Adding Code

Overview

Teaching: 10 min
Exercises: 10 min

Questions

• How do I add to an existing project?

Objectives

• Add the rest of your ATLAS code

• Compile and test it within the ATLAS environment

• Push the code to GitLab

This episode assumes

• You’ve uploaded a readme to GitLab
• You did the pre-workshop material
• You downloaded the test file. Note you can download it with

  wget https://cernbox.cern.ch/index.php/s/FR0cyGhtE3PNPty
  

Add ATLAS code to your repository

Now we’ll add the example we gave as pre-course material to your versioned code. Copy the AnalysisPayload.cxx and CMakeLists.txt files from that material into your repository.

Then run

git status

which should print something like

On branch master
Your branch is up to date with 'origin/master'.

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	AnalysisPayload.cxx
	CMakeLists.txt

nothing added to commit but untracked files present (use "git add" to track)

Let’s add these and commit them:

git add .
git commit -m "Add payload and CMakeLists"

If you run git status now, git should indicate that you’re one commit ahead of master.

Should I add my data files?

NO!! No no no! You should not add your DAOD files, or root files, to your repositories. This is a big no no in ATLAS and goes under the name of adding “binaries” because they are data files that are only machine readable. Due to the way that things get versioned, this can cause repositories to explode and during Run1 of the LHC/ATLAS, this caused for the entire ATLAS version control system (at that time is was SVN-Subversion) to crash. People crashed the mainframe because they did this. Not to mention that it just quickly makes a repository large and bloated and very cumbersome (large) to clone.

Now, unfortunately some people still do this. We will pick on the luminosity group in this instance gonzales/mblumi. If you find a colleague is doing this, please try to educate them. #greatergood

As an alternative, try storing your large data files in your EOS space wich maps automatically to CERNBox.

Set up the ATLAS Environment

Remember that we created some keys in the ~/.ssh directory a while back? We’re going to need to use these to push code updates to GitLab while in the docker container where we run ATLAS code.

First copy the keys into the Bootcamp directory, make sure you do this from the Bootcamp directory and not from the bootcamp-example code, which is going to be versioned (i.e. it would suck to accidentally push all the contents of your .ssh directory to GitLab). Also copy your git configuration file, so that your commits include your name and email.

cp -r ~/.ssh ssh-credentials
cp ~/.gitconfig gitconfig

Then we’ll have to launch a docker image:

docker run --rm -it -w /home/atlas/Bootcamp -v \
    $PWD:/home/atlas/Bootcamp atlas/analysisbase:21.2.125 \
    bash -c 'cp -r ssh-credentials ~/.ssh; cp gitconfig ~/.gitconfig ; bash'

We’ll come back to this in a few days, but let’s unpack what we just did there, since it was a very long command. docker run, runs a container, but we supplied a few named arguments:

• --rm: tells docker to delete the container when you exit
• -it: two arguments, run interactive with attached terminal
• -w: sets the directory you’ll be in when the container starts
• -v: mounts your current directory within the image so you can access files on your laptop

There were also a few positional arguments (those without a -* flag).

The first points to a container: in this case we’re using an ATLAS release which includes all the libraries we’ll need for analysis work.

The second argument tells the container what to run in the container. This one is more complicated than what you might have seen before because we have to copy our credentials into a place in the image where git will find them¹.

Exercise: Script the docker run command

You might have to call this quite a few times throughout the remainder of the week, so it would be advisable to write a shell script so that it’s reduced to running ./run-docker.sh

However, we’ll learn a lot more about what these commands are doing later this week. So if you are a bit unsure of this, then don’t worry, for now let’s just worry about “getting it to work”. But if Thursday comes and you are still unsure, then keep asking until you are sure.

Compile this code

It’s good practice to do a few things before you push code to your public repository:²

1. make sure it compiles
2. make sure it runs

You want to do this so that if a colleague of yours clones your repository, they are not left with a frustrating situation of debugging your code that was checked in hastily after “just making that one small change” that actually broke things and caused a segfault later on. Don’t be “that colleague”. Next cd to /home/atlas/Bootcamp. You should see amber-example here.

As we learned in the pre-workshop material, you should build code from a directory which is on the same level as your code repository. Create the build directory and build your code.

mkdir build
cd build
source ~/release_setup.sh
cmake ../amber-example
make

Now, if everything worked you should see an executable called AnalysisPayload.

Try running it just to make sure it works.

What if something doesn’t work?

If something is broken you should fix it! If you have to fix anything you can commit your changes with git commit -am "fix bug" which is a bit of short hand and has mashed together the -a argument (which effectively performs a git add -u) and the git commit command with a commit message. Don’t forget to make the commit message verbose, “fix bug” itself is not so verbose given that you will probably be fixing many bugs during your time in the experiment.

Push the code

Assuming everything compiles and you can run the resulting executable, you can push your new code to your repository.

git push origin master

Notes

Key Points

• Your credentials can be used within an image

• Always compile and test code before pushing