Jupyter Notebook usage tips

Usage tips

Memory management

• to free up memory used by large Python notebooks, put this line at the end of your notebook:
  • %reset -f

Custom conda environment

• Instructors: if a large class needs a specific custom environment please notify us to create a single shared one to conserve space
• to create a custom conda environment, open a fresh Jupyter terminal and run these commands

  # load anaconda environment into the shell
  module load anaconda3
  # create personal conda env installed at ~/.conda/envs/myconda
  # feel free to pick a name other than myconda
  conda create --name myconda -c conda pip ipykernel
  # activate your myconda so the python command uses it
  conda activate myconda
  # add personal icon to the Jupyter launcher for 'myconda' (relogin to Jupyter to see it)
  python -m ipykernel install --user --name 'myconda' --display-name 'myconda'
  

• to add more to a custom environment later, open a terminal and run

  # activate previously-created environment
  module load anaconda3
  conda activate myconda
  # install custom package, e.g., lmfit
  pip install lmfit
  

• read more about conda environments

Installing personal software

There are various ways you might install software in your own account. Here are some examples.

• configuring and building C code that comes with a GNU configure script

  ./configure --prefix=${HOME}/.local
  make --prefix=${HOME}/.local
  

• three different ways of using Python and pip

  • pip install --user packagename
    

  • pip3 install --update --user packagename

  • python3 -m pip install --user packagename

• using the NPM package manager

  • npm install -g --prefix=${HOME}/.local packagename

• R will use your home directory when installing packages. Examples:

  • # basic example
    if(!require(somepackage)) {
        install.packages("somepackage")
        library(somepackage)
    }
    

  • # source code example
    if (!require("EMMIXskew")) {
        install.packages('https://cran.r-project.org/src/contrib/Archive/EMMIXskew/EMMIXskew_1.0.3.tar.gz', repos = NULL, type="source")
        library(EMMIXskew)
    }
    

  • # install_github might need you to configure a lib path
    remotes::install_github("rspatial/rspatial")
          

  • # shell command-line example
    R -q -e "install.packages('GGIR', repos='http://cran.utstat.utoronto.ca/')"