Merge branch 'conda_cleanup' into 'master'

Update conda notes

See merge request !380

content/applications/user_software/using_anaconda_package_manager.md

@@ -21,9 +21,12 @@ straightforward.
 - [Creating custom Anaconda Environments](#creating-custom-anaconda-environments)
 - [Using /common for environments](#using-common-for-environments)
 - [Adding and Removing Packages from an Existing Environment](#adding-and-removing-packages-from-an-existing-environment)
+- [Moving and Recreating Existing Environment](#moving-and-recreating-existing-environment)
+- [Remove Unused Anaconda Packages and Caches](#remove-unused-anaconda-packages-and-caches)
 - [Creating custom GPU Anaconda Environment](#creating-custom-gpu-anaconda-environment)
 - [Creating custom MPI Anaconda Environment](#creating-custom-mpi-anaconda-environment)
 - [Using an Anaconda Environment in a Jupyter Notebook](#using-an-anaconda-environment-in-a-jupyter-notebook)
+- [Using Mamba](#using-mamba)
 
 ### Using Anaconda
 
@@ -203,6 +206,71 @@ conda remove -n mynumpy --all
 {{< /highlight >}}
 {{% /panel %}}
 
+### Moving and Recreating Existing Environment
+
+Sometimes conda environments need to be moved (e.g., from `$HOME` to `$COMMON` in order to reduce used space in `$HOME`) 
+or recreated (e.g., when shared with someone). This is done using `environment.yml` file as shown below.
+
+{{% panel theme="info" header="Activate the conda environment to export" %}}
+{{< highlight bash >}}
+conda activate mynumpy
+{{< /highlight >}}
+{{% /panel %}}
+
+Then export the active conda environment to file `environment.yml`.
+
+{{% panel theme="info" header="Export conda environment" %}}
+{{< highlight bash >}}
+conda env export > environment.yml
+{{< /highlight >}}
+{{% /panel %}}
+
+Next, deactivate the conda environment.
+
+{{% panel theme="info" header="Exit current environment" %}}
+{{< highlight bash >}}
+conda deactivate
+{{< /highlight >}}
+{{% /panel %}}
+
+The file `environment.yml` contains both `pip` and `conda` packages installed in the activated environment.
+This file can now be shared or used to recreate the conda environment elsewhere.
+
+The exported environment can be recreated in `$COMMON` with:
+
+{{% panel theme="info" header="Recreate conda environment in $COMMON" %}}
+{{< highlight bash >}}
+conda env create -p $COMMON/mynumpy -f environment.yml
+{{< /highlight >}}
+{{% /panel %}} 
+
+After the conda environment has been exported or recreated, if needed, the original conda environment can be removed.
+
+{{% panel theme="info" header="Remove conda environment" %}}
+{{< highlight bash >}}
+conda remove -n mynumpy --all
+{{< /highlight >}}
+{{% /panel %}}
+
+### Remove Unused Anaconda Packages and Caches
+
+By default, conda environments are installed in the user’s home directory at `~/.conda/envs`.
+conda caches and package tarballs are stored in `~/.conda/` as well.
+For larger or many conda environments, the size of the directory `~/.conda/` can easily reach the `$HOME` space quota limit of 20GB per user.
+
+In addition to [Moving and Recreating Existing Environment](#moving-and-recreating-existing-environment), one can remove unused conda packages and caches.
+
+{{% panel theme="info" header="Remove unused conda packages and caches" %}}
+{{< highlight bash >}}
+conda clean --all
+{{< /highlight >}}
+{{% /panel %}}
+
+{{% notice info %}}
+Please note that this command will only remove index cache, and unused cache packages and tarballs and will not
+affect nor break the current conda environments you have.
+{{% /notice %}}
+
 ### Creating Custom GPU Anaconda Environment
 
 We provide GPU versions of various frameworks such as `tensorflow`, `keras`, `theano`, via [modules](../../modules). 
@@ -357,3 +425,22 @@ Jupyter Notebook. To do so, follow the steps below, replacing
     corner.  
     {{< figure src="/images/24151931.png" height="400" class="img-border">}}
 
+### Using Mamba
+[Mamba](https://mamba.readthedocs.io/en/latest/) is an alternative to Conda that is in general faster and performs better at resolving dependencies in conda environments.
+Mamba is available as part of the `anaconda` modules on Swan.
+
+Mamba can be used by simply replacing `conda` with `mamba` in all `conda` commands provided here.
+
+{{% panel theme="info" header="Load the Anaconda module to start using Mamba" %}}
+{{< highlight bash >}}
+module load anaconda
+{{< /highlight >}} 
+{{% /panel %}}
+
+To create a new environment called 'mynumpy' and install NumPy version 1.17, along with any required dependencies, the command is:
+
+{{% panel theme="info" header="Create a new environment by providing a name and package specification" %}}
+{{< highlight bash >}}
+mamba create -n mynumpy numpy=1.17
+{{< /highlight >}} 
+{{% /panel %}}