This documentation is under active development, meaning that it can change over time as we refine it. Please email firstname.lastname@example.org if you require assistance.
Python and conda on M3: Frequently Asked Questions (FAQ)#
If you are unable to resolve your problem independently or don’t see your question answered here, please contact the helpdesk at email@example.com so we can investigate further.
My $HOME directory is full of conda packages and my desktop won’t start.#
You can see how much of your quota has been used by running
user_info Home directory usage +----------------+---------+---------+----------+ | Path | Usage | Quota | % Used | |----------------+---------+---------+----------| | /home/user | 6 GB | 10 GB | 60 % | +----------------+---------+---------+----------+
If your home directory is full, you may experience unexpected behaviour including desktops failing to start.
Sometimes this happens as a result of conda packages being installed in a
.conda directory in your $HOME folder by default.
If you have already installed conda, you can remedy this issue with the following steps.
Export your conda environment to a yaml file. You will need to do this for each environment you have created and intend to keep. To do this:
# Activate your conda environment as usual # Insert environment activation here # Once your environment is activated, run: conda env export > environment.yml
Remove your current install of conda, including the
Reinstall conda following the Anaconda or Miniconda install instructions under “create the conda environment with packages from a .yml file”.
Note: In our Anaconda instructions we include two commands which ensure you packages are not installed in your $HOME folder. These lines are also included within the Miniconda install script that we provide per the instructions. Specifically, these are the lines to pay attention to:
# These commands prevent your environments and packages being stored in $HOME conda config --add envs_dirs $CONDA_ENVS/conda/envs conda config --add pkgs_dirs $CONDA_ENVS/conda/pkgs
If you need any assistance with this process, please contact the helpdesk at firstname.lastname@example.org
conda init and my desktop session no longer starts#
To resolve this problem, follow these instructions.
ssh into M3.
.bashrcfile using your favourite editor.
Comment out the ‘conda’ lines using a # at the start of the lines. Below is a sample
.bashrcwith the comments
# .bashrc # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi # User specific aliases and functions # Give bash history a decent size export HISTFILESIZE=10000 # Helpful alias for users to quickly see their queue status alias squ='squeue -u $USER' # >>> conda initialize >>> # !! Contents within this block are managed by 'conda init' !! #__conda_setup="$('/usr/local/anaconda/2019.03-Python3.7-gcc5/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" #if [ $? -eq 0 ]; then # eval "$__conda_setup" #else # if [ -f "/usr/local/anaconda/2019.03-Python3.7-gcc5/etc/profile.d/conda.sh" ]; then # . "/usr/local/anaconda/2019.03-Python3.7-gcc5/etc/profile.d/conda.sh" # else # export PATH="/usr/local/anaconda/2019.03-Python3.7-gcc5/bin:$PATH" # fi #fi #unset __conda_setup # <<< conda initialize <<<
Save the file and exit your ssh session.
Restart your Desktop session.
If you are not comfortable updating your
.bashrc file, please
see Help and Support to obtain assistance.