index: Splitting sessions to smaller sessions

content/binding_folders.rst

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+Binding folders into your container
+===================================
+
+.. objectives::
+
+   * Learn how you can bind folders into containers
+
+When you launch a program in a container, the program runs in a contained
+environment. The file system in the container might not have the same
+folders structure as the machine that runs the container.
+
+So, when you want to work on your data, you need to bring it with you into
+this contained world inside the container.
+
+This is done via method called **mount binding**.
+
+Binding means that a folder from the host system is mapped into a folder
+inside the container.
+
+.. figure:: img/default_mounts.png
+
+   Figure 1: Only some folders are mounted by default
+
+By default, ``$HOME``, ``$CWD`` (current working directory)
+``/tmp`` and
+`few other paths <https://apptainer.org/docs/user/main/bind_paths_and_mounts.html#system-defined-bind-paths>`__
+are bound to the image.
+
+If you want to do additional mappings you need to do it by giving an
+extra arguments to the command you're running.
+
+The following would bind folder ``/scratch`` from the host system to
+``/scratch`` in the container:
+
+.. code-block:: console
+
+   $ apptainer exec --bind /scratch example.sif ls /scratch
+
+.. figure:: img/bind_example.png
+
+   Figure 2: Binding a directory inside a container
+
+Setting ``--bind``-argument works for ``apptainer run``- and
+``apptainer shell``-commands as well.
+
+You can also bind directories to different places. This is especially
+helpful if, for example. the code in container expects that data
+should be in ``/data``:
+
+.. code-block:: console
+
+   $ apptainer exec --bind /scratch:/data example.sif ls /data
+
+.. warning::
+
+   Bind mounts **are the same folders inside and outside** of the image.
+
+   Deleting file from the folder that you bound inside the image will
+   delete the file completely.
+
+.. admonition:: Key points to remember
+
+   - By default only some folders are bound inside the container.
+   - You'll need to manually ``--bind``-folders from outside of
+     the container if you want to use them inside the container.
+   - Bound folders are the same folders inside and outside of the
+     container.
+