GridUnesp - User Documentation
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
Index
Index