GridUnesp - User Documentation Logo
  • Quick Start Guide
    • Welcome to GridUnesp
      • 1. Create an Account
      • 2. First Login
      • 3. Your First Job
      • 4. Essential Commands
      • 5. Cluster Resources
      • 6. Next Steps

Getting Started

  • Presentation
    • About GridUnesp
    • Team of Specialists
    • Contributions
  • Usage Policy
    • Preamble
    • Objectives
    • User Responsibilities
      • Account and Access
      • Acceptable Use of Resources
      • Fair Use
    • Prohibited Activities
    • Citation Policy
    • Backup and Data Responsibility
      • Backup Policy
      • Recommendations:
    • Data Protection (LGPD)
    • Software Responsibility
    • Cooperation
    • Obligation to Report Incidents
      • Confidentiality
    • Privacy and Monitoring
      • Privacy Policy
      • Activity Monitoring
    • Sanctions and Penalties
    • Final Provisions
      • Validity
      • Policy Updates
      • Acceptance
      • Questions and Clarifications
    • Statement of Awareness
  • Security
    • Password Change
      • Importance of a Secure Password
      • How to Change Your Password
    • User Lockout (Fail2Ban)
      • What is Fail2Ban?
      • Identifying a Lockout
    • Security Notification
      • Obligation to Report
      • Confidentiality
    • Privacy Policy
      • User Data
    • Security Best Practices
      • Protecting Your Account
      • Security in Remote Access
      • Phishing and Social Engineering
    • Activity Monitoring
      • Suspicious Jobs
      • Recent Logins
    • Physical Security
    • Compliance with the Usage Policy

First Steps

  • Registration
    • Registered Projects
    • Registering New Projects
    • Registering New Users
      • Who Can Apply
      • Registration Procedure
      • Approval Flow
    • Citation Policy
      • Acknowledgment Templates
  • Accessing the Cluster
    • Access via Linux/Unix/macOS
    • Access via Microsoft Windows
      • PuTTY Configuration
      • WinSCP Configuration
    • Security Confirmation
      • First Access
      • Server Key Change
    • Access Troubleshooting
      • Connection Refused
      • Permission Denied
  • Transferring Files
    • Transferring to GridUnesp
      • Linux/Unix/macOS (command line)
      • Windows (WinSCP)
    • Transferring from GridUnesp
      • Linux/Unix/macOS (command line)
      • Windows (WinSCP)
    • Data Care
    • Command Summary

User Manual

  • User Manual
    • Chapter Overview
    • Typical Workflow
    • Where to Find Help
    • Practical Examples
    • Next Steps
  • Installing Applications
    • Installation Options
    • Installation via Modules (Already Installed)
      • Listing Available Modules
      • Loading a Module
      • Checking Loaded Modules
      • Unloading a Module
    • Local Installation in /home/
      • Using –prefix (configure/make)
    • Installation via Conda
      • Creating an Environment
      • Installing Packages
      • Listing Environments and Packages
      • Using in Submission Scripts
    • Installation via Apptainer (Containers)
      • Creating an Image
      • Running a Container
    • Requesting a Global Installation
    • Command Summary
  • Running Simulations
    • Basic Workflow
    • First Job: Simple Example
    • Monitoring Jobs
      • squeue command
      • scontrol command
      • scancel command
    • Queue System (Partitions)
    • File Systems
    • Basic Command Summary
  • Improving the Submission Script
    • SBATCH Options
    • job-nanny Script
      • Why use job-nanny?
      • Required Variables
      • Optional Variables
      • Examples of Using job-nanny
    • Choosing Between /tmp/ and /store/
    • Queue System (Detailed)
    • Storage Information (Detailed)
      • /tmp/ Partition
      • /store/ Partition
    • Important Considerations
  • Priority Policy
    • Fair Share Concept
    • Viewing Fair Share
      • sshare Command
      • Filtering the View
    • How Priority Affects Jobs
      • Listing Jobs in Priority Order
    • Factors That Influence Priority
    • Tips to Improve Your Priority
    • Understanding the 14-Day Half-Life
    • Practical Example
    • Command Summary
  • Optimizing Performance
    • Why Optimize?
    • Factors to Consider
    • Practical Optimization Example
      • Test 1: 24 processes on 12 nodes (1 CPU per process)
      • Test 2: 24 processes on 8 nodes (1 CPU per process)
      • Test 3: 24 processes on 12 nodes (2 CPUs per process)
      • Test 4: 24 processes on 1 node (2 CPUs per process)
      • Comparative Table
    • Optimization Strategies
    • HTC: “Breaking Up” Large Inputs (HTC)
    • Trade-offs Between /tmp/ and /store/
    • Optimization Checklist
  • Shared Memory
    • Basic Concepts
    • OpenMP
      • Example in C
      • Compiling
    • Submission Script
    • Important Variables
    • Limitations
    • When to Use Shared Memory
    • Practical Example: Matrix Product
    • Optimization Tips
  • Distributed Memory
    • Basic Concepts
    • MPI
      • Example in C
      • Compiling
    • Submission Script
    • Process Distribution
      • Option 1: Specify the total number of processes
      • Option 2: Specify processes per node
      • Option 3: Specify minimum and maximum nodes
    • Communication Between Processes
      • Example: Distributed Sum
    • Hybrid: MPI + OpenMP
    • When to Use Distributed Memory
    • Scalability
      • Amdahl’s Law
      • Testing Scalability
    • Common Problems
    • Optimization Tips
  • Job Array
    • Concept
    • When to Use a Job Array
    • Basic Syntax
    • Array Formats
    • Practical Examples
      • Example 1: Processing Multiple Files
      • Example 2: Parameter Sweep
      • Example 3: Job Array with a Simultaneous Limit
      • Example 4: Job Array with Dependencies
    • Environment Variables
    • Monitoring Job Arrays
      • View all jobs in the array
      • Cancel a job array
      • View details of a task
    • Limitations
    • Best Practices
    • Comparison: Job Array vs Individual Jobs
  • GPU Usage
    • GPU Infrastructure
    • GPU Partition
    • Basic GPU Script
    • Example with PyTorch
      • Creating the Conda environment
      • Example Python code
      • Submission script for PyTorch
    • Example with TensorFlow
      • Creating the environment
      • Python code
      • Submission script
    • Example with CUDA (C/C++)
      • Simple CUDA code
      • Compilation and execution
    • GPU Monitoring
    • GPU Optimization
    • Common Problems
  • Containers
    • Why Use Containers?
    • Apptainer vs Docker
    • Basic Concepts
    • Obtaining Images
      • Method 1: Pull from Docker Hub
      • Method 2: Build from a definition file
    • Running Containers
    • Sharing Files
    • Containers with GPU
    • Containers with MPI
    • Containers for Specific Applications
      • Example: GROMACS in a container
      • Example: Python with specific libraries
    • Best Practices with Containers
    • Troubleshooting
  • Installed Applications
    • Module System
    • List of Applications by Category
      • Libraries, Compilers and Languages
      • Bioinformatics
      • Computational Chemistry and Materials
      • Physics and Engineering
      • Geosciences
      • Environments and Tools
      • Other Applications
    • Quick Usage Examples
      • Example 1: GROMACS (Molecular Dynamics)
      • Example 2: Quantum ESPRESSO
      • Example 3: Python with scientific packages
      • Example 4: R for statistical analysis
      • Example 5: MATLAB
      • Example 6: VASP
    • Requesting New Applications
    • Installed Scientific Applications and More Complete Examples
      • Amber
        • Description
        • Available Versions
        • Serial Job Submission
        • MPI Job Submission
        • GPU Job Submission
        • MPI + GPU Job Submission
        • Example Input File
        • References
      • Anaconda
        • Description
        • Available Versions
        • Basic Commands
        • Serial Job Submission
        • OpenMP Job Submission
        • MPI Job Submission
        • Example Python Script with MPI
        • Creating an Environment with Specific Packages
        • Using in Submission Scripts
        • References
      • ANSYS
        • Description
        • Available Versions
        • Components
        • Environment Setup
        • Job Submission with ANSYS Fluent (MPI)
        • Example Journal File for Fluent
        • Job Submission with ANSYS Mechanical (APDL)
        • Example APDL Input File
        • Job Submission with CFX
        • References
      • BEAST
        • Description
        • Available Versions
        • Job Submission with BEAST 1.x
        • Job Submission with BEAST 2
        • Job Submission with BEAGLE (acceleration)
        • Job Array for Multiple Runs
        • Example XML File
        • Analysis Tools
        • References
      • Bowtie2
        • Description
        • Available Versions
        • Job Submission
        • Paired-end Alignment
        • Script Processing
        • Important Options
        • References
      • BUSCO
        • Description
        • Available Versions
        • Job Submission
        • Execution Modes
        • Transcriptome Mode
        • Available Databases
        • Job Array for Multiple Samples
        • Results Analysis
        • References
      • CCDC
        • Description
        • Available Versions
        • Components
        • Job Submission with GOLD
        • Example GOLD Configuration File
        • Job Submission with GOLD (MPI)
        • Batch Processing of Multiple Ligands
        • Accessing the CSD (Cambridge Structural Database)
        • Analysis with Mercury (text mode)
        • Preparation with Hermes
        • Mapping with SuperStar
        • References
      • CHARMM
        • Description
        • Available Versions
        • Serial Job Submission
        • Parallel Job Submission
        • GPU Job Submission
        • Example Input File
        • Job Array for Multiple Simulations
        • References
      • ClustalW
        • Description
        • Available Versions
        • Serial Job Submission
        • MPI Job Submission
        • Important Options
        • Alignment with Specific Parameters
        • ClustalW with Profiles
        • Job Array for Multiple Alignments
        • References
      • CP2K
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • MPI Job Submission
        • OpenMP Job Submission
        • Hybrid Job Submission (MPI+OpenMP)
        • GPU Job Submission (version 2026.1.gpu)
        • Multi-GPU Job Submission
        • Hybrid Job Submission (MPI + GPU)
        • Environment Variables
        • Example Input File
        • Example Input File with GPU Configuration
        • Job Array for Parameter Scan
        • Job Array for Parameter Scan with GPU
        • GPU Performance Optimization
        • Performance Comparison
        • References
      • Crystal
        • Description
        • Available Versions
        • Serial Job Submission
        • MPI Job Submission
        • MPI Job Submission with Multiple Nodes
        • Example Input File
        • Job Array for Multiple Systems
        • Results Analysis
        • References
      • CUDA
        • Description
        • Available Versions
        • Environment Setup
        • Compiling CUDA Code
        • Example CUDA Code
        • CUDA Job Submission
        • Multi-GPU
        • GPU Information
        • Compiling for Multiple Architectures
        • Using CUDA with Python (CuPy)
        • Example with CuPy
        • Debugging and Profiling
        • References
      • DFTB+
        • Description
        • Available Versions
        • Serial Job Submission
        • MPI Job Submission
        • Example Input File (HSD)
        • Job Array for Multiple Geometries
        • References
      • DIRAC
        • Description
        • Available Versions
        • Serial Job Submission
        • SMP (OpenMP) Job Submission
        • MPI Job Submission
        • Example Input File
        • Coordinates File (XYZ)
        • Job Array for Multiple Molecules
        • References
      • ESPResSo
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • MPI Job Submission
        • Tcl Script Example
        • Simulation with LB (Lattice Boltzmann)
        • Job Array for Parameter Scan
        • References
      • ExaBayes
        • Description
        • Available Versions
        • MPI Job Submission
        • Serial Job Submission
        • Example Configuration File
        • Alignment File (PHYLIP)
        • Important Options
        • Job Array for Multiple Runs
        • Results Analysis
        • References
      • Exciting
        • Description
        • Available Versions
        • MPI Job Submission
        • Serial Job Submission
        • Example XML Input File
        • Specific Properties Calculation
        • Job Array for Parameter Scan
        • References
      • fastStructure
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • Analysis for Multiple K Values
        • Job Array for Different K Values
        • Choosing the Best K
        • Input Data Format
        • Results Visualization
        • References
      • Foam-Extend
        • Description
        • Available Versions
        • Serial Job Submission
        • Parallel Job Submission
        • Exemplo de Caso: Cavidade
        • GPU Job Submission
        • Job Array for Multiple Cases
        • Results Analysis
        • References
      • g_mmpbsa
        • Description
        • Available Versions
        • Serial Job Submission
        • Example MDP File
        • Index for Decomposition
        • Residue Decomposition Analysis
        • Job Array for Different Temperatures
        • Processing with Multiple Trajectories
        • Statistical Analysis
        • References
      • GAMESS
        • Description
        • Available Versions
        • MPI Job Submission
        • Example Input File
        • Job Array for Multiple Molecules
        • Geometry Optimization
        • Frequency Calculation
        • References
      • GAMIT
        • Description
        • Available Versions
        • Serial Job Submission
        • Execution Script (run.sh)
        • Job Array for Multiple Periods
        • Batch Processing
        • Results Analysis
        • References
      • Gaussian
        • Description
        • Available Versions
        • Serial Job Submission
        • SMP (OpenMP) Job Submission
        • Job Submission with Linda (Distributed Parallel)
        • Example Input File (.com)
        • Specific Properties Calculation
        • Job Array for Parameter Scan
        • Excited States Calculation (TD-DFT)
        • References
      • GCC
        • Description
        • Available Versions
        • Loading Modules
        • Basic Compilation
        • Compilation with OpenMP
        • Compilation with MPI
        • Compilation with External Libraries
        • Common Optimization Flags
        • Job for Compiling and Running
        • Job Array for Testing Different Flags
        • References
      • GROMACS
        • Description
        • Available Versions
        • Serial Job Submission
        • OpenMP Job Submission
        • MPI Job Submission
        • Hybrid Job Submission (MPI+OpenMP)
        • GPU Job Submission
        • MDP Parameter Files
        • Job Array for Multiple Simulations
        • Trajectory Analysis
        • References
      • HMMER
        • Description
        • Available Versions
        • Serial Job Submission
        • OpenMP Job Submission
        • Main HMMER Commands
        • Full Example: Domain Analysis
        • Alignment with HMM
        • Building Profile from Alignment
        • Job Array for Multiple Searches
        • Results Analysis
        • References
      • Intel
        • Description
        • Available Versions
        • Components
        • Loading Modules
        • Compilation with Intel Compilers
        • Compilation with OpenMP
        • Compilation with Intel MPI
        • Execution with Intel MPI
        • Using Intel MKL
        • OneAPI (Modern Version)
        • Intel Optimization Flags
        • Job Array for Testing Different Flags
        • References
      • Kraken2
        • Description
        • Available Versions
        • Serial Job Submission
        • OpenMP Job Submission
        • Paired-end Classification
        • Database Building
        • Pre-built Databases
        • Job Array for Multiple Samples
        • Post-processing
        • Visual Analysis with Krona
        • References
      • LAMMPS
        • Description
        • Available Versions
        • Serial Job Submission
        • MPI Job Submission
        • GPU Job Submission
        • Example Input File
        • Example Input for ReaxFF
        • Job Array for Temperature Scan
        • Property Calculation
        • References
      • Mathematica
        • Description
        • Available Versions
        • Serial Job Submission
        • Job Submission with MathKernel
        • Job Submission with Parallelism
        • Mathematica Script Example
        • Job Array for Multiple Parameters
        • Batch Data Processing
        • Data Visualization
        • References
      • MATLAB
        • Description
        • Available Versions
        • Serial Job Submission
        • Job Submission with .m File
        • Parallel Job Submission (Parallel Computing Toolbox)
        • MATLAB Script Example
        • Image Processing with Parallel Computing Toolbox
        • Job Array for Multiple Parameters
        • Using Specific Toolboxes
        • Compiling MATLAB Applications
        • Running Compiled Application
        • References
      • MFannot
        • Description
        • Available Versions
        • Loading the Module
        • Required Input Files
        • Job Submission
        • Annotation with Different Genetic Codes
        • Annotation with Similarity Search
        • Job Array for Multiple Sequences
        • Results Interpretation
        • Post-processing with Python
        • Results Visualization
        • References
      • Miniconda
        • Description
        • Available Versions
        • Loading the Module
        • Basic Conda Commands
        • Job Submission with Conda Environment
        • Creating an Environment with Specific Packages
        • Machine Learning Environment
        • Job Array with Different Environments
        • Managing Multiple Environments
        • Environment with GPU Support
        • References
      • MOPAC
        • Description
        • Available Versions
        • Serial Job Submission
        • OpenMP Job Submission
        • Example Input File (.mop)
        • Main MOPAC Keywords
        • Thermodynamic Properties Calculation
        • Job Array for Conformational Scan
        • Molecular Orbital Calculation
        • Results Analysis
        • References
      • NAMD
        • Description
        • Available Versions
        • Serial Job Submission (Multicore)
        • MPI Job Submission (TCP)
        • Hybrid Job Submission (SMP + TCP)
        • Example NAMD Configuration File
        • Energy Minimization
        • Equilibration with Restraints
        • Job Array for Multiple Temperatures
        • Trajectory Analysis with VMD
        • References
      • NetCDF
        • Description
        • Available Versions
        • Loading Modules
        • Compilation with NetCDF
        • C Code Example
        • Fortran Code Example
        • Batch Processing Script
        • Command Line Tools
        • Job Array for Parallel Processing
        • References
      • OpenFOAM
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • Parallel Job Submission
        • Example: Cavity Case (icoFoam)
        • Case Configuration Files
        • Job Array for Multiple Cases
        • Post-processing
        • References
      • OpenMPI
        • Description
        • Available Versions
        • Loading the Module
        • Compilation with OpenMPI
        • MPI Code Example (C)
        • MPI Code Example (Fortran)
        • MPI Job Submission
        • Collective Communication (Example)
        • MPI + OpenMP (Hybrid)
        • Job Array for Scalability Tests
        • References
      • ORCA
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • Parallel Job Submission (OpenMP)
        • MPI Job Submission
        • Example Input File
        • DFT Calculation with Optimization
        • Properties Calculation (NMR, TD-DFT)
        • Job Array for Parameter Scan
        • Results Analysis
        • References
      • PartitionFinder
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • Example Configuration File
        • Job Array for Multiple Alignments
        • Results Analysis
        • References
      • PFinderUCE-SWSC-EN
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission
        • Job Array for Multiple Alignments
        • Input File Format (NEXUS)
        • Processing with PartitionFinder
        • References
      • Phyluce
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission
        • Example Configuration File
        • Complete UCE Analysis Pipeline
        • Job Array for Parallel Processing
        • Post-processing Tools
        • References
      • PLUMED
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission with PLUMED + GROMACS
        • Job Submission with PLUMED + NAMD
        • Example PLUMED File
        • Metadynamics with Free Energy Reconstruction
        • Umbrella Sampling
        • WHAM Analysis
        • References
      • Quantum ESPRESSO
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • MPI Job Submission
        • Example Input File (SCF)
        • Band Structure Calculation
        • Vibrational Properties Calculation
        • Geometry Optimization
        • Job Array for Parameter Scan
        • References
      • quest-qmc
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission
        • Example Input File
        • Geometry File
        • Job Array for Parameter Scan
        • Results Analysis
        • References
      • R
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • Job Submission with Parallelism
        • R Script Example
        • Example with Parallelism
        • Job Array for Multiple Analyses
        • Package Installation
        • Bioconductor
        • References
      • RAxML
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • MPI Job Submission
        • Job Submission with Bootstrap
        • Example Input File (PHYLIP)
        • Main Options
        • Rapid Analysis with Bootstrap
        • Job Array for Multiple Genes
        • Results Analysis
        • References
      • RAxML-NG
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission
        • Best Tree Search
        • Bootstrap
        • Full Analysis (Search + Bootstrap)
        • Available Models
        • Job Array for Multiple Alignments
        • Results Analysis
        • References
      • RNXCMP
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission
        • Batch Processing
        • Decompression
        • Job Array for Multiple Files
        • Integrity Verification
        • References
      • ROOT
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission
        • ROOT Script Example (C++)
        • ROOT Script with Python (PyROOT)
        • Batch Processing
        • Job Array for Simulations
        • RDataFrame Analysis
        • References
      • RSEM
        • Description
        • Available Versions
        • Loading the Module
        • Index Preparation
        • Single Sample Quantification
        • Batch Processing with Script
        • Job Array for Multiple Samples
        • Analysis with EBSeq
        • Results Extraction
        • References
      • Salmon
        • Description
        • Available Versions
        • Loading the Module
        • Transcriptome Indexing
        • Quantification (mapping-based mode)
        • Single-end Quantification
        • Batch Processing with Script
        • Job Array for Multiple Samples
        • Library Type Detection
        • Results Analysis
        • References
      • Siesta
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • MPI Job Submission
        • Example Input File (FDF)
        • Geometry Optimization
        • Band Structure Calculation
        • Density of States
        • Job Array for Parameter Scan
        • Results Analysis
        • References
      • SPAdes
        • Description
        • Available Versions
        • Loading the Module
        • Basic Assembly
        • Assembly with Careful Mode
        • Assembly with Multiple Libraries
        • Single-end Assembly
        • Metagenomic Assembly
        • Assembly with RNA-seq (rnaSPAdes)
        • Job Array for Multiple Samples
        • Results Analysis
        • References
      • Stacks
        • Description
        • Available Versions
        • Loading the Module
        • Basic Pipeline with Stacks
        • Script Processing
        • Population Map File (popmap)
        • Job Array for Multiple Samples
        • Population Analysis
        • SNP Filtering
        • Results Analysis
        • References
      • Structure
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission
        • Job Array for Multiple K Values
        • Multiple Runs for Each K
        • Input File (mainparams)
        • Input File (extraparams)
        • Data File
        • Results Analysis
        • Q-matrix Plot
        • References
      • SU2
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • MPI Job Submission
        • Example Configuration File
        • Shape Optimization
        • Job Array for Parameter Scan
        • Results Analysis
        • References
      • SWAN
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • OpenMP Job Submission
        • MPI Job Submission
        • Example Input File
        • Bathymetry File
        • Output Points File
        • Input Spectrum File
        • Job Array for Multiple Simulations
        • Results Analysis
        • References
      • Tesseract
        • Description
        • Available Versions
        • Loading the Module
        • PDF to Image Conversion
        • Basic Job Submission
        • Batch Image Processing
        • Job Array for Multiple Images
        • Multiple Languages
        • Advanced Settings
        • PDF Processing with Leptonica
        • Available Leptonica Tools
        • Example Conversion with Leptonica
        • References
      • TrimGalore
        • Description
        • Available Versions
        • Loading the Module
        • Job Submission
        • Job Array for Multiple Samples
        • Job Array for Paired-end (Multiple Samples)
        • Main Options and Features
        • Output Files
        • Optimization Tips
        • References
      • Trinity
        • Description
        • Available Versions
        • Loading the Module
        • Basic Assembly
        • Strand-specific Assembly
        • Single-end Assembly
        • Assembly with Multiple Samples
        • Including Unpaired Reads
        • Abundance Quantification
        • Differential Expression Analysis
        • Job Array for Multiple Samples
        • Results Analysis
        • References
      • VASP
        • Description
        • Available Versions
        • Loading the Module
        • Serial Job Submission
        • MPI Job Submission
        • Input Files
        • Geometry Optimization
        • Band Structure Calculation
        • Density of States (DOS)
        • Job Array for Parameter Scan
        • Results Analysis
        • References
      • VCFtools
        • Description
        • Available Versions
        • Loading the Module
        • Basic Filtering
        • Depth Filtering
        • Population Filtering
        • Statistics Calculation
        • Format Conversion
        • Job Array for Multiple Chromosomes
        • PCA Analysis
        • References
      • Weka
        • Description
        • Available Versions
        • Loading the Module
        • Classification
        • Regression
        • Clustering
        • Cross-Validation
        • Attribute Selection
        • Job Array for Multiple Algorithms
        • Hyperparameter Optimization
        • Results Analysis
        • Useful Commands
        • References
      • xtb
        • Description
        • Available Versions
        • Loading the Module
        • Simple Energy Calculation
        • Geometry Optimization
        • Frequency Calculation
        • Simple MD (meta-dynamics)
        • Solvent Screening (GBSA)
        • Electronic Properties
        • Coordinate Scan
        • Job Array for Multiple Molecules
        • Results Analysis
        • References
  • Using job-nanny
    • Why Use job-nanny?
    • How It Works
      • Workflow
    • Required Variables
      • INPUT
      • OUTPUT
    • Optional Variables
    • Choosing Between /tmp/ and /store/
    • Usage Examples
      • Example 1: Simple Serial Job
      • Example 2: Job with Multiple Files
      • Example 3: Job with Large Files
      • Example 4: MPI Job (Multiple Nodes)
      • Example 5: Job with Frequent Checkpoints
      • Example 6: Debug Job
    • job-nanny Log File
    • Common Errors and Solutions
      • Error: “INPUT is missing”
      • Error: “OUTPUT is missing”
      • Error: “No space left on device”
      • OUTPUT Files Do Not Appear in /home/
      • Error: “Permission denied” on /store/
    • Frequently Asked Questions
  • Authentication with SSH Keys
    • How SSH Keys Work
    • Generating an SSH Key Pair
      • Linux and macOS
      • Windows (PowerShell)
      • Windows (PuTTYgen)
    • Copying the Public Key to GridUnesp
      • Method 1: ssh-copy-id (Linux/macOS)
      • Method 2: Manual Copy
    • Configuring the ~/.ssh/config File
    • Using ssh-agent
      • Linux/macOS
      • Windows (PowerShell)
    • Troubleshooting
      • Incorrect Permissions
      • Connection Still Asks for Password
      • Error: “Permissions 0644 for ‘id_rsa’ are too open”
      • Error: “Agent admitted failure to sign”
    • Security Best Practices
    • Verifying Fingerprints
  • Partitions and Resource Limits
    • Basic Concepts
    • Available Partitions
    • Querying Partitions
      • sinfo Command
      • scontrol Command
    • Specifying Resources in the Script
      • Partition
      • Execution Time
      • Nodes and Processes
      • Memory
      • GPUs
    • Practical Examples
      • Example 1: Serial Job
      • Example 2: OpenMP Parallel Job
      • Example 3: MPI Job
      • Example 4: GPU Job
      • Example 5: Job Array with Concurrency Limit
    • Checking Limits and Usage
      • Running Jobs
      • Resources in Use
    • Why Is My Job Not Starting?
    • Optimizing Resource Usage
  • Complete Storage Guide
    • Storage Systems
    • /home/ - Personal Directory
      • Characteristics
      • What to Store in /home/
      • Suggested Organization:
    • /tmp/ - Temporary Local Storage
      • Characteristics
      • When to Use /tmp/
      • Using /tmp/ Correctly
    • /store/ - Shared Storage
      • Characteristics
      • When to Use /store/
      • Using /store/
    • Managing Disk Space
      • Checking Disk Usage
      • Cleaning Up Files
    • Sharing Data with Other Users
    • Automatic Cleanup Policy
    • Backup Strategies
      • Option 1: Manual Backup with rsync
      • Option 2: Git for Code
      • Option 3: Cloud Storage (rclone)
      • Option 4: Periodic Tarball
    • Best Practices
      • 3-2-1 Rule
      • Backup Checklist
    • I/O Optimization
    • Troubleshooting
    • Frequently Asked Questions
  • Complete SLURM Directive Reference
    • Introduction
    • Basic Script Structure
    • Essential Directives
      • Job Identification
      • Compute Resources
      • Partition and Time
      • Memory
      • Special Resources
    • Advanced Directives
      • E-mail and Notifications
      • Job Arrays
      • Job Dependencies
      • Resource Control
      • Task Distribution
      • Output Control
      • Restart and Checkpoints
    • Complete Practical Examples
      • Simple Serial Job
      • OpenMP Parallel Job
      • MPI Parallel Job
      • Hybrid MPI + OpenMP Job
      • GPU Job
      • Multi-GPU Job
      • Job Array
      • Job Array with Concurrency Limit
      • Jobs with Dependencies
      • Job with E-mail Notification
    • SLURM Environment Variables
      • Identification
      • Resources
      • Nodes and Location
      • Arrays
      • Usage Example
    • Useful SLURM Commands
      • Submission and Control
      • Monitoring
      • History and Accounting
    • Tips and Best Practices
      • Estimating Resources
      • Optimizing Wait Time
      • Avoiding Common Mistakes
      • Organizing Outputs
      • Debugging
    • References

Resources and Support

  • Infrastructure
    • Data Center
      • Projects in the Data Center
    • Team
    • The GridUnesp Cluster
      • Definitions
      • Operation
      • Node Configuration
        • Worker Nodes (Processing Nodes)
      • Specifications Summary
    • Network
    • Energy Consumption
    • Cooling System
    • Future Acquisitions
      • Incorporation Policy
    • Unsupported Services
  • Best Practices
    • Sharing Access
    • Requesting Support
    • Data Maintenance
      • Backup Policy
      • Disk Space Management
    • Processing on the Access Server
    • Best Practices Summary
  • Frequently Asked Questions
    • Accessing GridUnesp
      • 1) How do I get help using GridUnesp?
      • 2) How do I log in to GridUnesp?
      • 3) I forgot my password. How do I reset it?
      • 4) “The authenticity of host… can’t be established” — What does this mean?
      • 5) “WARNING: POSSIBLE DNS SPOOFING DETECTED!” — What should I do?
      • 6) Why can’t I log in?
      • 7) I was connected and the terminal froze. Why?
      • 8) I don’t know what to do after logging in. Can you help?
      • 9) Can I access GridUnesp via a browser?
    • File Transfer
      • 10) How do I transfer files to my account?
      • 11) How do I transfer files from GridUnesp to my computer?
    • Installing Programs
      • 12) I don’t have administrator permission. How do I install software?
      • 13) How do I install a specific piece of software?
    • Job Processing
      • 14) Can I process jobs in /home?
      • 15) How do I run jobs on GridUnesp?
      • 16) How do I create a submission script?
    • Job Monitoring
      • 17) How long can my job run?
      • 18) How many partitions are there?
      • 19) How do I know my job has started running?
      • 20) Why does my job take a long time to start?
      • 21) Is there an estimated start time for my job?
      • 22) Why do other users have many jobs running while I don’t?
    • Processing Failures
      • 23) My job was cancelled due to TIMEOUT. What does that mean?
      • 24) My job was cancelled due to missing INPUT. What does that mean?
      • 25) My job was cancelled due to missing OUTPUT. What does that mean?
      • 26) Why did my job fail?
    • Job Optimization
      • 27) How can I speed up my job?
      • 28) How many CPUs can I request?
      • 29) Does GridUnesp have GPUs?
      • 30) How do I use multiple CPUs in a job?
      • 31) How do I run jobs in parallel?
      • 32) How do I use MPI?
      • 33) How do I specify the number of nodes?
      • 34) Can I submit multiple jobs at once?
      • 35) Why is my job faster on 1 node than on multiple nodes?
      • 36) Does GridUnesp use InfiniBand or Ethernet?
    • Best Practices
      • 37) My files are very large. Is that a problem?
      • 38) How do I use /store/ instead of /tmp/?
      • 39) How do I use /tmp/ instead of /store/?
      • 40) Can I leave files stored on GridUnesp?
      • 41) How do I delete files from my account?
      • 42) How can I contribute to the smooth running of the cluster?
    • Other Questions
      • 43) Does GridUnesp use Ubuntu?
      • 44) What is the operating system?
      • 45) Can I use interactive programs?
      • 46) How do I open visual applications?
      • 47) Can I have a video call with the support team?
  • Troubleshooting
    • Access Problems
      • SSH Authentication Error
      • Connection Refused
      • Slow or Unstable Connection
    • Job Problems
      • Job Stuck in PENDING State for a Long Time
      • Job Fails Immediately
      • Job Cancelled (CANCELLED)
      • Library Error in Job
      • Compilation Problems
    • Storage Problems
      • No Disk Space
      • Files Disappeared
      • Permission Error
    • Performance Problems
      • Very Slow Job
      • Out of Memory (OOM)
    • Module Problems
      • Module Not Found
      • Module Conflict
    • job-nanny Problems
      • Required INPUT/OUTPUT
      • Using /store/ vs /tmp/
    • Network Problems
      • Slow Transfer
      • Interrupted Transfer
    • General Problems
      • Command Not Found
      • Default Shell
      • System Language
    • When to Contact Support
  • Contact
    • Support
      • Why use the support list?
      • Information to include in your e-mail
    • Location
    • Operating Hours
    • Social Media and Communication

Additional Information

  • Statistics
    • Projects and Users
      • Evolution of Registered Projects
      • Evolution of Registered Users
    • Fields of Knowledge
      • Distribution of Projects by Field
      • Evolution by Field
      • Distribution of Users by Field
      • Cumulative Evolution of Users by Field
      • Distribution by Campus
    • Processing
      • Cumulative CPU Hours
      • Use by International Collaborations
    • User Connections
      • Global Distribution
      • Connection Map
      • Connections by Unesp Campus
  • History
    • 2008 - Infrastructure Announcement
    • 2009 - Start of Operations
    • 2010 - Expansion and Outreach
    • 2011 - Accelerated Growth
    • 2012 - International Recognition
    • 2013 - Consolidation and New Services
    • 2014 - Accessibility
    • 2015 - Expressive Milestones
    • 2016 - Upgrade and Scientific Achievements
    • 2017 - Upgrade Completion
    • 2018 - Expansion and Statistics
    • 2019 - Science Outreach
    • 2020 - Pandemic and Accelerated Demand
    • 2021 - Remote Continuity
    • 2022 - Return and Consolidation
    • 2023-2024 - Continuous Expansion
    • 2025 - New Milestones
  • Publications
    • Citation Policy
      • Requirement
      • Acknowledgment Templates
    • Reporting Publications
      • Procedure
      • Previous Publications Without Acknowledgment
    • Publication Statistics
      • Cumulative Data
    • Complete List of Publications
      • Articles in Journals
        • 2026
        • 2025
        • 2024
        • 2023
        • 2022
        • 2021
        • 2020
        • 2019
        • 2018
        • 2017
        • 2016
        • 2015
        • 2014
        • 2013
        • 2012
        • 2011
      • Conference Proceedings
        • 2025
        • 2024
        • 2023
        • 2022
        • 2021
        • 2020
        • 2019
        • 2018
        • 2017
        • 2014
        • 2013
        • 2012
        • 2011
        • 2010
        • 2009
      • Master’s Dissertations and Doctoral Theses
        • Doctoral Theses
        • Master’s Dissertations
        • Submitted Articles (Theses and Dissertations)
      • Scientific Initiation
        • Scientific Initiation Projects
      • Articles Submitted for Publication
        • 2026
        • 2025
        • 2024
        • 2023
        • 2022
    • Importance of Reporting
      • Why report your publications?
      • Impact of GridUnesp on Scientific Output
  • Satisfaction Survey
    • Overview
    • Areas Evaluated
    • Results
      • Support Documentation for GridUnesp Users
        • Context
        • Improvements Implemented
        • Upcoming Improvements
      • Job Submission
        • Overview
        • Factors Affecting Wait Time
        • Job Queue Dynamics
        • Practical Example
        • Recommendations to Reduce Wait Time
      • Support for GridUnesp Users
        • Response Time
        • Solution Delivery
        • Improvements Implemented During the Survey
        • Support Channels
        • Tips for Efficient Support
      • NPS Index (Net Promoter Score)
        • What is NPS?
        • User Classification
        • NPS Calculation
        • GridUnesp Results
        • Comparison with Companies
        • Interpretation of Results
        • Post-Survey Actions
    • Net Promoter Score (NPS)
    • Key Strengths
    • Improvement Opportunities
    • Implemented Actions
    • Participate!

COVID-19

  • COVID-19
    • Operation During the Pandemic
      • Adaptations Made
    • Statistics for the Period
    • Impact on Research
  • Registration of New Projects and Users in the Pandemic
    • Overview
    • New Scientific Projects
    • New Users
      • Monthly Evolution
    • Distribution by Field of Knowledge
    • Impact of the Pandemic
  • Data Processing and Simulations in the Pandemic
    • Overview
    • Processing Statistics
    • Monthly Evolution
    • Analysis by Period
      • 2020: First Year of the Pandemic
      • 2021: Consolidation of Remote Work
      • 2022: First Quarter
    • Monthly Average
    • Comparison with the Pre-pandemic Period
  • User Support During the Pandemic
    • Overview
    • Support Volume
    • Types of Requests
    • New Applications Installed
    • Impact of Support During the Pandemic
    • User Testimonials
    • Team Adaptation
GridUnesp - User Documentation
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© Copyright 2025, GridUnesp Team - NCC/Unesp. Last updated on September 10, 2026.

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