AQUA
  • 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
AQUA
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