.. _running_simulations:

===================
Running Simulations
===================

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

This section presents the fundamental concepts for processing jobs on GridUnesp, from environment preparation to execution monitoring.

.. important::
   The server **access.grid.unesp.br** is exclusively for access and preparation.
   
   **NEVER run simulations directly on access.** Always use the queue system (SLURM) to submit jobs to the processing nodes.

Basic Workflow
==============

.. raw:: html

   <embed width="630px" height="354.3px" src="../_static/Acesso_ao_cluster.svg" />

The typical workflow on GridUnesp follows these steps:

1. **Access** the access server (``ssh``)
2. **Prepare** your files and scripts in ``/home/``
3. **Submit** the job with ``sbatch``
4. **Monitor** execution with ``squeue``
5. **Retrieve** results after completion

First Job: Simple Example
=========================

Let's create a test job that simply displays the date and waits 60 seconds.

**Step 1: Create the submission script**

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

   #!/bin/bash
   #SBATCH -t 5:00        # Maximum time: 5 minutes

   date
   sleep 60

**Step 2: Submit the job**

.. code-block:: bash

   sbatch first_job.sh

**Step 3: Check the status**

.. code-block:: bash

   squeue -u $USER

**Step 4: View the result**

.. code-block:: bash

   cat slurm-*.out

.. note::
   The output file follows the pattern ``slurm-JOBID.out``.

.. _monitoring_jobs:

Monitoring Jobs
===============

squeue command
--------------

.. code-block:: bash

   # View all jobs
   squeue -a

   # View only your jobs
   squeue -u $USER

   # View jobs in detailed format
   squeue -u $USER -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R"

**Job states:**

- **PD** (PENDING): Waiting for resources
- **R** (RUNNING): Running
- **CG** (COMPLETING): Finishing
- **F** (FAILED): Failed
- **TO** (TIMEOUT): Exceeded time limit

**Example output:**

.. code-block:: text

   JOBID    PARTITION        NAME   USER  ST      TIME  NODES  NODELIST
   2848879      short  vulcano.sh  spock   R      0:09      1   node011
   2841620       long   crucio.sh  vader   R  10:02:40      1   node018

scontrol command
----------------

To get full details of a job:

.. code-block:: bash

   scontrol show job JOBID

**Example partial output:**

.. code-block:: text

   JobId=2848879 JobName=vulcano.sh
     UserId=spock(11992) GroupId=enterprise(11006)
     JobState=RUNNING
     RunTime=00:00:18 TimeLimit=00:05:00
     NodeList=node011
     Command=/home/spock/vulcano.sh

scancel command
---------------

To cancel a job:

.. code-block:: bash

   scancel JOBID

To cancel all your jobs:

.. code-block:: bash

   scancel -u $USER

.. _basic_queue_system:

Queue System (Partitions)
=========================

GridUnesp organizes jobs into partitions based on maximum execution time:

.. list-table:: Available partitions
   :header-rows: 1
   :widths: 20 30 50

   * - Partition
     - Limit
     - Recommended use
   * - **short**
     - 24 hours
     - Tests, quick jobs (default)
   * - **medium**
     - 7 days
     - Medium-duration simulations
   * - **long**
     - 30 days
     - Long simulations
   * - **gpu**
     - 24 hours
     - Exclusively for the GPU server

.. important::
   - If not specified, the job goes to the **short** partition with a 24h limit
   - When the limit is reached, the job is **automatically cancelled** (TIMEOUT)
   - Always specify a **realistic** time (shorter jobs have priority)

Specifying time:

.. code-block:: bash

   #SBATCH -t 30:00                 # 30 minutes
   #SBATCH -t 12:00:00              # 12 hours
   #SBATCH -t 2-12:00:00            # 2 days and 12 hours
   #SBATCH -t 30-00:00:00           # 30 days

.. _storage_info:

File Systems
============

During execution, jobs use different storage areas:

.. list-table:: Mount points
   :header-rows: 1
   :widths: 20 20 60

   * - Location
     - Capacity
     - Use
   * - ``/home/``
     - 120 TB
     - Job preparation (accessible from access server)
   * - ``/tmp/``
     - ~180 GB/node
     - Single-node jobs (fast, temporary)
   * - ``/store/``
     - 7 TB
     - Multi-node jobs and large files

.. tip::
   See :ref:`storage_guide` for details on how to optimize the use of each area.

Basic Command Summary
=====================

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

   * - Command
     - Description
   * - ``sbatch script.sh``
     - Submit job
   * - ``squeue -u $USER``
     - View your jobs
   * - ``scancel JOBID``
     - Cancel job
   * - ``scontrol show job JOBID``
     - Job details
   * - ``sacct -j JOBID``
     - Job history (after completion)

.. seealso::

   - :ref:`improving_submission_script` - More configuration options
   - :ref:`monitoring_jobs` - Advanced monitoring
   - :ref:`priority_policy` - How priority works
   - :ref:`best_practices` - Usage recommendations