Anaconda

Anaconda is a software manager that allows you download and execute packages in your home directory.

If you use the Nevis Linux cluster, then you should consider using environment modules over Anaconda, if for no other reason than to save disk space (see below). But if you're on a different system, or the Nevis environment modules don't offer the package or version you're looking for, Anaconda is a better choice. All the Nevis Linux cluster systems running CentOS 7 have conda installed.

If you're not at Nevis, you can also separately install Anaconda.

Once you've installed Anaconda, you’ll probably have to include conda-forge. The following commands set it up:

conda config --add channels conda-forge
conda config --set channel_priority strict

To install Jupyter/ROOT:

conda create --name jupyter-pyroot jupyter python root

Note that the name jupyter-pyroot is arbitrary; you can use any name for the conda environment that you wish.

There are additional standard packages that you’ll probably want to include in your conda environment (note that conda install adds more packages to an environment you've already created):

conda install --name jupyter-pyroot jupyterlab numpy scipy matplotlib 

Your working group may use additional packages. For example, the VERITAS group at Nevis might want to use (in addition to the above):

conda install --name jupyter-pyroot astropy gammapy 

You only have to go through the above steps once to define an environment (e.g., jupyter-pyroot). Afterwards, once per login session, it’s necessary to activate it:

conda activate jupyter-pyroot

Once activated, you should be able to run ROOT by simply typing:

root

You can run jupyter with:

jupyter notebook

jupyter notebook --no-browser --port=XXXX

Warnings

• If you’re installing packages that have been pre-compiled by the maintainers of conda and conda-forge, then this process usually works well. However, if you’re using a system that does not have a pre-compiled version, conda will compile them on your computer. Not only can this take some time, but the results can be unreliable; I’ve seen a computer pause for many hours to re-compile ROOT only to finish with a program that issued errors every time I tried to run it.
• A conda environment can take up a lot of disk space, since it not only installs the packages you list, but any other packages that they depend on. On my desktop computer, the minimal Jupyter/ROOT container described above takes up 3G. This may not seem like much, but summer students at Nevis have a disk quota of 10G. It’s possible to run into disk-space problems, especially if you’re sharing disk space with other users, if you add more packages to your environment, or begin to define multiple environments for different projects.
• Anaconda changes your shell’s execution environment. It may be incompatible with other environment setups (such as MicroBooNE’s LArSoft, ATLAS’ Athena, or Nevis’ module load command).
• Your shell’s prompt will be changed by conda. Even when you’re not using conda, the text (base) will appear at the beginning of the prompt. If this doesn’t bother you, then ignore it. If it does, you can try:

  conda config --set auto_activate_base false
  

  You’ll have to log off then log in again to see the change. If you don’t want conda to alter your prompt even when you’re using an environment, this command will suppress conda’s prompt changes:

  conda config --set changeps1 False