tactus docs

Contents:

  • DEODE
    • About
    • Set up environment
    • Installation
      • Important
    • Usage
      • The Configuration File
      • Command line options
    • Examples
      • Running ecflow suite on ATOS or LUMI
      • Running the "Forecast" task from the hpc-login’s command line
  • LUMI
    • Introduction
    • Step 1. Getting on LUMI
      • 1.1 SSH to LUMI
      • 1.2 Setup Github access
    • Step 2. Request access to ecflow server
      • 2.1 Generate a new SSH keys pair without passphrase, using the RSA protocol
      • 2.2 Send the public key to ECMWF
      • 2.3 Verification step: ssh ecflow servers
    • Step 3. Configure access to ecflow server from ecflow_client
      • 3.1 Retrieve the encrypted ecflow certificates
      • 3.2 Decode the encrypted files:
      • 3.3 Copy decrypted files to their current location:
      • 3.4 Create soft links for both certificate files:
      • 3.5 Define the following variables:
      • 3.6 Initialize the modules
      • 3.7 Verification test: ping the ecflow server
    • Step 4. Configure Ecflow UI
      • 4.1 Start ecflow_ui
      • 4.2 Add the servers in Ecflow UI
    • Step 5. Setup Deode
    • Step 6. Running Deode
      • Running a complete suite
      • Standalone task example (forecast)
    • Configuration
      • Ecflow server selection
      • Ecflow scheduler
      • Data
      • Production user (lrb_465000527_efprd)
    • Troubleshooting
      • 1. If you can not perform an ssh to the ecflow servers
      • 2. If you can not start ecflow UI
      • 3. If you can not connect to your ecflow servers
      • 4. If you can not start a deode suite
    • Contacts
  • Development guidelines
    • Best practices
      • Requesting and accepting/declining reviews
      • Checklist for assignee
      • Checklist for reviewers
      • Checklist for assignee after completed review
    • Local testing
      • Run and fix toml-formatter errors in place
      • Run linters and exit with an error if non-linted code is detected
      • Run linters and attempt to fix eventually encountered errors
      • Runthe typical checks for things you need to fix prior to a push
      • Run tests
      • Generate and view the documentation to be published to our docpages
  • Testing on Atos and LUMI
    • Testing before tagging
    • Git Branching Structure and Workflow
      • Branching Structure
        • Branches in the Upstream Repository
        • Branches in Developers’ Forks
      • Workflow
        • Developing New Features
        • Fixing Bugs
        • Creating a Hotfix
        • Creating a New Release
      • Summary of Branch Responsibilities
  • Misc
    • DEODE environment variables
    • Local installations
      • Adding a new host
      • Setup ecflow
      • freja
        • Installing under mamba
      • LEONARDO
        • Preparations
        • Install and activate micromamba
        • Get and install the Deode-Workflow
        • Access the ecflow server with port forwarding
    • Available tasks
      • Preparations
      • Preparation of static files
        • Surfex
        • E923
      • Input data
      • Forecasting
      • Postprocessing
      • Archiving
      • Cleaning
    • Configure cases
      • The case setup
      • Adding a new host
      • Time handling
    • EPS Configuration by design
      • Running a minimal ensemble
      • Adjusting which member uses which IFSENS member data
      • Common or member specific mars data retrieval
      • Member specific static data
      • Construct ensemble from modification files
      • Configuring EPS in general terms
        • 1. Single value -> all members get the same setting
        • 2. List of values -> first member gets first item, second member gets second item, etc. (with “circular boundary condition”)
        • 3. Dict of mbr/value pairs -> a given member get the value of the mbr key
        • 4. Python subclass of deode.eps.custom_generators.BaseGenerator. Generates member settings based on list of members.
    • Domain configuration
      • Define new domains
    • Handling of binaries
      • Compilation and external sources
      • How to specify binaries
    • Computational parameters in config file
    • Namelist handling in deode
      • Internal usage
      • Get a specific namelist from command line
      • Add your own namelist
      • Modify a namelist from config
    • Configure selection of timings in output settings
      • Example
    • Configure selection of fields from fullpos
      • Overview
      • The fullpos config files
        • NAMFPC settings
        • Selection
        • Combine selection files
      • Example
    • e923 Update
      • Original instructions:
    • Adding a New Task
      • Code requirements
      • Handling output
      • Submission rules for a task
    • Plug-ins
      • Plugin capablilities
      • Running your own suite
      • Enable your own plug-in
    • Impact models
      • General design
      • EHYPE
      • Deode-EPS-Upscaling
    • Cleaning of experiment
      • Cleaning task to clean experiment files
      • Cleaning settings are separeted to general default settings and folder specific settings:
      • Settings for the working folder
      • Settings for the archive folder
    • Removal of a complete case
    • Some notes about using the FDB archive
      • Preparing the fdb tool
      • How to list available data
      • How to retrieve archived data from FDB:
      • Archive data in FDB
        • How to exclude variables from being archived
      • How to remove data
      • Notes about georef
    • Config
      • Property Config > general
        • Property Config > general > times
        • Property Config > general > accept_static_namelists
        • Property Config > general > case
        • Property Config > general > member_str
        • Property Config > general > member
        • Property Config > general > cnmexp
        • Property Config > general > loglevel
        • Property Config > general > e923_optional_sections
        • Property Config > general > surfex
        • Property Config > general > keep_workdirs
        • Property Config > general > csc
        • Property Config > general > cycle
        • Property Config > general > event_type
        • Property Config > general > famodel
        • Property Config > general > initfile
        • Property Config > general > initfile_sfx
        • Property Config > general > namelist
        • Property Config > general > output_settings
        • Property Config > general > remove_sections
        • Property Config > general > windfarm
        • Property Config > general > fullpos_windpower
        • Property Config > general > upd_sst_sic
        • Property Config > general > surfex_sea_ice
      • Property Config > suite_control
        • Property Config > suite_control > suite_definition
        • Property Config > suite_control > compile
        • Property Config > suite_control > do_creategrib_static
        • Property Config > suite_control > do_soil
        • Property Config > suite_control > do_pgd
        • Property Config > suite_control > mode
        • Property Config > suite_control > interpolate_boundaries
        • Property Config > suite_control > do_interpolsstsic
        • Property Config > suite_control > do_marsprep
        • Property Config > suite_control > do_extractsqlite
        • Property Config > suite_control > do_mergesqlite
        • Property Config > suite_control > create_static_data
        • Property Config > suite_control > create_time_dependent_suite
        • Property Config > suite_control > split_mars
        • Property Config > suite_control > do_cleaning
        • Property Config > suite_control > n_io_merge
        • Property Config > suite_control > n_creategrib
        • Property Config > suite_control > n_addcalculatedfields
        • Property Config > suite_control > member_specific_static_data
        • Property Config > suite_control > member_specific_mars_prep
        • Property Config > suite_control > mirror_globalDT
        • Property Config > suite_control > mirror_host_case
        • Property Config > suite_control > mirror_offline
        • Property Config > suite_control > max_static_data_tasks
        • Property Config > suite_control > DeodeCleaningSuiteDefinition
      • Property Config > clean_old_data
        • Property Config > clean_old_data > cases_period
        • Property Config > clean_old_data > ignore
        • Property Config > clean_old_data > scratch_ext
        • Property Config > clean_old_data > force_delete_period
        • Property Config > clean_old_data > dw_case_prefixes
      • Property Config > system
        • Property Config > system > forecast_dir_link
        • Property Config > system > bdfile_sfx_template
        • Property Config > system > bdfile_sst_template
        • Property Config > system > bdfile_template
        • Property Config > system > sstfile_template
        • Property Config > system > bddir_sfx
        • Property Config > system > bddir
        • Property Config > system > intp_bddir
        • Property Config > system > intp_bddir_sfx
        • Property Config > system > climdir
        • Property Config > system > bindir
        • Property Config > system > bdclimdir
        • Property Config > system > wrk
        • Property Config > system > fullpos_config_file
        • Property Config > system > archive_timestamp
        • Property Config > system > archive
        • Property Config > system > logs
        • Property Config > system > namelists
        • Property Config > system > global_sfcdir
        • Property Config > system > prev_case
        • Property Config > system > sfx_input_definition
        • Property Config > system > forecast_input_definition
        • Property Config > system > c903_input_definition
        • Property Config > system > e923_input_definition
        • Property Config > system > e927_input_definition
      • Property Config > compile
        • Property Config > compile > ial_dir
        • Property Config > compile > git_repo
        • Property Config > compile > git_token
        • Property Config > compile > git_branch
        • Property Config > compile > arch
      • Property Config > boundaries
        • Property Config > boundaries > bdint
        • Property Config > boundaries > bdshift
        • Property Config > boundaries > bdshift_sfx
        • Property Config > boundaries > lbc_per_task
        • Property Config > boundaries > max_interpolation_tasks
        • Property Config > boundaries > bdmodel
        • Property Config > boundaries > bdmodel_sfx
        • Property Config > boundaries > sstmodels
        • Property Config > boundaries > sst_is_lsm
        • Property Config > boundaries > humi_gp
        • Property Config > boundaries > lam
        • Property Config > boundaries > ifs
        • Property Config > boundaries > bd_has_surfex
        • Property Config > boundaries > do_slaf
        • Property Config > boundaries > slaflag
        • Property Config > boundaries > slafdiff
        • Property Config > boundaries > slafk
      • Property Config > collectlogs
        • Property Config > collectlogs > staticlogs
        • Property Config > collectlogs > hourlogs
      • Property Config > pgd
        • Property Config > pgd > npatch
        • Property Config > pgd > one_decade
        • Property Config > pgd > use_osm
      • Property Config > fullpos
        • Property Config > fullpos > config_path
        • Property Config > fullpos > main
        • Property Config > fullpos > selection
        • Property Config > fullpos > domain_name
      • Property Config > troika
        • Property Config > troika > config_file
        • Property Config > troika > troika
      • Property Config > include
      • Property Config > gribmodify
        • Property Config > gribmodify > conversions
        • Property Config > gribmodify > gribmodify_rules_file
        • Property Config > gribmodify > fullpos.1
        • Property Config > gribmodify > fullpos.2
        • Property Config > gribmodify > fullpos.3
        • Property Config > gribmodify > fullpos.4
        • Property Config > gribmodify > fullpos.5
        • Property Config > gribmodify > fullpos.6
        • Property Config > gribmodify > fullpos.7
        • Property Config > gribmodify > surfex.1
        • Property Config > gribmodify > surfex.2
        • Property Config > gribmodify > surfex.3
        • Property Config > gribmodify > surfex.4
        • Property Config > gribmodify > surfex.5
        • Property Config > gribmodify > surfex.6
        • Property Config > gribmodify > surfex.7
        • Property Config > gribmodify > surfex.8
      • Property Config > archiving
        • Property Config > archiving > prefix
        • Property Config > archiving > hour
      • Property Config > cleaning
        • Property Config > cleaning > defaults
        • Property Config > cleaning > Cleaning_example
      • Property Config > creategrib
        • Property Config > creategrib > CreateGrib
        • Property Config > creategrib > CreateGribStatic
      • Property Config > domain
        • Property Config > domain > gridtype
        • Property Config > domain > gridtype_oro
        • Property Config > domain > orographic_smoothing_method
        • Property Config > domain > name
        • Property Config > domain > number
        • Property Config > domain > nzsfilter
        • Property Config > domain > nimax
        • Property Config > domain > njmax
        • Property Config > domain > xdx
        • Property Config > domain > xdy
        • Property Config > domain > ilone
        • Property Config > domain > ilate
        • Property Config > domain > nbzong
        • Property Config > domain > nbzonl
        • Property Config > domain > tstep
        • Property Config > domain > xloncen
        • Property Config > domain > xlatcen
        • Property Config > domain > xlon0
        • Property Config > domain > xlat0
        • Property Config > domain > xbeta
        • Property Config > domain > spectral_smoothing_by_gridtype
        • Property Config > domain > truncation_by_gridtype
        • Property Config > domain > dtf_lead_time
      • Property Config > eps
        • Property Config > eps > general
      • Property Config > extractsqlite
        • Property Config > extractsqlite > parameter_list
        • Property Config > extractsqlite > sqlite_model_name
        • Property Config > extractsqlite > sqlite_path
        • Property Config > extractsqlite > sqlite_template
        • Property Config > extractsqlite > selection
      • Property Config > fdb
        • Property Config > fdb > negative_rules
        • Property Config > fdb > expver_restrictions
        • Property Config > fdb > grib_set
        • Property Config > fdb > databridge_user
      • Property Config > file_templates
        • Property Config > file_templates > duration
        • Property Config > file_templates > ddh_dl
        • Property Config > file_templates > ddh_gl
        • Property Config > file_templates > ddh_zo
        • Property Config > file_templates > fullpos
        • Property Config > file_templates > interpolated_boundaries
        • Property Config > file_templates > history
        • Property Config > file_templates > pgd
        • Property Config > file_templates > pgd_prel
        • Property Config > file_templates > pgd_host
        • Property Config > file_templates > surfex
      • Property Config > json2tab
        • Property Config > json2tab > enabled
        • Property Config > json2tab > force_rewrite
        • Property Config > json2tab > config_file
        • Property Config > json2tab > loglevel
        • Property Config > json2tab > input
        • Property Config > json2tab > output
      • Property Config > macros
        • Property Config > macros > select
      • Property Config > mars
        • Property Config > mars > HRES
        • Property Config > mars > IFSENS
        • Property Config > mars > ATOS_DT
        • Property Config > mars > atos_bologna_DT
        • Property Config > mars > DT12
        • Property Config > mars > i5qp
        • Property Config > mars > i7u4
        • Property Config > mars > i7ye
        • Property Config > mars > i8hy
        • Property Config > mars > lumi_DT
      • Property Config > platform
        • Property Config > platform > archive_types
        • Property Config > platform > ecoclim_data_path
        • Property Config > platform > tactus_home
        • Property Config > platform > pgd_data_path
        • Property Config > platform > soilgrid_data_path
        • Property Config > platform > global_sfcdir
        • Property Config > platform > topo_data_path
        • Property Config > platform > topo_source
        • Property Config > platform > ecosg_data_path
        • Property Config > platform > climdata
        • Property Config > platform > static_data
        • Property Config > platform > e923_data
        • Property Config > platform > ncdir
        • Property Config > platform > rrtm_dir
        • Property Config > platform > rttov_coefdir
        • Property Config > platform > scratch
        • Property Config > platform > task_name
        • Property Config > platform > flake_dir
        • Property Config > platform > albnir_soil_dir
        • Property Config > platform > albnir_veg_dir
        • Property Config > platform > albvis_soil_dir
        • Property Config > platform > albvis_veg_dir
        • Property Config > platform > install_dir
        • Property Config > platform > lai_dir
        • Property Config > platform > osm_data_eu
        • Property Config > platform > tree_height_dir
        • Property Config > platform > windfarm_path
        • Property Config > platform > eclipse_data_dir
        • Property Config > platform > archive_root
        • Property Config > platform > unix_group
      • Property Config > remove
        • Property Config > remove > defaults
        • Property Config > remove > remove_from_scheduler
        • Property Config > remove > remove_not_completed_suites
        • Property Config > remove > Cleaning_example
      • Property Config > scheduler
        • Property Config > scheduler > ecfvars
        • Property Config > scheduler > mirror_globalDT
        • Property Config > scheduler > mirror_offline
        • Property Config > scheduler > mirror_host_case
      • Property Config > submission
        • Property Config > submission > account
        • Property Config > submission > bindir
        • Property Config > submission > bindir_gl
        • Property Config > submission > compiler
        • Property Config > submission > precision
        • Property Config > submission > ial_version
        • Property Config > submission > gl_version
        • Property Config > submission > nproma
        • Property Config > submission > lfftw
        • Property Config > submission > module_initfile
        • Property Config > submission > module_initpath
        • Property Config > submission > default_submit_type
        • Property Config > submission > task_exceptions
        • Property Config > submission > types
        • Property Config > submission > iomerge
      • Property Config > vertical_levels
        • Property Config > vertical_levels > nlev
        • Property Config > vertical_levels > ahalf
        • Property Config > vertical_levels > bhalf
    • Troubleshooting
      • Cannot run poetry
      • Command not found when trying to run deode or some related command
      • ImportError or ModuleNotFoundError when running the package’s executable
      • poetry update or poetry update fail
      • Failing linting checks
      • Failing tests
      • Failing CI checks on github
        • Failing coverage checks on CI
  • CHANGELOG
    • Unreleased
      • Added
      • Changed
      • Fixed
    • [0.25.0] - 2026-02-13
      • Added
      • Changed
      • Fixed
    • [0.24.1] - 2025-12-19
      • Fixed
    • [0.24.0] - 2025-12-16
      • Added
      • Changed
      • Fixed
    • [0.23.0] - 2025-11-24
      • Added
      • Changed
      • Fixed
    • [0.22.0] - 2025-10-21
      • Added
      • Fixed
      • Added
      • Changed
      • Fixed
    • [0.21.0] - 2025-09-25
      • Added
      • Changed
      • Fixed
    • [0.20.0] - 2025-09-18
      • Added
      • Changed
      • Fixed
    • [0.19.0] - 2025-08-14
      • Added
      • Fixed
    • [0.18.1] - 2025-07-22
      • Fixed
    • [0.18.0] - 2025-07-16
      • Added
      • Fixed
    • [0.17.0] - 2025-06-13
      • Added
      • Changed
      • Fixed
    • [0.16.1] - 2025-05-23
      • Fixed
    • [0.16.0] - 2025-05-21
      • Added
      • Changed
      • Fixed
    • [0.15.0] - 2025-04-24
      • Added
      • Changed
      • Fixed
    • [0.14.0] - 2025-03-27
      • Added
      • Changed
      • Fixed
    • [0.13.2] - 2025-03-21
      • Changed
    • [0.13.1] - 2025-02-27
      • Changed
    • [0.13.0] - 2025-02-26
      • Added
      • Changed
      • Fixed
    • [0.12.1] - 2025-02-21
    • [0.12.0] - 2025-02-21
      • Added
      • Changed
      • Fixed
    • [0.11.0] - 2025-02-13
      • Changed
      • Fixed
    • [0.10.0] - 2024-12-17
      • Added
      • Fixed
      • Changed
    • [0.9.1] - 2024-11-22
      • Fixed
    • [0.9.0] - 2024-11-20
      • Added
      • Changed
      • Fixed
    • [0.8.0] - 2024-10-31
      • Added
      • Changed
      • Removed
    • [0.7.1] - 2024-10-17
      • Added
    • [0.7.0] - 2024-10-09
      • Added
      • Changed
      • Fixed
      • Fixed
    • [0.6.1] - 2024-09-24
      • Fixed
    • [bugfix_v0.6.1] - 2024-09-24
    • [0.6.0] - 2024-09-19
      • Added
      • Changed
      • Fixed
      • Removed
    • [0.5.0] - 2024-05-06
      • Added
      • Changed
      • Fixed
    • [0.4.0] - 2024-03-01
      • Breaking changes
      • Added
      • Changed
      • Removed
      • Fixed
      • Maintenance
    • [0.3.0] - 2023-11-28
      • Added
      • Changed
      • Fixed
    • [0.2.0] - 2023-10-27
      • Added
      • Changed
      • Removed
      • Fixed
    • [0.1.0] - 2023-10-11
      • Added
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