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This repository holds code for defining tasks, applications, tools, workflows, and other aspects of the FRE2 postprocessing ecosystem.

Instructions to postprocess FMS history files on GFDL's PP/AN

These instructions are targeted at workflow developers. If you are a user simply looking to run a specific workflow, see fre-cli.

1. Clone fre-workflows repository

git clone https://github.com/NOAA-GFDL/fre-workflows.git
cd fre-workflows

Do not clone to a temporary directory - the directory must be readable by slurm from all nodes. Directories on local \vftmp are not, while those on /home, /work, and /xtmp are.

2. Load Cylc, the backend workflow engine used by FRE2

cylc lets us parse workflow template files (*.cylc) and their configurations into modular, interdependent batch jobs. Tools used by those jobs (e.g. fre-nctools or xarray) should be loaded by those jobs as part of their requirements and do not need to be loaded at this time unless desired.

To run this repository's code, we need cylc accessible and somewhere in out PATH environment variable. One way is to activate a conda environment with cylc-flow, cylc-rose, and metomi-rose installed. At GFDL's PP/AN, it is sufficient to do

module load cylc

3. Fill in rose-suite configuration fields

With your favorite text editor, open up rose-suite.conf and set variables to desired values. These values will be passed to task definitions within flow.cylc and taken as configuration settings to instruct task execution.

Key values include:

  • SITE set to "ppan" to submit jobs to PP/AN cluster
  • HISTORY_DIR directory path to your raw model output
  • HISTORY_SEGMENT amount of time covered by a single history file (ISO8601 datetime)
  • PP_CHUNK_A amount of time covered by a single postprocessed file (ISO8601 datetime)
  • PP_CHUNK_B secondary chunk size for postprocessed files, if desired (ISO8601 datetime)
  • PP_START start of the desired postprocessing (ISO8601 datetime)
  • PP_STOP end of the desired postprocessing (ISO8601 datetime)
  • PP_COMPONENTS space-separated list of user-defined components, discussed in more detail below
  • PP_GRID_SPEC path to FMS grid definition tarfile
  • PP_DEFAULT_XYINTERP default target resolution for regridding, if the resolution is not specified elsewhere
  • FRE_ANALYSIS_HOME For locating shared analysis scripts (only define if DO_ANALYSIS=True)

It is common to not know exactly what to set PP_COMPONENTS to when configuring a new workflow from scratch. Later steps in this guide can help inform how to adjust these settings. The Rose configuation file format is described in full elsewhere

If one is looking to hit the ground running at GFDL's PP/AN, copy/paste the code block here into your rose-suite.conf, replacing YOUR.USERNAME with your own where applicable:

SITE="ppan"
EXPERIMENT='FOO'
PLATFORM='BAR'
TARGET='BAZ'

DO_STATICS=True
DO_TIMEAVGS=True
DO_ATMOS_PLEVEL_MASKING=True
DO_MDTF=False

DO_REFINEDIAG=False
REFINEDIAG_SCRIPTS="\$CYLC_WORKFLOW_RUN_DIR/etc/refineDiag/refineDiag_atmos_cmip6.csh"

DO_PREANALYSIS=False
PREANALYSIS_SCRIPT="\$CYLC_WORKFLOW_RUN_DIR/etc/refineDiag/refineDiag_data_stager_globalAve.csh"

DO_ANALYSIS=False
DO_ANALYSIS_ONLY=False
FRE_ANALYSIS_HOME="/home/fms/local/opt/fre-analysis/test"
ANALYSIS_DIR='/nbhome/YOUR.USERNAME/fre/FMS2023.04_om5_20240410/ESM4.2JpiC_om5b04r1'

CLEAN_WORK=True

PTMP_DIR='/xtmp/$USER/ptmp'

HISTORY_DIR='/archive/Ian.Laflotte/fre/FMS2023.04_om5_20240410/ESM4.2JpiC_om5b04r1/gfdl.ncrc5-intel23-prod-openmp/history'
HISTORY_SEGMENT='P1Y'

PP_DIR='/archive/YOUR.USERNAME/fre/FMS2023.04_om5_20240410/ESM4.2JpiC_om5b04r1/gfdl.ncrc5-intel23-prod-openmp/pp'
PP_CHUNK_A='P2Y'
PP_COMPONENTS='atmos atmos_scalar land land_static'
PP_START="00010101"
PP_STOP="00020101"
PP_DEFAULT_XYINTERP="360,180"
PP_GRID_SPEC='/work/Ian.Laflotte/mosaic_generation/exchange_grid_toolset/workdir/mosaic_c96om5b04v20240410.20240423.an105/mosaic_c96om5b04v20240410.20240423.an105.tar'

4. Create history file manifest (optional but highly recommended)

For more complete validation of workflow settings, we create a manifest for our history file archives with

tar -tf /path/to/history/YYYYMMDD.nc.tar | grep -v "tile[2-6]" | sort > history-manifest

The history-manifest contains a list of source files contained within the targeted history files. This can be helpful for validating settings on a component-by-component basis in the next step(s).

5. Define your desired postprocessing components for remap-pp-components

Users define their own postprocessing components for their workflow, which represent a group of source files to be postprocessed together. This grouping is typically united by a common gridding, which may be the current "native" gridding of the source files, or a desired target gridding to achieve via regridding. If history-manifest was created, it will be used to check that the source files specified in the components are actually present in the history files.

User-defined components are configured within app/remap-pp-components/rose-app.conf. An example set of components could be:

[command]
default=remap-pp-components

[atmos]
sources=atmos_month
grid=regrid-xy/default

[atmos_scalar]
sources=atmos_scalar atmos_global_cmip
grid=native

[land]
sources=land_month_cmip
grid=regrid-xy/288_180.conserve_order1

[land_static]
sources=land_static
grid=regrid-xy/288_180.conserve_order1
freq=P0Y

Here we've defined the atmos component as being a set of one source file, atmos_month. The grid field shows we wish to have these two source files regridded to the default resolution specified in rose-suite.conf. By contrast, the atmos_scalar component contains two source files, and specifies a native grid. This indicates that atmos_scalar and atmos_global_cmip source files will not be regridded when processing them for the atmos_scalar component.

Note- it is not uncommon for a specific component to be named after a source file contained in it's sources field, but it does not imply anything special about the relationship between the source file and the component.

The third component is land, and will be regridded to a resolution corresponding to a 180x288 lat/lon grid, using an interpolation scheme which is conservative to a first-order approximation. The last is the land_static component, and will be similarly handled to land. Since land_static is time-independent, it will require freq=P0Y, as the name is not used to determine if a component involves static data. Statics will only be processed if DO_STATICS=True in rose-suite.conf.

The setting for PP_COMPONENTS should reflect information in app/remap-pp-components/rose-app.conf. From our example, a good list that passes validation would be PP_COMPONENTS=atmos atmos_scalar land land_static.

6. Provide more specifics for regrid-xy

Any component specified in app/remap-pp-components/rose-app.conf requesting regridding requires a corresponding entry in app/regrid-xy/rose-app.conf, providing further information. A full set of options one can specify in this configuration can be found in app/regrid-xy/README.md.

Following up on our example in the previous step, we would not have an extry in app/regrid-xy/rose-app.conf for atmos_scalar, but we will for atmos, land and land_static components:

[command]
default=regrid-xy

[atmos]
inputGrid=cubedsphere
inputRealm=atmos
interpMethod=conserve_order2
outputGridLat=180
outputGridLon=288
outputGridType=default
sources=atmos_month

[land]
inputGrid=cubedsphere
inputRealm=land
interpMethod=conserve_order1
outputGridLat=180
outputGridLon=288
outputGridType=288_180.conserve_order1
sources=land_month_cmip

[land_static]
inputGrid=cubedsphere
inputRealm=land
interpMethod=conserve_order1
outputGridLat=180
outputGridLon=288
outputGridType=288_180.conserve_order1
sources=land_static

Note that the atmos_scalar component does not have an entry here, as we requested a native regridding for source files in that component. Full documentation on the available input configuration fields is available in the app/regrid-xy directory, but some things worth noting above:

  • inputGrid can be cubedsphere or tripolar.
  • inputRealm attribute is used for identifying the land, atmos, or ocean grid mosaic file.
  • The interpMethod should be conserve_order1, conserve_order2, or bilinear.
  • OutputGridType is the grid label referenced in the app/remap-pp-components/rose-app.conf file.
  • OutputGridLat and OutputGridLon identify the target grid if OutputGridType is not specified

7. Validate your workflow configuration

Rose can validate the configuration by checking the field values against a list of rules defined by the devlopers of this repository. It's crucial to note that while this list of rules is determined by the requirements of th

One can wait until this step in this guide, or validate as they go along at any point in the previous instructions

rose macro --validate

Common errors include non-existent directories and time intervals that are not ISO8601 datetimes. It is recommended to address any/all complaints. If history-manifest exists, rose macro --validate will report on source files referenced by components that are not present in the history tar file archives. Whether a missing file is a show-stopper or a toothless complaint is at the discretion of the user. If a source file is missing, consider reconfiguring the component definition(s), remove the source file from the component, or simply removing the component altogether.

8. Validate/Install/Run the configured workflow templates with cylc

Validate the workflow with cylc by entering:

cylc validate .

If the Cylc validation fails but the Rose validation passes, please raise an issue on this repository, as it is better to catch configuration issues at the rose macro --validate step, and the validation rules can be updated to match the task definition requirements.

We install the workflow with:

cylc install .

This creates a workflow directory in ~/cylc-run.

After successful installation, the workflow is launched with:

cylc play fre-workflows/run1

If on PP/AN, cylc launches a scheduler daemon on a workflow1 server, via ssh, triggering the login banner to be printed. This daemon submits and runs jobs based on the task dependencies defined in flow.cylc.

9. Inspect workflow progress with an interface (GUI or TUI)

The workflow will run and shutdown when all tasks are complete. If tasks fail, the workflow may stall, in which case it will shutdown in error after a period of time.

cylc has two workflow viewing interfaces (full GUI and text UI), and a variety of CLI commands that can expose workflow and task information. The text-based GUI can be launched via:

cylc tui fre-workflows/run1

The full GUI can be launched on jhan or jhanbigmem (an107 or an201).

cylc gui --ip=`hostname -f` --port=`jhp 1` --no-browser

Then, navigate to one of the two links printed to screen in your web browser. If one just wants a quick look at the state of their workflow, the user-interfaces can be completely avoided by using the workflow-state command, two examples of which are:

cylc workflow-state -v fre-workflows/run1                # show all jobs
cylc workflow-state -v fre-workflows/run1 | grep failed  # show only failed ones

10. Inspect workflow progress with a terminal CLI

Various other cylc commands are useful for inspecting a running workflow. Try cylc help, and cylc <command> --help for more information on how to use these tools to your advantage!

  • cylc scan Lists running workflows
  • cylc cat-log fre-workflows/run1 Show the scheduler log
  • cylc list Lists all tasks
  • cylc report-timings