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Sample Notebooks

This is a set of example notebooks that do various things in ROOT and larsoft analysis (via gallery). All this is just playing around by W. Ketchum ([email protected]). No guarantees or anything, but you can always message me if you have questions or whatever.

These are mostly made using the ROOT kernel for jupyter notebooks. You can read a tiny bit about that here:

Setup

Typically, you want to setup the version of larsoft you will be using first. For MicroBooNE, that's something like:

source /cvmfs/uboone.opensciencegrid.org/products/setup_uboone.sh
setup uboonecode v08_55_00 -qe19:prof

Consult your experiment's documentation/local expert/slack channel for what you should do.

Then, you likely will need to add python modules beyond what comes in the pre-packaged version of python with larsoft. Often you may not have write access to the python install area, but you can instead setup a "user" area into which you can install what's needed. Note: this should work for all different kinds of python modules, not just what's done here.

You can do that setup blindly by executing the setup script included:

source setup_user_python.sh

Details on setup

Want to know what that does? First it creates and sets the paths for a user area:

#create a python user area
#change this to be what you like, but this is probably a good default on gpvm
export PYTHONUSERBASE=/$EXPERIMENT/app/users/$USER/python_libs
mkdir -p $PYTHONUSERBASE

#add your python area to the path ... maybe this is done automatically, but
#I've had trouble in the past so just to be sure
export PYTHONPATH=$PYTHONUSERBASE/bin:$PYTHONPATH
export PATH=$PYTHONUSERBASE/bin:$PATH

Then for running ROOT notebooks, you will need to make sure Jupyter, Metakernel, and ZMQ are installed. Do this:

#install the modules you want. These are the ones needed for the ROOT notebook.
#if they're already installed, it'll just print a bunch of stuff to tell you so
pip install --user jupyter metakernel zmq

Starting the ROOT notebook the impatient way

In the directory where you have your notebooks, do the following:

root --notebook

OK, when you do that, you should see an output like:

[I 17:33:53.217 NotebookApp] Serving notebooks from local directory: ***
[I 17:33:53.217 NotebookApp] 0 active kernels
[I 17:33:53.217 NotebookApp] The Jupyter Notebook is running at:
[I 17:33:53.217 NotebookApp] http://localhost:8888/?token=e393f2b1f6145dffa5a2958ba5112bcd203ddd20bd5263f7

Also, it will try to start a browser locally. Just exit out of it as soon as it pops up unless you want to use a browser over the connection. If not, move on to setting up the port forwarding.

Starting the ROOT notebook, the Jupyter way

You may prefer to just the typical jupyter command to startup the notebook (since maybe you don't even want to start a ROOT kernel!). You can do that by doing:

jupyter notebook --no-browser

and you should see a similar message to the above, except with no annoying browser popping up. You can also checkout jupyter documenation for specifying a port and etc.

But, you will likely need to add some configuration information to get the ROOT kernel working within that. First, copy in the kernel info by doing the following:

mkdir -p ~/.jupyter/kernels
cp -r $ROOTSYS/etc/notebook/kernels/root ~/.jupyter/kernals/

Then, to get some of the javascript magic working, you may also need to add this line to the jupyter config file (typically in ~/.jupyter/jupyter_notebook_config.py, create it if it's not there)

c.NotebookApp.extra_static_paths = ['$ROOTSYS/js']

Port forwarding

Note the port number in that link in the above example: it's 8888. Then, from your machine, do something like:

ssh -L localhost:8888:localhost:8888 <remote_machine>.fnal.gov

Where the 8888 matches the port number, and <remote_machine> is the gpvm or whatever you started the notebook from. Then, copy the link from the ROOT notebook start into your local browser (it contains a token to authenticate that you have write access to that area), and you should see the notebook area in a nice browsable format!

Using the notebooks

Walk through some of the examples a bit, and lookup online for more information on ROOT, PyROOT, notebookes, and the like. The suggested order is:

  1. ROOT_Example.ipynb
  2. ROOT_CPP_Kernel_Example.ipynb
  3. Analyze_MCTruth.ipynb
  4. SpaceCharge_Example.ipynb

Have fun!