.. _user_manual:

===========
User Manual
===========

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

Welcome to the GridUnesp User Manual! This section gathers all the information you need to access the cluster, install applications, create submission scripts, monitor your jobs, and optimize your processing.

.. note::
   If you are new to GridUnesp, we recommend starting with the :ref:`quick_start` for an overview of the process.

.. (Commented-out toctree — kept for reference only)

Chapter Overview
================

**Getting Started:**

- :ref:`accessing_the_cluster` - How to log in to GridUnesp
- :ref:`transferring_files` - How to transfer data to/from the cluster

**Preparing the Environment:**

- :ref:`installing_applications` - How to install software and libraries
- :ref:`ssh_authentication` - Advanced SSH configuration

**Job Submission:**

- :ref:`running_simulations` - Basic submission concepts
- :ref:`improving_submission_script` - SBATCH directives
- :ref:`job_array` - Submitting multiple jobs
- :ref:`partitions_limits` - System partitions and limits

**Parallelism and Optimization:**

- :ref:`shared_memory` - OpenMP and threads
- :ref:`distributed_memory` - MPI and distributed processes
- :ref:`gpu_usage` - Using GPUs
- :ref:`optimizing_performance` - Optimization techniques

**Advanced Topics:**

- :ref:`containers` - Using containers (Singularity)
- :ref:`installed_applications` - Examples with specific applications
- :ref:`job_nanny_script` - Wrapper script for jobs

**Reference:**

- :ref:`storage_guide` - Details about the file systems
- :ref:`slurm_reference` - SLURM reference commands
- :ref:`priority_policy` - How job priority works

Typical Workflow
================

A typical workflow on GridUnesp follows these steps:

1. **Access the cluster** via SSH (:ref:`accessing_the_cluster`)
2. **Transfer your data** and scripts (:ref:`transferring_files`)
3. **Prepare the environment** by loading modules or installing applications (:ref:`installing_applications`)
4. **Create a submission script** with the appropriate directives (:ref:`running_simulations`)
5. **Submit the job** with ``sbatch``
6. **Monitor the execution** with ``squeue`` and ``scontrol`` (:ref:`monitoring_jobs`)
7. **Retrieve the results** after completion
8. **Transfer the results** to your local machine

Where to Find Help
==================

.. list-table::
   :header-rows: 1
   :widths: 30 70

   * - Resource
     - Description
   * - :ref:`faq`
     - Answers to the most common questions
   * - :ref:`troubleshooting`
     - Diagnosis and resolution of problems
   * - :ref:`best_practices`
     - Recommendations for responsible use
   * - ``support.ncc@unesp.br``
     - Direct support from the team

.. important::
   Before requesting support, check the :ref:`faq` and :ref:`troubleshooting` sections. Most questions have already been answered there.

Practical Examples
==================

Throughout the manual, you will find practical examples for different scenarios:

- **Basic scripts:** Simple serial jobs
- **Scripts with modules:** Loading software
- **Parallel jobs:** OpenMP and MPI
- **Job arrays:** Batch processing
- **GPU jobs:** Using accelerators
- **Containers:** Running with Apptainer

.. tip::
   Adapt the examples to your specific needs. The scripts are provided as a starting point.

Next Steps
==========

We recommend reading the first chapters in sequence for beginners. Advanced users can navigate directly to the topics of interest.

**Start with:** :ref:`accessing_the_cluster`

.. seealso::

   - :ref:`infrastructure` - Details about the available hardware
   - :ref:`statistics` - Cluster usage data
   - :ref:`contact` - Support channels