Create 03_apptainer_files.mdx

Author: Amanda-dong

docs/hpc/15_tutorial_apptainer/03_apptainer_files.mdx

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+# Files in Apptainer Containers
+Apptainer is designed to work closely with the host filesystem. In most cases, your home directory and current working directory remain accessible from within the container.
+
+## Accessing Your Files
+
+While inside a container, check your current directory:
+
+```bash
+pwd
+```
+
+You can also list files in your home directory:
+
+```bash
+ls ~
+```
+
+The files and directories you see should match those available outside the container.
+
+Files created in these mounted directories remain available after the container exits.
+
+## Binding Additional Directories
+
+Sometimes you may need access to additional directories that are not automatically available inside the container.
+
+Apptainer allows additional directories to be mounted using the `-B` option:
+
+```bash
+apptainer shell \
+    -B /scratch:/scratch \
+    /share/apps/images/ubuntu-24.04.3.sif
+```
+
+This makes `/scratch` available inside the container.
+
+You can also mount a directory at a different location:
+
+```bash
+apptainer shell \
+    -B /scratch:/data \
+    /share/apps/images/ubuntu-24.04.3.sif
+```
+
+In this example, files stored in `/scratch` on the host system are accessible through `/data` inside the container.
+
+## Why This Matters
+
+Container images are typically read-only. Research data, scripts, notebooks, and output files usually remain outside the container.
+
+By making host directories available inside the container, Apptainer allows applications to access data stored on Torch while maintaining a reproducible software environment.