Preferably, in your nobackup area (in LPC) or in your local computer:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
# Follow the instructions to finish the installation
# Make sure to choose `yes` for the following one to let the installer initialize Miniconda3
# > Do you wish the installer to initialize Miniconda3
# > by running conda init? [yes|no]
# disable auto activation of the base environment
conda config --set auto_activate_base false
Verify the installation is successful by running conda info and check if the paths are pointing to your Miniconda installation.
If you cannot run conda command, check if you need to add the conda path to your PATH variable in your bashrc/zshrc file, e.g.,
export PATH="$HOME/miniconda3/bin:$PATH"
# create a new conda environment
conda create -n coffea-env python=3.8
# activate the environment
conda activate coffea-env
# install packages
pip install numpy pandas scikit-learn coffea correctionlib pyarrow
pip install tritonclient['all']
# install xrootd
conda install -c conda-forge xrootd
First, copy the executable script from lpcjobqueue: https://github.com/CoffeaTeam/lpcjobqueue
curl -OL https://raw.githubusercontent.com/CoffeaTeam/lpcjobqueue/main/bootstrap.sh
bash bootstrap.sh
This creates two new files in this directory: shell and .bashrc.
The ./shell executable can then be used to start a singularity shell with a coffea environment.
In order to be able to write to eos add the following line (replacing $USER with your username):
-B /eos/uscms/store/user/$USER/boostedhiggs:/myeosdir
in the shell executable.
e.g.
singularity exec -B ${PWD}:/srv -B /uscmst1b_scratch -B /eos/uscms/store/user/cmantill/boostedhiggs:/myeosdir --pwd /srv \
/cvmfs/unpacked.cern.ch/registry.hub.docker.com/${COFFEA_IMAGE} \
/bin/bash --rcfile /srv/.bashrc