !! Attention: QT installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/qt/5.9.1/5.9.1/clang_64/lib not found !! Attention: ROOT installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/root/6.12.06/bin/root-config not found !! Attention: SCONS installation check /opt/jlab_software/2.2/scons_bm/1.6/site_tools not found !! Attention: XERCESC installation check /opt/jlab_software/2.2/Darwin_macosx10.13-x86_64-clang9.0.0/xercesc/3.2.0/lib not found
cd $JLAB_ROOT/2.2/ce and open settings.xcconfig in a text editor. Change the geant4 version to whatever is the latest version from here. Do the same with the file versions.env.
You should now be able to run the
go_<package> scripts in $JLAB_VERSION/install. It is recommended that you open the
go_all script and manually run each individual script in the order found there. Watch for further instructions in the terminal output. Remember to also run
The common environment should now be installed. Ensure that the message that displays when opening a new terminal reflects that.
Should you experience any segfault errors while attempting to build, ensure that awk is set to gawk:
sudo update-alternatives --config awk
These instructions setup GEMC and the clas12Tags repository so that you may easily start simulating clas12 runs.
If you haven't already, first complete the CE install above, then:
cd $JLAB_ROOT git clone https://github.com/gemc/clas12Tags cd clas12Tags/4a.2.3/source/physics
Here you are going to open PhysicsList.cc and uncomment the line
auto theParticleIterator = GetParticleIterator();. Then:
cd ../.. scons -j4 OPT=1
This should result in an exectuable file simply called gemc in the directory 4a.2.3/source. When running GEMC, you will be wanting to run this file. So, either always use the full path to target this executable, or set the environmental variable $GEMC to the absolute path to it.
All of these assume that you start in the JLabSoftware/COATJAVA directory.
Download the desired version from here.
cp ~/Downloads/clas12-offline-software-<version>.tar.gz . tar -xzf clas12-offline-software-<version>.tar.gz cd clas12-offline-software-<version> bash build-coatjava.sh
The tools should be in the directory ./coatjava/bin
Note: While this appears to build correctly, it would seem that I must use
bash instead of
./ to run any of the executables in bin.
Official Github Version
mkdir clas12-offline-software-official git clone -b master https://github.com/JeffersonLab/clas12-offline-software.git clas12-offline-software-official cd clas12-offlone-software-official ./build-coatjava.sh
Forking Your Own Version
First, create a Github account if you don't already have one. Then go to JeffersonLab/clas12-offline-software and hit the fork button. You should now have a repository at
git clone -b master https://github.com/<your-username>/clas12-offline-software cd clas-12-offline-software ./build-coatjava.sh
The upstream repository (JLab's) can be added as follows:
git remote add upstream https://github.com/JeffersonLab/clas12-offline-software.git
To update your development build with the Jlab updates:
git fetch upstream git checkout master git merge upstream/master
And to push your local repository to your github repo:
When you want to push your changes to JLab's repo, you need to go to your github page and push the "pull request" button.
Netbeans Setup Instructions
Can be found here.
Starting from the directory JLabSoftware:
cd CED wget https://userweb.jlab.org/~heddle/ced/builds/ced.1.003d.tar.gz tar -xzf ced.1.003d.tar.gz cd cedbuild sudo chmod 764 ced.sh
You should now be able to run CED by using
Note: For some reason I don't appear to have the full functionality I would expect (e.g. magnification doesn't seem to work).
The purpose of setting up a local database is so that you may run simulations without having to rely on JLab's database. This gives you a constant setup that won't be changed without your knowledge.
Procuring the Database
To get the official versions, you must have a JLab account and have access to the clas12 software. Assuming that that isn't the case, copies of several iterations of the database can be found on lds3. The instructions for getting the database onto a local machine are as follows:
cd /path/to/JLabSoftware/DB ssh firstname.lastname@example.org scp email@example.com:/home/lds/src/CLAS/DB/clas12.sqlite.<date> . exit scp firstname.lastname@example.org:/home/daq/clas12.sqlite.<date> .
Setup for Running Via Command Line
The environmental variables CCDB_CONNECTION and CCDB_DATABASE must be defined and must point to the right spot. Before running a program which relies on the database (such as COATJAVA or GEMC), you must export (or setenv or what-have-you) the following in some fashion:
sqlite:///chupa is a relative path and
sqlite:////thingy is an absolute path.
Setup for Running Via NetBeans
Assuming that your IDE is setup such that the working directory is
- In the projects tab, right click on "clas12detector-dc" -> Properties
- In the Actions section:
- Add the environmental variable CCDB_CONNECTION=sqlite:///../../DB/clas12.sqlite.<date>
- Add the environmental variable CCDB_DATABASE=../../DB/clas12.sqlite.<date>
- In the Actions section: