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-# Instructions to postprocess FMS history output on PP/AN or gaea
+<!-- 
+based on: https://gitlab.gfdl.noaa.gov/fre2/workflows/postprocessing/-/raw/d51df76e537222a3c78405b5749fe59306e6d2bd/README.md
+-->
+This repository holds code for defining tasks, applications, tools, workflows, and other aspects of the FRE2 postprocessing
+ecosystem. 
 
-1. Checkout postprocessing workflow template
-This will clone the postprocessing repository into `/home/$USER/cylc-src/EXPNAME__PLATFORM__TARGET`.
+
+<!-- ______________________________________________________________________________________________________________________ -->
+# 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`](https://github.com/NOAA-GFDL/fre-cli). 
+
+
+
+<!-- ______________________________________________________________________________________________________________________ -->
+## 1. Clone `fre-workflows` repository
 ```
-module load fre/canopy
-fre pp checkout -e EXPNAME -p PLATFORM -t TARGET
+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. Configure pp template with either XML or pp.yaml
 
+
+<!-- ______________________________________________________________________________________________________________________ -->
+## 2. Load Cylc, the backend workflow engine used by FRE2
+[`cylc`](https://cylc.github.io/cylc-doc/stable/html/) 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
 ```
-fre pp configure-xml -e EXPNAME -p PLATFORM -t TARGET -x XML
-```
-or
+module load cylc
 ```
-fre pp configure-yaml -e EXPNAME -p PLATFORM -t TARGET -y YAML 
 
-```
 
-3. (OPTIONAL BUT RECCOMENDED) Create `history-manifest` for config validation
+<!-- ______________________________________________________________________________________________________________________ -->
+## 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`)
 
-Create a `history-manifest` of a single tar file archive first for use in the validation. 
-This list represents the available source files within the history tar archives, and enables the 
-validation procedure to catch a wider variety of potential errors. This can be done like so-
+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](https://metomi.github.io/rose/doc/html/api/configuration/rose-configuration-format.html)
+
+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:
 ```
-tar -tf /archive/$USER/path/to/history/files/YYYYMMDD.nc.tar | grep -v tile[2-6] | sort > /home/$USER/cylc-src/EXPNAME__PLATFORM__TARGET/history-manifest
+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. Validate the configuration
+
+
+<!-- ______________________________________________________________________________________________________________________ -->
+## 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
 ```
-fre pp validate -e EXPNAME -p PLATFORM -t TARGET
+tar -tf /path/to/history/YYYYMMDD.nc.tar | grep -v "tile[2-6]" | sort > history-manifest
 ```
 
-Warnings related to directories are probably valid and should be fixed in `rose-suite.conf`, or created as necessary via `mkdir`.
+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).
+
 
-If you are running postprocessing gaea, you'll need to change the `SITE` variable in `rose-suite.conf` from `ppan` to `gaea`.
 
-5. Install the workflow
+<!-- ______________________________________________________________________________________________________________________ -->
+## 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:
 ```
-fre pp install -e EXPNAME -p PLATFORM -t TARGET
+[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
 ```
 
-If you are attempting this on gaea, you'll need to make two one-time changes before installing.
-- Currently, `cylc`, `rose`, and `isodatetime` must be in your PATH for new shells. One approach to do this is
-to symlink the fms-user-installed fre-cli cylc/rose/isodatetime scripts into your local `~/bin` directory,
-and then add that `~/bin` directory to your PATH in your `.bashrc` or `.cshrc`. (If you don't do this, Cylc tasks
-will fail complaining those 3 tools are not available.)
+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:
 ```
-cd ~/bin
-ln -s /ncrc/home2/Flexible.Modeling.System/conda/envs/fre-cli/bin/{cylc,rose,isodatetime} .
-echo 'setenv PATH ${PATH}:~/bin' >> ~/.cshrc
+[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
 ```
-- Currently, the cylc available on gaea (through `module load cylc` or the `PATH` trick above) does not
-include any global configuration, so you'll need to create a file `~/.cylc/flow/global.cylc` that contains the following.
-If you don't do this, Cylc will use your home directory for the scratch space and rapidly fill your quota.)
+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](https://github.com/NOAA-GFDL/fre-workflows/tree/update.README/app/regrid-xy), 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
 ```
-[install]
-    [[symlink dirs]]
-        [[[localhost]]]
-            run = /gpfs/f5/scratch/gfdl_f/$USER
+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.
+
+
+
+
 
-6. Run the workflow
 
+
+
+<!-- ______________________________________________________________________________________________________________________ -->
+## 8. Validate/Install/Run the configured workflow templates with `cylc`
+Validate the workflow with `cylc` by entering: 
 ```
-fre pp run -e EXPNAME -p PLATFORM -t TARGET
+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.
 
-7. Report status of workflow progress
+We install the workflow with:
+```
+cylc install .
+```
+This creates a workflow directory in `~/cylc-run`. 
 
+After successful installation, the workflow is launched with:
 ```
-fre pp status -e EXPNAME -p PLATFORM -t TARGET
+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`. 
+
+
+
+
 
-8. Launch GUI
 
+<!-- ______________________________________________________________________________________________________________________ -->
+## 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
 ```
-TODO: fre pp gui?
 
 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`
+
+
+
+
+
+