Merge pull request #4 from ARCTraining/modules-section

draft modules section, need to edit exercises

Author: murphyqm

book/modules-software.md

@@ -1,9 +1,133 @@
 # Session 4: Modules and Software
 
-## What are modules and how to use them?
+In this session we will learn about software on Aire, and how to access software via the module system. We will also discuss some alternatives to install software yourself on the system.
 
-## other ways to get/run software
-### spack/easybuild
-### download
-### self build
-### container
+`````{tab-set}
+````{tab-item} Introduction to Modules
+- **What are Modules?**
+  - Modules are a way to manage different software environments on HPC systems.
+  - They allow users to load and unload software packages dynamically.
+  - This helps in managing different versions of software and their dependencies.
+
+- **Why Use Modules?**
+  - Simplifies the user environment.
+  - Avoids conflicts between software versions.
+  - Provides a consistent and reproducible environment.
+
+:::: exercise
+**Exercise 1:** List all available modules on Aire.
+::::
+
+:::: solution
+```bash
+module avail
+```
+::::
+````
+
+````{tab-item} Using Modules
+- **Loading a Module:**
+  - To use a software package, load its module.
+  - Example:
+    ```bash
+    module load python/3.8
+    ```
+
+- **Unloading a Module:**
+  - To remove a software package from your environment.
+    ```bash
+    module unload python/3.8
+    ```
+
+- **Listing Loaded Modules:**
+  - To see which modules are currently loaded.
+    ```bash
+    module list
+    ```
+
+:::: exercise
+**Exercise 2:** Load the `gcc` module and verify it's loaded.
+::::
+
+:::: solution
+```bash
+module load gcc
+module list
+```
+::::
+````
+
+````{tab-item} Requesting New Modules
+- **Centralized Management:**
+  - Popular software is centrally installed by the Research Computing team.
+  - Ensures optimized performance and avoids conflicts.
+
+- **Requesting New Software:**
+  - If a required software is not available, users can request its installation.
+  - Submit a Research Computing Query with details about the software.
+
+:::: exercise
+**Exercise 3:** Identify a software you need that's not available and draft a request.
+::::
+
+:::: solution
+Provide the software name, version, and a brief justification for its use in your research.
+::::
+````
+
+````{tab-item} Alternative Software Management
+- [**Spack:**](https://spack.io/)
+  - A flexible package manager for HPC systems.
+  - Allows users to install software without admin privileges.
+  - Supports complex dependency management.
+
+- [**EasyBuild:**](https://easybuild.io/)
+  - Framework for building and installing software on HPC systems.
+  - Automates the build process using configuration files.
+
+- **Downloading and Self-Building:**
+  - Users can manually download and compile software.
+  - Requires knowledge of build systems and dependencies.
+
+- **Containers:**
+  - Encapsulate software environments using tools like [Apptainer](https://apptainer.org/).
+  - Ensures portability and consistency across systems.
+
+:::: exercise
+**Exercise 4:** Choose a simple software package and outline steps to install it using Spack.
+::::
+
+:::: solution
+1. Load Spack module: `module load spack`
+2. Install software: `spack install htop`
+3. Load the installed package: `spack load htop`
+::::
+````
+
+````{tab-item} Best Practices
+- **Environment Management:**
+  - Use modules to manage software environments effectively.
+  - Unload modules when they are no longer needed to avoid conflicts.
+
+- **Reproducibility:**
+  - Document the modules and versions used in your research.
+  - Use containers for complex environments to ensure consistency.
+
+- **Collaboration:**
+  - Share module load commands with collaborators to replicate environments.
+  - Use version-controlled scripts to manage workflows.
+
+:::: exercise
+**Exercise 5:** Create a script that loads necessary modules for your project.
+::::
+
+:::: solution
+```bash
+#!/bin/bash
+module load gcc
+module load python/3.8
+# Add other module load commands as needed
+```
+::::
+````
+`````

book/storage.md

@@ -1,8 +1,7 @@
 # Session 3: Storage on Aire
 
-::: note  
-**Objectives:** Understand the main file areas on Aire (home, scratch, etc.), learn the purpose and differences of each storage type, practice navigating between storage areas and checking disk quotas, and learn commands for copying and transferring data to/from Aire.  
-:::
+In this session, we will work to understand the main file areas on Aire (home, scratch, etc.), learn the purpose and differences of each storage type, practice navigating between storage areas and checking disk quotas, and learn commands for copying and transferring data to/from Aire.  
+
 
 `````{tab-set}
 ````{tab-item} 1. Structure