Welcome to AQUA’s documentation!

• Introduction
  • Overview of AQUA
  • Purpose
  • Key Features
  • Contributing
• Installation
  • Prerequisites
  • Installation with Miniforge
  • Update of the environment
  • Installation on LUMI HPC
  • Installation on Levante HPC at DKRZ
  • Installation on MareNostrum 5 (MN5) HPC at BSC
  • Installation and use of the AQUA container
• Getting Started
  • Basic Concepts
  • Python installation
  • Catalog installation
    • Set up the configuration folder
    • Add a catalog
  • Set up Jupyter kernel
• Example use case
• The Reader class
  • The Reader
  • Input and Output formats
  • Catalog exploration
  • Reader basic usage
  • Dask and Iterator access
• Configuration and catalog manager
  • The AQUA console
  • aqua install
  • aqua avail
  • aqua add <catalog>
  • aqua remove <catalog>
  • aqua set <catalog>
  • aqua uninstall
  • aqua list
  • aqua update
  • aqua fixes {add,remove} <fixes-file>
  • aqua grids {add,remove} <grid-file>
  • aqua lra -c <config_file> <lra-options>
• Regrid and interpolation capabilities
  • Basic usage
  • Concept
  • Available target grids
  • Oceanic grid files naming scheme
    • Elements Description
    • Examples
  • Vertical interpolation
• Fixer functionalities
  • Concept
  • Convention file structure
  • Fixer file structure
  • AQUA variables convention
  • Metadata Correction
    • Merge of convention and fixer
    • Variables block structure
  • Data Model and Coordinates/Dimensions Correction
  • Develop your own fix
• Other core functionalities
  • Time Statistics
  • Detrending
  • Spatial Averaging
  • Time selection
  • Level selection
  • Streaming of data
    • Basic usage
    • Iterator streaming
  • Accessors
    • Basic usage
    • Usage with multiple Reader instances
  • Parallel Processing
  • Graphic tools
    • Single map
    • Single map with differences
    • Time series
    • Seasonal cycle
    • Multiple maps
• Container
  • Download the container image
  • Load the container
    • Load container script
  • Generate a Personal Access Token (PAT)
  • Advanced Topics
    • Running Jupyter Notebook
    • Running Jupyter Notebook within VSCode
    • Temporary Upgrade of Any Package
• Diagnostics
  • Overview of Available Diagnostics
    • Frontier Diagnostics
      • SSH variability
      • Tropical Cyclones detection, tracking and zoom in diagnostic
      • Tropical rainfall diagnostic
    • State-of-the-art diagnostics
      • Global Biases Diagnostic
      • ECmean4 Performance Metrics
      • Timeseries
      • Ocean3D
      • Radiation Budget Diagnostic
      • Sea ice extent
      • Teleconnections diagnostic
  • Running Diagnostics
  • Minimum Data Requirements
  • Creating Custom Diagnostics
    • Standards for new diagnostics
      • Automatic Standardized File Naming
      • Configuration Files and AQUA console
• Adding new data
  • File-based sources
  • FDB-based sources
  • Experiment metadata
  • Regridding capabilities
  • Grid definitions
  • Compact catalogs with YAML override
  • Intake capabilities and kwargs data access
  • DE_340 source syntax convention
    • Models (model key)
    • Experiments (exp key)
    • Sources (source key)
• Catalog Generator
  • aqua catgen -c <config_file> -p <portfolio>
    • Basic usage
  • Configuration file
• Low Resolution Archive
  • Basic Concepts
  • Access to the LRA
  • Generation of the LRA
    • Usage
    • Parallel LRA tool
• AQUA analysis wrapper
  • Basic usage
  • Additional options
  • Configuration file
    • Job
    • Cluster
    • Diagnostics
• Dashboard
  • General description and main components
  • Automatic uploading of figures and documentation to aqua-web
    • Basic usage
    • Additional options
    • Grouping configuration file
    • AWS credentials file
  • Pushing to LUMI-O or another S3 bucket
    • Basic usage
    • Options
  • Multiple experiment analysis submitter
    • Basic usage
    • Options
• Examples and Tutorials
  • Jupyter Notebooks for Various Use Cases
• Command Line Interface tools
  • Benchmarker
  • Grids management
    • Grids downloader
    • Checksum verifications for obs and grids
    • Generation of grid from data
    • Grids synchronization
    • Grids uploader
    • ORCA grid generator
  • HPC container utilities
  • LUMI conda installation
  • Weights generator
  • Orography generator
• Advanced Topics
  • Set up the configuration file
  • Adding a new catalog
    • Creation of the catalog folder
    • Populating the catalog
    • Adding the catalog to the AQUA package
    • Download of grids
  • Dask access to FDB or GSV
  • Iterator access to data
  • Level selection and regridding
  • Reader prepocessing option
  • Slurm utilities
    • The Slurm Class
    • Dask-Job Initialization
    • Submitting Jobs on Different Machines
      • Submit a Job Using Predefined Configurations
      • Submit a Job with Maximum Available Resources per Node
    • Change default attributes
    • Path to the Output
    • Canceling the Dask Job
    • Modifying and Adding Machine Configurations in YAML
  • Enable regrid capabilities in a new machine
    • Set the machine in the catalog machine file
    • Download the grids
  • Developer notes
    • Set up environment variables
    • Add new catalogs as developer
  • ecCodes
    • ecCodes fixer
• API Reference
  • LRAgenerator
    • LRAgenerator.check_integrity()
    • LRAgenerator.create_catalog_entry()
    • LRAgenerator.create_zarr_entry()
    • LRAgenerator.dask
    • LRAgenerator.generate_lra()
    • LRAgenerator.get_filename()
    • LRAgenerator.retrieve()
    • LRAgenerator.write_chunk()
  • Reader
    • Reader.detrend()
    • Reader.fldmean()
    • Reader.info()
    • Reader.instance
    • Reader.reader_fdb()
    • Reader.reader_intake()
    • Reader.regrid()
    • Reader.retrieve()
    • Reader.set_default()
    • Reader.vertinterp()
  • Streaming
    • Streaming.generator()
    • Streaming.reset()
    • Streaming.stream()
    • Streaming.stream_chunk()
  • catalog()
  • inspect_catalog()
  • job()
  • max_resources_per_node()
  • output_dir()
  • plot_hovmoller()
  • plot_maps()
  • plot_single_map()
  • plot_single_map_diff()
  • plot_timeseries()
  • scancel()
  • squeue()
• Troubleshooting and FAQ
  • I am getting an error when trying to install AQUA on LUMI
    • Resource is busy
    • Pip dependency resolution
    • Permission denied
  • I am getting an error MissingGridDefinitionPathError
  • I am getting TypeError: ‘GeometryCollection’ object is not subscriptable when using plot_single_map function
  • How do I cite AQUA in my research or publications?
• Contributing to AQUA
  • Reporting Bugs
  • Suggesting Features
  • Contributing Code
  • Documentation and Tutorials
  • Testing
    • Running Tests Locally
    • Writing Tests
• References and Acknowledgments
  • Citing AQUA
  • Acknowledgments