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flow.cylc
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#!jinja2
{# fre version should be programatically set, not hard-coded. #}
{% set FRE_VERSION = 2025.01 %}
{# things written between hash and single braces is a Jinja comment. #}
{# Jinja code between single braces is run. #}
{# Jinja code with two braces is printed. #}
{# The site-specific file (stored in site/ subdir) is included at the end of this file. When working in the main #}
{# branch, the ppan site file should be specified. The ppan site comprises of gfdl specific tools. Other available #}
{# sites include ppan, gfdl-ws, and generic. The generic.cylc site file is used for a portable flow.cylc. #}
{# (Probably, we should use similar mechanisms where sensible, e.g. for shared items among workflows) #}
{% set SITE = SITE %}
{# Calculate the number of history segments per a-chunk #}
{% set HIST_SEGMENTS_PER_CHUNK_A = (PP_CHUNK_A | duration_as('s') / HISTORY_SEGMENT | duration_as('s')) | int %}
{# secs_per_365cal_month #}
{% set SECS_PER_365CAL_MONTH = (365 / 12 * 24 * 60 * 60) %}
{# months_per_hist_segment #}
{% set MOS_PER_HIST_SEGMENT = (HISTORY_SEGMENT | duration_as('s') / SECS_PER_365CAL_MONTH) | int %}
{# months_per_chunk_a #}
{% set MOS_PER_CHUNK_A = (PP_CHUNK_A | duration_as('s') / SECS_PER_365CAL_MONTH) | int %}
{# Calculate the number of a-chunks per b-chunk (if desired) #}
{% set DO_SECONDARY_PP = False %}
{% if PP_CHUNK_B is defined and PP_CHUNK_B != PP_CHUNK_A %}
{% set CHUNK_AS_PER_CHUNK_B = (PP_CHUNK_B | duration_as('s') / PP_CHUNK_A | duration_as('s')) | int %}
{% set DO_SECONDARY_PP = True %}
{# months_per_chunk_b #}
{% set MOS_PER_CHUNK_B = (PP_CHUNK_B | duration_as('s') / SECS_PER_365CAL_MONTH) | int %}
{% else %}
{% set MOS_PER_CHUNK_B = -1 %}
{% endif %}
{# Set ANALYSIS_START and ANALYSIS_STOP if they do not exist #}
{% if ANALYSIS_START is not defined %}
{% set ANALYSIS_START = PP_START %}
{% endif %}
{% if ANALYSIS_STOP is not defined %}
{% set ANALYSIS_STOP = PP_STOP %}
{% endif %}
{# The combined yaml is the definitive configuration source #}
{% set YAML = EXPERIMENT + '.yaml' %}
[meta]
title = "Postprocessing Example 1"
description = """
Postprocessing example that includes Bronx-like functionality,
"""
URL = https://gitlab.gfdl.noaa.gov/fre2/workflows/postprocessing
[scheduler]
{# Implicit tasks are tasks without explicit runtime definitions in [runtime], often typos. #}
{# (For prototyping and graphing, change this to True.) #}
allow implicit tasks = False
{# Configure the directories and files to be included in the remote file installation #}
install = app/*, bin/*, etc/*, lib/*
UTC mode = True
# When the stall timeout is reached, a stalled workflow will exit
# and remove the /xtmp working directory.
[[events]]
stall timeout = P1W
[task parameters]
{# The task parameters (except for component) depend on configuration in Rose apps, #}
{# so custom Jinja triggers are used to form the lists. Cylc and custom Jinja triggers have these rules: #}
{# 1. Triggers live in Jinja2Filters/ and must be python #}
{# 2. The trigger filename must be <trigger-name>.py #}
{# 3. In the file, trigger must be defined as a function with the same name #}
{# 4. First argument is passed through as a pipe, and the rest are passed through in the trigger arguments. #}
{# More info: #}
{# The python loaded within Cylc has access to some useful Cylc utilities (e.g. metomi.isodatetime.parsers). #}
{# For development/testing, use "module load conda; conda activate cylc". Then the Cylc python will be loaded. #}
{% set REGRID = "regrid-xy" | form_task_parameters('temporal', PP_COMPONENTS) %}
{% set REGRID_STATIC = "regrid-xy" | form_task_parameters('static', PP_COMPONENTS) %}
{% set DO_REGRID = REGRID|length %}
{% if DO_REGRID %}
regrid = {{ REGRID }}
{% if DO_STATICS %}
regrid_static = {{ REGRID_STATIC }}
{% endif %}
{% endif %}
{% set NATIVE = "native" | form_task_parameters('temporal', PP_COMPONENTS) %}
{% set NATIVE_STATIC = "native" | form_task_parameters('static', PP_COMPONENTS) %}
{% set DO_NATIVE = NATIVE|length %}
{% if DO_NATIVE %}
native = {{ NATIVE }}
{% if DO_STATICS %}
native_static = {{ NATIVE_STATIC }}
{% endif %}
{% endif %}
{# Standard Jinja2 triggers are also available (e.g. "replace") #}
component = {{ PP_COMPONENTS | replace(' ', ', ') }}
[scheduling]
initial cycle point = {{ PP_START }}
final cycle point = {{ PP_STOP }}
# max number of active cycle points (default 5)
# this should be something sensible assuming tasks with required outputs
# (i.e. not marked as "ok to fail") such as analysis scripts.
# But until the analysis scripts can be marked optional then a workaround
# is to set this to be very high, ~100 cycle points.
# However, the cost of keeping many cycle points active at once are starting
# stage-history tasks first, possibly filling /xtmp before the clean tasks run.
runahead limit = P20
[[queues]]
# limit the entire workflow to 100 active tasks at once
[[[default]]]
limit = 100
{# Graph strings are organized by recurrence interval-- when to run the tasks. #}
{# Currently, we use 4 intervals: every history-file segment, once (for statics), #}
{# every chunk-a, and every chunk-b. #}
[[graph]]
{% if DO_ANALYSIS_ONLY %}
{% if DO_SECONDARY_PP %}
{{ YAML | get_analysis_info('task-graph', PP_COMPONENTS, PP_DIR, PP_START, PP_STOP, PP_CHUNK_A, PP_CHUNK_B, DO_ANALYSIS_ONLY) }}
{% else %}
{{ YAML | get_analysis_info('task-graph', PP_COMPONENTS, PP_DIR, PP_START, PP_STOP, PP_CHUNK_A, None, DO_ANALYSIS_ONLY) }}
{% endif %}
{% else %}
#
# Recurrence interval: every history-file segment
#
{{ HISTORY_SEGMENT }} = """
{# Within a recurrence interval, task dependencies are specified with => (depends on), & (and), and | (or). #}
{# Tasks in a dependency can be single tasks, task families (by convention, in all caps), #}
{# or "ensembles" expanded by the parameters above. #}
{# All tasks in the STAGE-HISTORY family (staging history and staging history-refined) are started #}
{# once the pp-starter task succeeds. #}
pp-starter => STAGE-HISTORY
{# Jinja is useful to include or exclude parts of the configuration. In this case, the lines between #}
{# if DO_REFINEDIAG and endif are used or not used, depending on the value of DO_REFINEDIAG (in rose-suite.conf). #}
{# All template variables in rose-suite.conf are available as Jinja variables. #}
{# If refineDiag generation is desired (DO_REFINEDIAG is True), then add these two task dependencies: #}
{# 1. All tasks in the REFINE-DIAG task family are started once the stage-history task succeeds. #}
{# 2. stage-history-refined task is started once all the refineDiag tasks succeed. #}
{% if DO_REFINEDIAG %}
stage-history => REFINE-DIAG
REFINE-DIAG:succeed-all => stage-history-refined
{% endif %}
{# If preAnalysis desired (vitals calculations is canonical case), #}
{# start all PRE-ANALYSIS tasks when stage-history succeeds. #}
{% if DO_PREANALYSIS %}
stage-history => PRE-ANALYSIS
{% endif %}
{# If task families are on the left side of the => then a qualifier must be used (e.g. :succeed-all) #}
{# The angle brackets define the "ensemble" axis, the task paramaters defined above. #}
{# The next two lines set the major processing for the native and regrid #}
{# (horizontal regridding) lists of history files. #}
{# Each history file to be regridded should be regridded once staging is done; then should be split and cataloged #}
{# (into a standard shards directory set by ISO8601 frequencies ). #}
{# Each history file needed for native grid processing is similar, except skipping the regridding. #}
{% if DO_REGRID %}
STAGE-HISTORY:succeed-all => regrid-xy<regrid> => split-netcdf-regrid<regrid> => rename-split-to-pp-regrid<regrid>
{% if DO_ATMOS_PLEVEL_MASKING %}
STAGE-HISTORY:succeed-all => mask-atmos-plevel<regrid> => regrid-xy<regrid>
{% endif %}
{% endif %}
{% if DO_NATIVE %}
STAGE-HISTORY:succeed-all => split-netcdf-native<native> => rename-split-to-pp-native<native>
{% if DO_ATMOS_PLEVEL_MASKING %}
STAGE-HISTORY:succeed-all => mask-atmos-plevel<native> => split-netcdf-native<native>
{% endif %}
{% endif %}
{# If HISTORY_DIR_REFINED is set, then use the next 3 lines. #}
{# Regridding and splitting native history files should not start until the history-refined output is available. #}
{% if HISTORY_DIR_REFINED is defined %}
{% if DO_REGRID %}
stage-history-refined => regrid-xy<regrid>
{% endif %}
{% if DO_NATIVE %}
stage-history-refined => split-netcdf-native<native>
{% endif %}
{% endif %}
{# If work-dir cleaning is desired, then remove what should now be safe to remove. #}
{# Once regridded history files are split, then the regridded history files can be removed. #}
{# Once the split (regridded and native) files are cataloged, then the (not-cataloged) split files can be removed. #}
{% if CLEAN_WORK %}
{% if DO_REGRID %}
regrid-xy<regrid> => clean-history-native
split-netcdf-regrid<regrid> => clean-history-regrid-xy
rename-split-to-pp-regrid<regrid> => clean-split-regrid-xy
{% endif %}
{% if DO_NATIVE %}
split-netcdf-native<native> => clean-history-native
rename-split-to-pp-native<native> => clean-split-native
{% endif %}
{% endif %}
"""
#
# Recurrence interval R1: run only once. useful for statics.
#
R1 = """
{# The static processing is similar to the "every history segment" processing, #}
{# except uses different history file lists. #}
pp-starter => STAGE-HISTORY
{% if DO_STATICS %}
{% if DO_REGRID %}
STAGE-HISTORY:succeed-all => regrid-xy<regrid_static> => split-netcdf-regrid<regrid_static> => rename-split-to-pp-regrid<regrid_static>
{% endif %}
{% if DO_NATIVE %}
STAGE-HISTORY:succeed-all => split-netcdf-native<native_static> => rename-split-to-pp-native<native_static>
{% endif %}
{# After cataloging the regridded and native statics, remap them to pp components as desired #}
{% if DO_NATIVE and DO_REGRID %}
rename-split-to-pp-regrid<regrid_static> & rename-split-to-pp-native<native_static> => remap-pp-components-static => combine-statics
{% elif DO_NATIVE %}
rename-split-to-pp-native<native_static> => remap-pp-components-static => combine-statics
{% elif DO_REGRID %}
rename-split-to-pp-regrid<regrid_static> => remap-pp-components-static => combine-statics
{% endif %}
{% endif %}
{# Similarly, if the history-refined is used, then don't process until the history-refined staging is done. #}
{% if HISTORY_DIR_REFINED is defined %}
{% if DO_STATICS %}
{% if DO_REGRID %}
stage-history-refined => regrid-xy<regrid_static>
{% endif %}
{% if DO_NATIVE %}
stage-history-refined => split-netcdf-native<native_static>
{% endif %}
{% endif %}
{% endif %}
{# If work-dir cleaning is set, then remove what should now be safe to remove. #}
{% if CLEAN_WORK and DO_STATICS %}
{% if DO_REGRID %}
regrid-xy<regrid_static> => clean-history-native
split-netcdf-regrid<regrid_static> => clean-history-regrid-xy
rename-split-to-pp-regrid<regrid_static> => clean-split-regrid-xy
{% endif %}
{% if DO_NATIVE %}
split-netcdf-native<native_static> => clean-history-native
rename-split-to-pp-native<native_static> => clean-split-native
{% endif %}
remap-pp-components-static => clean-shards-static
combine-statics => clean-pp-statics
{% endif %}
"""
#
# Recurrence interval: every CHUNK-A
#
{# Run the tasks to process CHUNK-A every CHUNK-A, starting after PP_CHUNK_A #}
+{{ PP_CHUNK_A | subtract_durations('P1Y') }}/{{ PP_CHUNK_A }} = """
{# Tasks can be split over multiple lines if the subsequent ones begin with =>, &, or | #}
{# The make-timeseries tasks for CHUNK-A depend on all segment processing for the time period succeeding. #}
{# This Jinja for loop expands to do this. #}
{% if DO_REGRID %}
rename-split-to-pp-regrid<regrid>
{% for SEGMENT in range(1, HIST_SEGMENTS_PER_CHUNK_A) %}
& rename-split-to-pp-regrid<regrid>[{{ HISTORY_SEGMENT | multiply_duration(-SEGMENT) }}]
{% endfor %}
{% if HISTORY_SEGMENT != PP_CHUNK_A %}
=> make-timeseries-regrid-{{ PP_CHUNK_A }}<regrid>
{% endif %}
{% if DO_TIMEAVGS %}
=> make-timeavgs-regrid-{{ PP_CHUNK_A }}<regrid>
{% endif %}
{% endif %}
{% if DO_NATIVE %}
rename-split-to-pp-native<native>
{% for SEGMENT in range(1, HIST_SEGMENTS_PER_CHUNK_A) %}
& rename-split-to-pp-native<native>[{{ HISTORY_SEGMENT | multiply_duration(-SEGMENT) }}]
{% endfor %}
{% if HISTORY_SEGMENT != PP_CHUNK_A %}
=> make-timeseries-native-{{ PP_CHUNK_A }}<native>
{% endif %}
{% if DO_TIMEAVGS %}
=> make-timeavgs-native-{{ PP_CHUNK_A }}<native>
{% endif %}
{% endif %}
{% if DO_REGRID %}
{{ "regrid-xy" | form_remap_dep('temporal', PP_CHUNK_A, PP_COMPONENTS, 'ts', HISTORY_SEGMENT) }}
{% if DO_TIMEAVGS %}
{{ "regrid-xy" | form_remap_dep('temporal', PP_CHUNK_A, PP_COMPONENTS, 'av', HISTORY_SEGMENT) }}
{% endif %}
{% endif %}
{% if DO_NATIVE %}
{{ "native" | form_remap_dep('temporal', PP_CHUNK_A, PP_COMPONENTS, 'ts', HISTORY_SEGMENT) }}
{% if DO_TIMEAVGS %}
{{ "native" | form_remap_dep('temporal', PP_CHUNK_A, PP_COMPONENTS, 'av', HISTORY_SEGMENT) }}
{% endif %}
{% endif %}
{% if DO_TIMEAVGS %}
remap-pp-components-av-{{ PP_CHUNK_A }}<component> => combine-timeavgs-{{ PP_CHUNK_A }}<component>
{% if CLEAN_WORK %}
COMBINE-TIMEAVGS-{{ PP_CHUNK_A }}:succeed-all => clean-pp-timeavgs-{{ PP_CHUNK_A }}
{% endif %}
{% endif %}
# 3 scenarios of CHUNK-A workdir cleaning
# 1. If secondary chunk is not used, then remove history and chunk-a shards after remapping ts and av
# 2. If chunk-a equals history segment, then do nothing- these will be removed after chunk-b generation
# 3. Otherwise, remove prereq history segments and leave the chunk-a shards for chunk-b generation
{% if CLEAN_WORK %}
{% if PP_CHUNK_B is not defined or PP_CHUNK_A != HISTORY_SEGMENT %}
REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_A }}:succeed-all => clean-shards-{{ HISTORY_SEGMENT }}
{% if DO_TIMEAVGS %}
REMAP-PP-COMPONENTS-AV-{{ PP_CHUNK_A }}:succeed-all => clean-shards-{{ HISTORY_SEGMENT }}
{% endif %}
{% endif %}
{% endif %}
REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_A }}:succeed-all => data-catalog
"""
#
# Recurrence interval: every CHUNK-B
#
{# If only one pp chunk is used, then skip the CHUNK-B processing. #}
{% if DO_SECONDARY_PP %}
{# Run the tasks to process CHUNK-B every CHUNK-B, starting after CHUNK-B time #}
+{{ PP_CHUNK_B | subtract_durations('P1Y') }}/{{ PP_CHUNK_B }} = """
{# The make-timeseries tasks for CHUNK-B depend on all CHUNK-A processing for the time period succeeding. #}
{% if DO_REGRID %}
{% if HISTORY_SEGMENT == PP_CHUNK_A %}
rename-split-to-pp-regrid<regrid>
{% else %}
make-timeseries-regrid-{{ PP_CHUNK_A }}<regrid>
{% endif %}
{% for CHUNK in range(1, CHUNK_AS_PER_CHUNK_B) %}
{% if HISTORY_SEGMENT == PP_CHUNK_A %}
& rename-split-to-pp-regrid<regrid>[{{ PP_CHUNK_A | multiply_duration(-CHUNK)}}]
{% else %}
& make-timeseries-regrid-{{ PP_CHUNK_A }}<regrid>[{{ PP_CHUNK_A | multiply_duration(-CHUNK)}}]
{% endif %}
{% endfor %}
=> make-timeseries-regrid-{{ PP_CHUNK_B }}<regrid>
{% if DO_TIMEAVGS %}
=> make-timeavgs-regrid-{{ PP_CHUNK_B }}<regrid>
{% endif %}
{% endif %}
{% if DO_NATIVE %}
{% if HISTORY_SEGMENT == PP_CHUNK_A %}
rename-split-to-pp-native<native>
{% else %}
make-timeseries-native-{{ PP_CHUNK_A }}<native>
{% endif %}
{% for CHUNK in range(1, CHUNK_AS_PER_CHUNK_B) %}
{% if HISTORY_SEGMENT == PP_CHUNK_A %}
& rename-split-to-pp-native<native>[{{ PP_CHUNK_A | multiply_duration(-CHUNK)}}]
{% else %}
& make-timeseries-native-{{ PP_CHUNK_A }}<native>[{{ PP_CHUNK_A | multiply_duration(-CHUNK)}}]
{% endif %}
{% endfor %}
=> make-timeseries-native-{{ PP_CHUNK_B }}<native>
{% if DO_TIMEAVGS %}
=> make-timeavgs-native-{{ PP_CHUNK_B }}<native>
{% endif %}
{% endif %}
{% if DO_TIMEAVGS %}
remap-pp-components-av-{{ PP_CHUNK_B }}<component> => combine-timeavgs-{{ PP_CHUNK_B }}<component>
{% if CLEAN_WORK %}
COMBINE-TIMEAVGS-{{ PP_CHUNK_B }}:succeed-all => clean-pp-timeavgs-{{ PP_CHUNK_B }}
{% endif %}
{% endif %}
{# Generate the per-component make-timeseries => remap-pp-component tasks using Jinja trigger form_remap_dep #}
{# Throw validation exception if PP_CHUNK_B is not in rose-app.conf #}
{% if DO_REGRID %}
{{ "regrid-xy" | form_remap_dep('temporal', PP_CHUNK_B, PP_COMPONENTS, 'ts') }}
{% if DO_TIMEAVGS %}
{{ "regrid-xy" | form_remap_dep('temporal', PP_CHUNK_B, PP_COMPONENTS, 'av') }}
{% endif %}
{% endif %}
{% if DO_NATIVE %}
{{ "native" | form_remap_dep('temporal', PP_CHUNK_B, PP_COMPONENTS, 'ts') }}
{% if DO_TIMEAVGS %}
{{ "native" | form_remap_dep('temporal', PP_CHUNK_B, PP_COMPONENTS, 'av') }}
{% endif %}
{% endif %}
# CHUNK-B work dir cleaning: remove CHUNK-A and CHUNK-B shards after saving the CHUNK-B products
{% if CLEAN_WORK %}
REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_B }}:succeed-all => clean-shards-{{ PP_CHUNK_B }}
{% if DO_TIMEAVGS %}
REMAP-PP-COMPONENTS-AV-{{ PP_CHUNK_B }}:succeed-all => clean-shards-{{ PP_CHUNK_B }}
{% endif %}
REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_B }}:succeed-all => clean-shards-{{ PP_CHUNK_A }}
{% if DO_TIMEAVGS %}
REMAP-PP-COMPONENTS-AV-{{ PP_CHUNK_B }}:succeed-all => clean-shards-{{ PP_CHUNK_A }}
{% endif %}
{% endif %}
REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_B }}:succeed-all => data-catalog
"""
{% endif %}
#
# Recurrence intervals for analysis tasks
#
{% if DO_ANALYSIS %}
{% if DO_SECONDARY_PP %}
{{ YAML | get_analysis_info('task-graph', PP_COMPONENTS, PP_DIR, PP_START, PP_STOP, PP_CHUNK_A, PP_CHUNK_B, DO_ANALYSIS_ONLY) }}
{% else %}
{{ YAML | get_analysis_info('task-graph', PP_COMPONENTS, PP_DIR, PP_START, PP_STOP, PP_CHUNK_A, None, DO_ANALYSIS_ONLY) }}
{% endif %}
{% endif %}
{% endif %}
[runtime]
[[pp-starter]]
inherit = PP-STARTER
# NOTE! script must appear *before* [[[enviroment]]] or else
# the job scripts will have quoting issues
script = """
# Returns 0 if ready, 1 if not
#
echo Arguments:
echo " INFO: trigger: $targetFile"
echo " INFO: cycle point: $CYLC_TASK_CYCLE_POINT"
# Resolve the date strings: YYYY, MM, DD, HH
IFS='-' read YYYY MM DD << DATES
$(cylc cycle-point --template CCYY-MM-DD)
DATES
HH=$(cylc cycle-point --template hh)
targetFileResolved=$(echo $targetFile | sed -e "s/YYYY/$YYYY/g" -e "s/MM/$MM/g" -e "s/DD/$DD/g" -e "s/HH/$HH/g")
echo " trigger (date expanded): $targetFileResolved"
# Look for target file
if ls $targetFileResolved; then
echo "Target ${targetFileResolved} is ready"
exit 0
else
echo "Error: target ${targetFileResolved} is not ready"
exit 1
fi
"""
[[[environment]]]
targetFile = {{ HISTORY_DIR }}/YYYYMMDD.nc.tar
[[STAGE-HISTORY]]
# Increase time limit for staging jobs to 8 hours
execution time limit = PT8H
script = """
set -euo pipefail
#Stage the contents of a tarfile to PTMP
echo Arguments:
echo " history dir: $historyDir"
echo " ptmp dir: $ptmpDir"
echo " cycle point: $CYLC_TASK_CYCLE_POINT"
echo " TMPDIR (not used yet): ${TMPDIR:=/tmp}"
echo Utilities:
type hsmget
type cylc
#Verify history directory exists and is a directory
if [[ ! -d $historyDir ]]; then
echo "Error: Archive directory ${historyDir} does not exist or isnt a directory"
exit 1
fi
#Verify history file exists
file=$historyDir/$(cylc cycle-point --template CCYYMMDD).nc.tar
if ls ${file}; then
echo "Going to stage ${file} to PTMP"
else
echo "Error: Could not locate ${file}"
exit 1
fi
#We want to stage the history files to PTMP without transferring to VFTMP.
#Calling hsmget on a file with wildcards that doesnt exist does this,
#e.g. "dummy*" as below, but prints a warning
if hsmget -v -t -a $historyDir -p $ptmpDir$historyDir -w $TMPDIR$historyDir $(basename -s .tar $file)/dummy\*; then
echo "History files in ${file} have been staged to PTMP successfully"
else
echo "Error: Cant stage history files in ${file} to PTMP"
exit 1
fi
# Setup PYTHONPATH and io lists for the data lineage tool
if [ ! -z "${EPMT_DATA_LINEAGE+x}" ] && [ "$EPMT_DATA_LINEAGE" == "1" ]; then
export PYTHONPATH=$CYLC_SUITE_DEF_PATH:$PYTHONPATH
export input_file_list=
export output_file_list=
echo "Set PYTHONPATH and created i/o lists"
fi
# Finally, link these files to $CYLC_WORKFLOW_SHARE_DIR
mkdir -p $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/history/native
cd $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/history/native
ln -f $ptmpDir/$historyDir/$(cylc cycle-point --template CCYYMMDD).nc/* . \
|| ln -sf $ptmpDir/$historyDir/$(cylc cycle-point --template CCYYMMDD).nc/* .
if [ ! -z "${EPMT_DATA_LINEAGE+x}" ] && [ "$EPMT_DATA_LINEAGE" == "1" ]; then
outputDir=$CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/history/native
start_time=$(date +%s)
for file in $(ls $outputDir); do
hash_val=$(/home/Cole.Harvey/.conda/envs/bloom-filter-env/bin/python \
-m data_lineage.bloomfilter.HashGen $outputDir/$file)
export output_file_list="${output_file_list}$file $hash_val,"
echo "[DATA LINEAGE] Added $file to output list with hash_val: $hash_val"
done
end_time=$(date +%s)
duration=$((end_time - start_time))
echo "Time spent hashing and creating the file list: $duration seconds"
epmt -v annotate EPMT_DATA_LINEAGE_OUT_PATH="$outputDir/"
echo "[DATA LINEAGE] Annotated $outputDir/ to EPMT_DATA_LINEAGE_OUT_PATH"
if [ -n "$output_file_list" ]; then
compressed_bytes=$(/home/Cole.Harvey/.conda/envs/bloom-filter-env/bin/python \
-m data_lineage.bloomfilter.StringCompression "${output_file_list}")
epmt -v annotate EPMT_DATA_LINEAGE_OUT="${compressed_bytes%*,}"
echo "[DATA LINEAGE] Annotated output files to EPMT_LINEAGE_OUT"
fi
fi
echo "Natural end of the history file staging"
exit 0
"""
[[stage-history]]
inherit = STAGE-HISTORY
[[[environment]]]
historyDir = {{ HISTORY_DIR }}
ptmpDir = {{ PTMP_DIR }}
{% if HISTORY_DIR_REFINED is defined %}
[[stage-history-refined]]
inherit = STAGE-HISTORY
post-script = """
"""
[[[environment]]]
historyDir = {{ HISTORY_DIR_REFINED }}
ptmpDir = {{ PTMP_DIR }}
{% endif %}
{% if DO_TIMEAVGS %}
[[MAKE-TIMEAVGS]]
pre-script = mkdir -p $outputDir
script = rose task-run --verbose --app-key make-timeavgs
{% if DO_NATIVE %}
[[MAKE-TIMEAVGS-NATIVE]]
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts/native
outputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/av/native
component = $CYLC_TASK_PARAM_native
{% endif %}
{% if DO_REGRID %}
[[MAKE-TIMEAVGS-REGRID]]
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts/regrid-xy
outputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/av/regrid-xy
component = $CYLC_TASK_PARAM_regrid
use_subdirs = 1
{% endif %}
[[MAKE-TIMEAVGS-{{ PP_CHUNK_A }}]]
[[[environment]]]
interval = {{ PP_CHUNK_A }}
{% if DO_NATIVE %}
[[MAKE-TIMEAVGS-NATIVE-{{ PP_CHUNK_A }}]]
inherit = MAKE-TIMEAVGS, MAKE-TIMEAVGS-NATIVE, MAKE-TIMEAVGS-{{ PP_CHUNK_A }}
[[make-timeavgs-native-{{ PP_CHUNK_A }}<native>]]
inherit = MAKE-TIMEAVGS-NATIVE-{{ PP_CHUNK_A }}, <native>
{% endif %}
{% if DO_REGRID %}
[[MAKE-TIMEAVGS-REGRID-{{ PP_CHUNK_A }}]]
inherit = MAKE-TIMEAVGS, MAKE-TIMEAVGS-REGRID, MAKE-TIMEAVGS-{{ PP_CHUNK_A }}
[[make-timeavgs-regrid-{{ PP_CHUNK_A }}<regrid>]]
inherit = MAKE-TIMEAVGS-REGRID-{{ PP_CHUNK_A }}, <regrid>
{% endif %}
{% if DO_SECONDARY_PP %}
[[MAKE-TIMEAVGS-{{ PP_CHUNK_B }}]]
[[[environment]]]
interval = {{ PP_CHUNK_B }}
{% if DO_NATIVE %}
[[MAKE-TIMEAVGS-NATIVE-{{ PP_CHUNK_B }}]]
inherit = MAKE-TIMEAVGS, MAKE-TIMEAVGS-NATIVE, MAKE-TIMEAVGS-{{ PP_CHUNK_B }}
[[make-timeavgs-native-{{ PP_CHUNK_B }}<native>]]
inherit = MAKE-TIMEAVGS-NATIVE-{{ PP_CHUNK_B }}, <native>
{% endif %}
{% if DO_REGRID %}
[[MAKE-TIMEAVGS-REGRID-{{ PP_CHUNK_B }}]]
inherit = MAKE-TIMEAVGS, MAKE-TIMEAVGS-REGRID, MAKE-TIMEAVGS-{{ PP_CHUNK_B }}
[[make-timeavgs-regrid-{{ PP_CHUNK_B }}<regrid>]]
inherit = MAKE-TIMEAVGS-REGRID-{{ PP_CHUNK_B }}, <regrid>
{% endif %}
{% endif %}
{% endif %}
{% if DO_REFINEDIAG or DO_PREANALYSIS %}
[[PRE-ANALYSIS]]
pre-script = """
env
set -x
mkdir -p $work $tempCache $refineDiagDir
cd $work/$hsmdate
ls
"""
[[[environment]]]
name = {{ EXPERIMENT }}
rtsxml = no-more-xml
work = $TMPDIR/work
tempCache = $TMPDIR/tempCache
root = $CYLC_WORKFLOW_RUN_DIR
archive = is-this-needed
scriptName = $CYLC_TASK_LOG_DIR/job
oname = $(cylc cycle-point --template CCYYMMDD)
hsmdate = $oname.nc
ptmpDir = {{ PTMP_DIR }}/{{ HISTORY_DIR }}
histDir = {{ HISTORY_DIR }}
platform = {{ PLATFORM }}
target = {{ TARGET }}
segment_months = {{ HISTORY_SEGMENT }}
basedate = is-this-needed
gridspec = {{ PP_GRID_SPEC }}
refineDiagDir = $TMPDIR/history_refineDiag/$hsmdate
catalog = {{ PP_DIR }}/catalog.json
{% endif %}
{% if DO_REFINEDIAG %}
[[REFINE-DIAG]]
inherit = PRE-ANALYSIS
post-script = """
cd $refineDiagDir
if ls *nc; then
refinedCount=$(ls -1 *nc | wc -l)
else
refinedCount=0
fi
if [[ $refinedCount > 0 ]]; then
for file in $(ls -1 *nc); do
list_ncvars.csh -st01234 $file |& tee $CYLC_WORKFLOW_SHARE_DIR/refineDiag.log
done
else
echo ERROR: RefineDiag script did not create any NetCDF files as it was expected to do
exit 1
fi
if [[ -f {{ HISTORY_DIR_REFINED }}/$oname.nc.tar ]]; then
echo "the contents of {{ PTMP_DIR }}/{{ HISTORY_DIR_REFINED }} is..."
ls {{ PTMP_DIR }}/{{ HISTORY_DIR_REFINED }}
echo "the contents of {{ PTMP_DIR }}/{{ HISTORY_DIR_REFINED }}/$oname.nc is..."
ls {{ PTMP_DIR }}/{{ HISTORY_DIR_REFINED }}/$oname.nc
mv -f * $TMPDIR/modify_refineDiag
mv -f $TMPDIR/modify_refineDiag/* .
rm -rf $TMPDIR/modify_refineDiag
fi
"""
{# The following section executes refineDiag tasks, whether single or multiple refineDiag paths are given #}
{# Create a 'macro' function to reduce code repeat #}
{% macro exec_refine(script_name) -%}
inherit = REFINE-DIAG
script = """
ls
echo NOTE: About to source user script
if csh {{ script_name }}; then
echo NOTE: User script exited normally
else
echo ERROR: User script got an error status $?
exit 1
fi
"""
{%- endmacro %}
{# Use the 'split' function to transform string into an iterable list, including of length 1 #}
{% set refineDiag_scripts = REFINEDIAG_SCRIPTS.split(' ') %}
{% for refineDiag_path in refineDiag_scripts %}
[[refineDiag-{{ refineDiag_path[refineDiag_path.rfind('/')+1:refineDiag_path.rfind('.')] | replace(".", "_") }}]]
{{ exec_refine(refineDiag_path) }}
{% endfor %}
{% endif %}
{% if DO_PREANALYSIS and PREANALYSIS_SCRIPT is defined %}
{% set preanalysis_name = PREANALYSIS_SCRIPT[PREANALYSIS_SCRIPT.rfind('/')+1:PREANALYSIS_SCRIPT.rfind('.')] | replace(".", "_") %}
[[preAnalysis-{{ preanalysis_name }}]]
inherit = PRE-ANALYSIS
script = """
ls
echo NOTE: About to source user script
if csh {{ PREANALYSIS_SCRIPT }}; then
echo NOTE: User script exited normally
else
echo ERROR: User script got an error status $?
exit 1
fi
"""
{% endif %}
[[MASK-ATMOS-PLEVEL]]
script = rose task-run --verbose --app-key mask-atmos-plevel
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/history/native
{% if DO_NATIVE %}
[[mask-atmos-plevel<native>]]
inherit = MASK-ATMOS-PLEVEL, <native>
[[[environment]]]
component = $CYLC_TASK_PARAM_native
{% endif %}
{% if DO_REGRID %}
[[mask-atmos-plevel<regrid>]]
inherit = MASK-ATMOS-PLEVEL, <regrid>
[[[environment]]]
component = $CYLC_TASK_PARAM_regrid
{% endif %}
[[SPLIT-NETCDF]]
pre-script = mkdir -p $outputDir
script = rose task-run --verbose --app-key split-netcdf
[[[environment]]]
date = $CYLC_TASK_CYCLE_POINT
{% if DO_NATIVE %}
[[SPLIT-NETCDF-NATIVE]]
inherit = SPLIT-NETCDF
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/history/native
outputDir = $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/split/native
component = $CYLC_TASK_PARAM_native
{% endif %}
{% if DO_REGRID %}
[[SPLIT-NETCDF-REGRID]]
inherit = SPLIT-NETCDF
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/history/regrid-xy
outputDir = $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/split/regrid-xy
use_subdirs = 1
component = $CYLC_TASK_PARAM_regrid
{% endif %}
{% if DO_NATIVE %}
[[split-netcdf-native<native>]]
inherit = SPLIT-NETCDF-NATIVE, <native>
{% if DO_STATICS %}
[[split-netcdf-native<native_static>]]
inherit = SPLIT-NETCDF-NATIVE, <native_static>
[[[environment]]]
component = $CYLC_TASK_PARAM_native_static
{% endif %}
{% endif %}
{% if DO_REGRID %}
[[split-netcdf-regrid<regrid>]]
inherit = SPLIT-NETCDF-REGRID, <regrid>
{% if DO_STATICS %}
[[split-netcdf-regrid<regrid_static>]]
inherit = SPLIT-NETCDF-REGRID, <regrid_static>
[[[environment]]]
component = $CYLC_TASK_PARAM_regrid_static
{% endif %}
{% endif %}
[[RENAME-SPLIT-TO-PP]]
pre-script = mkdir -p $outputDir
script = rose task-run --verbose --app-key rename-split-to-pp
{% if DO_NATIVE %}
[[RENAME-SPLIT-TO-PP-NATIVE]]
inherit = RENAME-SPLIT-TO-PP
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/split/native
outputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts/native
component = $CYLC_TASK_PARAM_native
{% endif %}
{% if DO_REGRID %}
[[RENAME-SPLIT-TO-PP-REGRID]]
inherit = RENAME-SPLIT-TO-PP
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/cycle/$CYLC_TASK_CYCLE_POINT/split/regrid-xy
outputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts/regrid-xy
component = $CYLC_TASK_PARAM_regrid
use_subdirs = 1
{% endif %}
{% if DO_NATIVE %}
[[rename-split-to-pp-native<native>]]
inherit = RENAME-SPLIT-TO-PP-NATIVE, <native>
{% if DO_STATICS %}
[[rename-split-to-pp-native<native_static>]]
inherit = RENAME-SPLIT-TO-PP-NATIVE, <native_static>
[[[environment]]]
component = $CYLC_TASK_PARAM_native_static
{% endif %}
{% endif %}
{% if DO_REGRID %}
[[rename-split-to-pp-regrid<regrid>]]
inherit = RENAME-SPLIT-TO-PP-REGRID, <regrid>
{% if DO_STATICS %}
[[rename-split-to-pp-regrid<regrid_static>]]
inherit = RENAME-SPLIT-TO-PP-REGRID, <regrid_static>
[[[environment]]]
component = $CYLC_TASK_PARAM_regrid_static
{% endif %}
{% endif %}
[[REMAP-PP-COMPONENTS]]
script = rose task-run --verbose --app-key remap-pp-components
[[[environment]]]
components = $CYLC_TASK_PARAM_component
[[REMAP-PP-COMPONENTS-TS]]
inherit = REMAP-PP-COMPONENTS
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts
outputDir = {{ PP_DIR }}
product = ts
dirTSWorkaround = 1
[[REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_A }}]]
inherit = REMAP-PP-COMPONENTS-TS
[[[environment]]]
begin = $(cylc cycle-point --offset=-{{ PP_CHUNK_A | subtract_durations(HISTORY_SEGMENT) }})
currentChunk = {{ PP_CHUNK_A }}
[[remap-pp-components-ts-{{ PP_CHUNK_A }}<component>]]
inherit = REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_A }}, <component>
{% if DO_SECONDARY_PP %}
[[REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_B }}]]
inherit = REMAP-PP-COMPONENTS-TS
[[[environment]]]
begin = $(cylc cycle-point --offset=-{{ PP_CHUNK_B | subtract_durations(HISTORY_SEGMENT) }})
currentChunk = {{ PP_CHUNK_B }}
[[remap-pp-components-ts-{{ PP_CHUNK_B }}<component>]]
inherit = REMAP-PP-COMPONENTS-TS-{{ PP_CHUNK_B }}, <component>
{% endif %}
[[REMAP-PP-COMPONENTS-AV]]
inherit = REMAP-PP-COMPONENTS
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/av
outputDir = $CYLC_WORKFLOW_SHARE_DIR/pp/av
product = av
[[REMAP-PP-COMPONENTS-AV-{{ PP_CHUNK_A }}]]
inherit = REMAP-PP-COMPONENTS-AV
[[[environment]]]
begin = $(cylc cycle-point --offset=-{{ PP_CHUNK_A | subtract_durations(HISTORY_SEGMENT) }})
currentChunk = {{ PP_CHUNK_A }}
[[remap-pp-components-av-{{ PP_CHUNK_A }}<component>]]
inherit = REMAP-PP-COMPONENTS-AV-{{ PP_CHUNK_A }}, <component>
{% if DO_SECONDARY_PP %}
[[REMAP-PP-COMPONENTS-AV-{{ PP_CHUNK_B }}]]
inherit = REMAP-PP-COMPONENTS-AV
[[[environment]]]
begin = $(cylc cycle-point --offset=-{{ PP_CHUNK_B | subtract_durations(HISTORY_SEGMENT) }})
currentChunk = {{ PP_CHUNK_B }}
[[remap-pp-components-av-{{ PP_CHUNK_B }}<component>]]
inherit = REMAP-PP-COMPONENTS-AV-{{ PP_CHUNK_B }}, <component>
{% endif %}
{% if DO_TIMEAVGS %}
[[COMBINE-TIMEAVGS]]
script = rose task-run --verbose --app-key combine-timeavgs
[[[environment]]]
end = $(cylc cycle-point --print-year)
outputDir = {{ PP_DIR }}/$CYLC_TASK_PARAM_component/av
[[COMBINE-TIMEAVGS-{{ PP_CHUNK_A }}]]
inherit = COMBINE-TIMEAVGS
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/pp/av
begin = $(cylc cycle-point --offset=-{{ PP_CHUNK_A | subtract_durations(HISTORY_SEGMENT) }} --print-year)
currentChunk = {{ PP_CHUNK_A }}
[[combine-timeavgs-{{ PP_CHUNK_A }}<component>]]
inherit = COMBINE-TIMEAVGS-{{ PP_CHUNK_A }}, <component>
[[[environment]]]
component = $CYLC_TASK_PARAM_component
{% if DO_SECONDARY_PP %}
[[COMBINE-TIMEAVGS-{{ PP_CHUNK_B }}]]
inherit = COMBINE-TIMEAVGS
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/pp/av
begin = $(cylc cycle-point --offset=-{{ PP_CHUNK_B | subtract_durations(HISTORY_SEGMENT) }} --print-year)
currentChunk = {{ PP_CHUNK_B }}
[[combine-timeavgs-{{ PP_CHUNK_B }}<component>]]
inherit = COMBINE-TIMEAVGS-{{ PP_CHUNK_B }}, <component>
[[[environment]]]
component = $CYLC_TASK_PARAM_component
{% endif %}
{% endif %}
{% if DO_STATICS %}
[[remap-pp-components-static]]
inherit = REMAP-PP-COMPONENTS-TS
[[[environment]]]
begin = $CYLC_TASK_CYCLE_POINT
currentChunk = P0Y
outputDir = $CYLC_WORKFLOW_SHARE_DIR/pp/static
components = {{ PP_COMPONENTS }}
product = static
dirTSWorkaround = ""
{% endif %}
[[data-catalog]]
script = """
fre catalog builder --overwrite $ppdir $ppdir/catalog
# workaround to replace P1M with monthly
sed -i.bak -e 's/,P1M,/,monthly,/' $ppdir/catalog.csv
"""
# when many data catalog jobs run simultaneously, they can fail
# this is not a good solution here
execution retry delays = PT5M, PT10M, PT15M
[[[environment]]]
ppdir = {{ PP_DIR }}
[[MAKE-TIMESERIES]]
pre-script = mkdir -p $outputDir
script = rose task-run --verbose --app-key make-timeseries
[[[environment]]]
fail_ok_components = grid_spec lumip_Lyr lumip_Lyr_crp lumip_Lyr_psl lumip_Lyr_pst
{% if DO_NATIVE %}
[[MAKE-TIMESERIES-NATIVE]]
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts/native
outputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts/native
component = $CYLC_TASK_PARAM_native
{% endif %}
{% if DO_REGRID %}
[[MAKE-TIMESERIES-REGRID]]
[[[environment]]]
inputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts/regrid-xy
outputDir = $CYLC_WORKFLOW_SHARE_DIR/shards/ts/regrid-xy
component = $CYLC_TASK_PARAM_regrid
use_subdirs = 1
{% endif %}
[[MAKE-TIMESERIES-{{ PP_CHUNK_A }}]]
[[[environment]]]
begin = $(cylc cycle-point --offset=-{{ PP_CHUNK_A | subtract_durations(HISTORY_SEGMENT) }})
inputChunk = {{ HISTORY_SEGMENT }}
outputChunk = {{ PP_CHUNK_A }}
{% if DO_NATIVE %}
[[MAKE-TIMESERIES-NATIVE-{{ PP_CHUNK_A }}]]
inherit = MAKE-TIMESERIES, MAKE-TIMESERIES-NATIVE, MAKE-TIMESERIES-{{ PP_CHUNK_A }}
[[make-timeseries-native-{{ PP_CHUNK_A }}<native>]]
inherit = MAKE-TIMESERIES-NATIVE-{{ PP_CHUNK_A }}, <native>
{% endif %}
{% if DO_REGRID %}
[[MAKE-TIMESERIES-REGRID-{{ PP_CHUNK_A }}]]
inherit = MAKE-TIMESERIES, MAKE-TIMESERIES-REGRID, MAKE-TIMESERIES-{{ PP_CHUNK_A }}
[[make-timeseries-regrid-{{ PP_CHUNK_A }}<regrid>]]
inherit = MAKE-TIMESERIES-REGRID-{{ PP_CHUNK_A }}, <regrid>
{% endif %}
{% if DO_SECONDARY_PP %}
[[MAKE-TIMESERIES-{{ PP_CHUNK_B }}]]
[[[environment]]]
begin = $(cylc cycle-point --offset=-{{ PP_CHUNK_B | subtract_durations(HISTORY_SEGMENT) }})
inputChunk = {{ PP_CHUNK_A }}
outputChunk = {{ PP_CHUNK_B }}
{% if DO_NATIVE %}
[[MAKE-TIMESERIES-NATIVE-{{ PP_CHUNK_B }}]]
inherit = MAKE-TIMESERIES, MAKE-TIMESERIES-NATIVE, MAKE-TIMESERIES-{{ PP_CHUNK_B }}
[[make-timeseries-native-{{ PP_CHUNK_B }}<native>]]
inherit = MAKE-TIMESERIES-NATIVE-{{ PP_CHUNK_B }}, <native>
{% endif %}
{% if DO_REGRID %}
[[MAKE-TIMESERIES-REGRID-{{ PP_CHUNK_B }}]]
inherit = MAKE-TIMESERIES, MAKE-TIMESERIES-REGRID, MAKE-TIMESERIES-{{ PP_CHUNK_B }}
[[make-timeseries-regrid-{{ PP_CHUNK_B }}<regrid>]]
inherit = MAKE-TIMESERIES-REGRID-{{ PP_CHUNK_B }}, <regrid>
{% endif %}
{% endif %}
{% if DO_REGRID %}
[[REGRID-XY]]