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CONDA user defined environments
Users or groups can build their own environments.
General template
General model that can be used to create personal or group environments:
- hpc-make-condaenv-template.sh
#!/bin/bash set -e module load miniconda3-test source "$CONDA_PREFIX/etc/profile.d/conda.sh" CONDAENV_NAME='template' CONDAENV_VERSION=$(date '+%Y.%m.%d') PYTHON_VERSION='3.6' CONDAENV="${CONDAENV_NAME}-${CONDAENV_VERSION}" if [ $UID = 0 ]; then CONDAENV_PREFIX="/hpc/share/tools/miniconda3/envs/$CONDAENV" CONDAENV_SYMLNK="/hpc/share/tools/miniconda3/envs/$CONDAENV_NAME" else if [ -z "$CONDA_ENVS_PATH" ]; then echo 'Error: the CONDA_ENVS_PATH envarionment variable is not set' 1>&2 exit 1 fi if [ -z "$CONDA_PKGS_DIRS" ]; then echo 'Error: the CONDA_PKGS_DIRS envarionment variable is not set' 1>&2 exit 1 fi echo "CONDA_ENVS_PATH: $CONDA_ENVS_PATH" echo "CONDA_PKGS_DIRS: $CONDA_PKGS_DIRS" CONDAENV_PREFIX="$CONDA_ENVS_PATH/$CONDAENV" CONDAENV_SYMLNK="$CONDA_ENVS_PATH/$CONDAENV_NAME" fi echo "CONDAENV_PREFIX: $CONDAENV_PREFIX" echo "CONDAENV_SYMLNK: $CONDAENV_SYMLNK" echo echo -n "Should we proceed with the creation of the condaenv '$CONDAENV_NAME' (yes/no)? " read ans case "$ans" in [yY]|[yY][Ee][Ss]) ;; [nN]|[nN][oO]) exit 1 ;; *) echo exec "$0" exit ;; esac conda info if [ $UID = 0 ]; then conda --version conda update conda conda --version fi if [ -d "$CONDAENV_PREFIX" ]; then conda env remove --name "$CONDAENV" fi conda create --yes --name "$CONDAENV" python=$PYTHON_VERSION conda activate "$CONDAENV" conda install --yes --name "$CONDAENV" \ --channel conda-forge \ 7zip conda list || true conda deactivate ln -sf "$CONDAENV_PREFIX" "$CONDAENV_SYMLNK" ls -la "$CONDAENV_SYMLNK"*
This script is located in
/hpc/share/tools/conda/bin/hpc-make-condaenv-template
Creating a user environment
Create a script from the template and run it.
Creating a group environment
Change group:
newgrp <GROUP>
Create a script from the template and run it.
Work session with conda
[<USER>@ui01 ~]$ module load miniconda3 [<USER>@ui01 ~]$ source "$CONDA_PREFIX/etc/profile.d/conda.sh" [<USER>@ui01 ~]$ conda --help [<USER>@ui01 ~]$ conda --version conda 4.9.2 [<USER>@ui01 ~]$ conda info [<USER>@ui01 ~]$ conda activate (base) [<USER>@ui01 ~]$ which python /hpc/share/tools/miniconda3/bin/python (base) [<USER>@ui01 ~]$ python -V Python 3.7.4 (base) [<USER>@ui01 ~]$ conda deactivate [<USER>@ui01 ~]$
Package search
conda search sklearn
Alternate channels
To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page.
To add a new channel:
conda config --add channels conda-forge
Environment
With conda, you can create, export, list, remove, and update environments that have different versions of Python and/or packages installed in them. Switching or moving between environments is called activating the environment.
Environments list
To see a list of all available environments run:
conda env list