Installing Miniconda

While the RDHPCS system have Anaconda/Conda available, you can install your own Miniconda.

The install process is rather simple (with a few notable warnings, see Cautionary Notes further below):

$ mkdir miniconda/
$ cd miniconda/
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod u+x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh -u -p ~/miniconda

  • The -p flag specifies the prefix path for where to install miniconda.

  • The -u updates any current installations at the -p location (not necessary if you didn’t do a mkdir beforehand)

Cautionary Notes

While running the installer, you will be prompted with something like this:

Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]

If “yes”, your .bashrc (or equivalent shell configuration file) will be updated with something like this:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init’ !! .
.
.
.
.
#unset __conda_setup
# <<< conda initialize <<<

Warning

By default, this will always initialize conda upon login, which clashes with other Python installations (e.g., if you use the other anaconda modules).

It is MUCH SAFER to say “no” and to just export the PATH manually to avoid clashing:

$ export PATH="/path/to/your/miniconda/bin:$PATH"

$ setenv PATH "/path/to/your/miniconda/bin:$PATH"

Note

If your .bashrc already has a similar block of code, then it will NOT modify your .bashrc

An additional recommendation is to set things to not activate your base environment by default (to help with the potential clashing):

# Only needs to be run once after exporting conda into your PATH
conda config --set auto_activate_base false

As always, if you encounter issue, don’t hesitate to contact help.