.. _installing_applications:

=======================
Installing Applications
=======================

.. contents:: In this section:
   :local:
   :depth: 2

On GridUnesp, you **do not have administrator (root) privileges**. This means you cannot install programs in the system's default directories (``/usr/``, ``/lib/``). However, there are several ways to install and use scientific applications in your own space.

Installation Options
====================

1. **Use already-installed modules** (recommended)
2. **Install locally** in your ``/home/``
3. **Use Conda** to manage environments
4. **Use containers** (Apptainer)
5. **Request a global installation** from the team

.. _installation_via_modules:

Installation via Modules (Already Installed)
============================================

GridUnesp has dozens of pre-installed applications available as modules.

Listing Available Modules
-------------------------

.. code-block:: bash

   module avail

To search for a specific module:

.. code-block:: bash

   module avail partial_name

Loading a Module
----------------

.. code-block:: bash

   module load module_name/version

**Example:**

.. code-block:: bash

   module load gcc/10.2.0
   module load openmpi/4.1.5

Checking Loaded Modules
-----------------------

.. code-block:: bash

   module list

Unloading a Module
------------------

.. code-block:: bash

   module unload module_name

.. tip::
   For more details on modules, see the :ref:`system_administrator_installation` section.

.. _local_installation:

Local Installation in /home/
============================

Many applications allow specifying an alternative installation directory.

Using --prefix (configure/make)
-------------------------------

.. code-block:: bash
   :caption: Example of local installation

   # Download and extraction
   wget https://example.com/application.tar.gz
   tar -xzf application.tar.gz
   cd application

   # Configure to install in /home/$USER/local
   ./configure --prefix=/home/$USER/local
   make
   make install

   # Add to PATH
   export PATH=/home/$USER/local/bin:$PATH
   export LD_LIBRARY_PATH=/home/$USER/local/lib:$LD_LIBRARY_PATH

To make the installation permanent, add the ``PATH`` and ``LD_LIBRARY_PATH`` lines to your ``~/.bashrc``.

.. _installation_via_conda:

Installation via Conda
======================

Conda is a package manager that allows you to create isolated environments.

Creating an Environment
-----------------------

.. code-block:: bash

   # Load the Conda module
   module load miniconda/24.4.0-libmamba

   # Create environment
   conda create -n my_environment python=3.9

   # Activate environment
   source activate my_environment

Installing Packages
-------------------

.. code-block:: bash

   conda install numpy pandas matplotlib
   conda install -c bioconda samtools  # Specific channel

Listing Environments and Packages
---------------------------------

.. code-block:: bash

   conda info --envs          # List environments
   conda list                 # List packages in current environment
   conda deactivate           # Exit the environment

Using in Submission Scripts
---------------------------

.. code-block:: bash
   :caption: conda_script.sh

   #!/bin/bash
   #SBATCH -J my_job
   #SBATCH -n 1
   #SBATCH -t 01:00:00

   export INPUT="input.dat"
   export OUTPUT="output.dat"

   module load miniconda/24.4.0-libmamba
   source activate my_environment

   job-nanny python my_script.py

.. _installation_via_apptainer:

Installation via Apptainer (Containers)
=======================================

Apptainer allows running applications in containers, useful when:

- The application depends on specific libraries from another Linux distribution
- You need a reproducible environment
- Conventional installation is too complex

Creating an Image
-----------------

.. code-block:: bash
   :caption: build_container_script.sh

   #!/bin/bash
   #SBATCH -J build_container
   #SBATCH -t 02:00:00
   #SBATCH -n 1

   export INPUT="ubuntu.def"
   export OUTPUT="ubuntu.sif"

   job-nanny apptainer build ubuntu.sif ubuntu.def

Definition file (ubuntu.def):

.. code-block:: text

   Bootstrap: docker
   From: ubuntu:20.04

   %post
       apt-get update
       apt-get install -y python3 python3-pip
       pip3 install numpy pandas

   %runscript
       python3 "$@"

Running a Container
-------------------

.. code-block:: bash
   :caption: run_container_script.sh

   #!/bin/bash
   #SBATCH -J run_container
   #SBATCH -t 01:00:00
   #SBATCH -n 1

   export INPUT="ubuntu.sif script.py data/"
   export OUTPUT="results/"

   job-nanny apptainer exec ubuntu.sif python3 script.py

.. tip::
   See the :ref:`containers` section for more advanced examples, including MPI and GPU.

.. _system_administrator_installation:

Requesting a Global Installation
================================

If the application:

- Is too complex for local installation
- Will be useful for several users
- Requires special system configuration

You can request from the GridUnesp team:

**Email:** ``support.ncc@unesp.br``

**Required information:**

- Application name
- Desired version
- Link to official documentation
- Installation instructions (if available)

.. note::
   The team will evaluate the request and may:

   - Install globally as a module
   - Suggest local installation
   - Provide specific guidance

Command Summary
===============

.. list-table:: Commands for module management
   :header-rows: 1
   :widths: 30 70

   * - Command
     - Description
   * - ``module avail``
     - List available modules
   * - ``module load name``
     - Load module
   * - ``module list``
     - View loaded modules
   * - ``module unload name``
     - Unload module
   * - ``module purge``
     - Unload all

.. seealso::

   - :ref:`installed_applications` - List of available applications
   - :ref:`containers` - Complete containers guide
   - :ref:`running_simulations` - How to use applications in jobs