#!/usr/bin/env python
# Copyright (c) 2017, Los Alamos National Security, LLC (LANS)
# and the University Corporation for Atmospheric Research (UCAR).
#
# Unless noted otherwise source code is licensed under the BSD license.
# Additional copyright and license information can be found in the LICENSE file
# distributed with this code, or at http://mpas-dev.github.com/license.html
#
"""
Runs MPAS-Analysis via a configuration file (e.g. `config.analysis`)
specifying analysis options.
"""
# Authors
# -------
# Xylar Asay-Davis, Phillip J. Wolfram
from __future__ import absolute_import, division, print_function, \
unicode_literals
import matplotlib as mpl
import argparse
import traceback
import sys
import pkg_resources
import shutil
import os
from collections import OrderedDict
from mpas_analysis.configuration import MpasAnalysisConfigParser
from mpas_analysis.shared.io.utility import build_config_full_path, \
make_directories
from mpas_analysis.shared.html import generate_html
from mpas_analysis.shared import AnalysisTask
[docs]def build_analysis_list(config, refConfig): # {{{
"""
Build a list of analysis tasks. New tasks should be added here, following
the approach used for existing analysis tasks.
Parameters
----------
config : ``MpasAnalysisConfigParser`` object
contains config options
refConfig : ``MpasAnalysisConfigParser`` object
contains config options for a reference run, or ``None`` if no config
file for a reference run was specified
Returns
-------
analyses : list of ``AnalysisTask`` objects
A list of all analysis tasks
"""
# Authors
# -------
# Xylar Asay-Davis
# choose the right rendering backend, depending on whether we're displaying
# to the screen
if not config.getboolean('plot', 'displayToScreen'):
mpl.use('Agg')
# analysis can only be imported after the right MPL renderer is selected
from mpas_analysis import ocean
from mpas_analysis import sea_ice
from mpas_analysis.shared.climatology import MpasClimatologyTask, \
RefYearMpasClimatologyTask
from mpas_analysis.shared.time_series import MpasTimeSeriesTask
analyses = []
# Ocean Analyses
oceanClimatolgyTask = MpasClimatologyTask(config=config,
componentName='ocean')
oceanTimeSeriesTask = MpasTimeSeriesTask(config=config,
componentName='ocean')
oceanIndexTask = MpasTimeSeriesTask(config=config,
componentName='ocean',
section='index')
oceanRefYearClimatolgyTask = RefYearMpasClimatologyTask(
config=config, componentName='ocean')
analyses.append(oceanClimatolgyTask)
analyses.append(oceanRefYearClimatolgyTask)
analyses.append(ocean.ClimatologyMapMLD(config, oceanClimatolgyTask,
refConfig))
analyses.append(ocean.ClimatologyMapSST(config, oceanClimatolgyTask,
refConfig))
analyses.append(ocean.ClimatologyMapSSS(config, oceanClimatolgyTask,
refConfig))
analyses.append(ocean.ClimatologyMapSSH(config, oceanClimatolgyTask,
refConfig))
analyses.append(ocean.ClimatologyMapOHCAnomaly(
config, oceanClimatolgyTask, oceanRefYearClimatolgyTask,
refConfig))
analyses.append(ocean.ClimatologyMapSoseTemperature(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapSoseSalinity(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapSoseMLD(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapSoseZonalVel(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapSoseMeridVel(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapSoseVelMag(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapArgoTemperature(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapArgoSalinity(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapSchmidtko(
config, oceanClimatolgyTask, refConfig))
analyses.append(ocean.ClimatologyMapAntarcticMelt(config,
oceanClimatolgyTask,
refConfig))
analyses.append(ocean.TimeSeriesAntarcticMelt(config, oceanTimeSeriesTask,
refConfig))
analyses.append(ocean.TimeSeriesTemperatureAnomaly(config,
oceanTimeSeriesTask))
analyses.append(ocean.TimeSeriesSalinityAnomaly(config,
oceanTimeSeriesTask))
analyses.append(ocean.TimeSeriesOHCAnomaly(config,
oceanTimeSeriesTask,
refConfig))
analyses.append(ocean.TimeSeriesSST(config, oceanTimeSeriesTask,
refConfig))
analyses.append(ocean.MeridionalHeatTransport(config, oceanClimatolgyTask,
refConfig))
analyses.append(ocean.StreamfunctionMOC(config, oceanClimatolgyTask,
refConfig))
analyses.append(ocean.IndexNino34(config, oceanIndexTask, refConfig))
# Sea Ice Analyses
seaIceClimatolgyTask = MpasClimatologyTask(config=config,
componentName='seaIce')
seaIceTimeSeriesTask = MpasTimeSeriesTask(config=config,
componentName='seaIce')
analyses.append(seaIceClimatolgyTask)
analyses.append(sea_ice.ClimatologyMapSeaIceConc(
config=config, mpasClimatologyTask=seaIceClimatolgyTask,
hemisphere='NH', refConfig=refConfig))
analyses.append(sea_ice.ClimatologyMapSeaIceThick(
config=config, mpasClimatologyTask=seaIceClimatolgyTask,
hemisphere='NH', refConfig=refConfig))
analyses.append(sea_ice.ClimatologyMapSeaIceConc(
config=config, mpasClimatologyTask=seaIceClimatolgyTask,
hemisphere='SH', refConfig=refConfig))
analyses.append(sea_ice.ClimatologyMapSeaIceThick(
config=config, mpasClimatologyTask=seaIceClimatolgyTask,
hemisphere='SH', refConfig=refConfig))
analyses.append(seaIceTimeSeriesTask)
analyses.append(sea_ice.TimeSeriesSeaIce(config, seaIceTimeSeriesTask,
refConfig))
return analyses # }}}
[docs]def determine_analyses_to_generate(analyses): # {{{
"""
Build a list of analysis tasks to run based on the 'generate' config
option (or command-line flag) and prerequisites and subtasks of each
requested task. Each task's ``setup_and_check`` method is called in the
process.
Parameters
----------
analyses : list of ``AnalysisTask`` objects
A list of all analysis tasks
Returns
-------
analysesToGenerate : list of ``AnalysisTask`` objects
A list of analysis tasks to run
"""
# Authors
# -------
# Xylar Asay-Davis
analysesToGenerate = OrderedDict()
# check which analysis we actually want to generate and only keep those
for analysisTask in analyses:
# update the dictionary with this task and perhaps its subtasks
add_task_and_subtasks(analysisTask, analysesToGenerate)
return analysesToGenerate # }}}
[docs]def add_task_and_subtasks(analysisTask, analysesToGenerate,
callCheckGenerate=True):
# {{{
"""
If a task has been requested through the generate config option or
if it is a prerequisite of a requested task, add it to the dictionary of
tasks to generate.
Parameters
----------
analysisTask : ``AnalysisTask``
A task to be added
analysesToGenerate : ``OrderedDict`` of ``AnalysisTask``
The list of analysis tasks to be generated, which this call may
update to include this task and its subtasks
callCheckGenerate : bool
Whether the ``check_generate`` method should be call for this task to
see if it has been requested. We skip this for subtasks and
prerequisites, since they are needed by another task regardless of
whether the user specifically requested them.
"""
# Authors
# -------
# Xylar Asay-Davis
key = (analysisTask.taskName, analysisTask.subtaskName)
if key in analysesToGenerate.keys():
# The task was already added
assert(analysisTask._setupStatus == 'success')
return
# for each anlaysis task, check if we want to generate this task
# and if the analysis task has a valid configuration
taskTitle = analysisTask.printTaskName
if callCheckGenerate and not analysisTask.check_generate():
# we don't need to add this task -- it wasn't requested
return
# first, we should try to add the prerequisites of this task and its
# subtasks (if they aren't also subtasks for this task)
prereqs = analysisTask.runAfterTasks
for subtask in analysisTask.subtasks:
for prereq in subtask.runAfterTasks:
if prereq not in analysisTask.subtasks:
prereqs.extend(subtask.runAfterTasks)
for prereq in prereqs:
add_task_and_subtasks(prereq, analysesToGenerate,
callCheckGenerate=False)
if prereq._setupStatus != 'success':
# a prereq failed setup_and_check
print("ERROR: prerequisite task {} of analysis task {}"
" failed during check,\n"
" so this task will not be run".format(
prereq.printTaskName, taskTitle))
analysisTask._setupStatus = 'fail'
return
# make sure all prereqs have been set up successfully before trying to
# set up this task -- this task's setup may depend on setup in the prereqs
try:
analysisTask.setup_and_check()
except (Exception, BaseException):
traceback.print_exc(file=sys.stdout)
print("ERROR: analysis task {} failed during check and "
"will not be run".format(taskTitle))
analysisTask._setupStatus = 'fail'
return
# next, we should try to add the subtasks. This is done after the current
# analysis task has been set up in case subtasks depend on information
# from the parent task
for subtask in analysisTask.subtasks:
add_task_and_subtasks(subtask, analysesToGenerate,
callCheckGenerate=False)
if subtask._setupStatus != 'success':
# a subtask failed setup_and_check
print("ERROR: a subtask of analysis task {}"
" failed during check,\n"
" so this task will not be run".format(taskTitle))
analysisTask._setupStatus = 'fail'
return
analysesToGenerate[key] = analysisTask
analysisTask._setupStatus = 'success'
# }}}
[docs]def update_generate(config, generate): # {{{
"""
Update the 'generate' config option using a string from the command line.
Parameters
----------
config : ``MpasAnalysisConfigParser`` object
contains config options
generate : str
a comma-separated string of generate flags: either names of analysis
tasks or commands of the form ``all_<tag>`` or ``no_<tag>`` indicating
that analysis with a given tag should be included or excluded).
"""
# Authors
# -------
# Xylar Asay-Davis
# overwrite the 'generate' in config with a string that parses to
# a list of string
generateList = generate.split(',')
generateString = ', '.join(["'{}'".format(element)
for element in generateList])
generateString = '[{}]'.format(generateString)
config.set('output', 'generate', generateString) # }}}
[docs]def run_analysis(config, analyses): # {{{
"""
Run all the tasks, either in serial or in parallel
Parameters
----------
config : ``MpasAnalysisConfigParser`` object
contains config options
analyses : OrderedDict of ``AnalysisTask`` objects
A dictionary of analysis tasks to run with (task, subtask) names as
keys
"""
# Authors
# -------
# Xylar Asay-Davis
# write the config file the log directory
logsDirectory = build_config_full_path(config, 'output',
'logsSubdirectory')
mainRunName = config.get('runs', 'mainRunName')
configFileName = '{}/config.{}'.format(logsDirectory, mainRunName)
configFile = open(configFileName, 'w')
config.write(configFile)
configFile.close()
taskCount = config.getWithDefault('execute', 'parallelTaskCount',
default=1)
isParallel = taskCount > 1 and len(analyses) > 1
for analysisTask in analyses.values():
if not analysisTask.runAfterTasks and not analysisTask.subtasks:
analysisTask._runStatus.value = AnalysisTask.READY
else:
analysisTask._runStatus.value = AnalysisTask.BLOCKED
tasksWithErrors = []
runningTasks = {}
# run each analysis task
while True:
# we still have tasks to run
for analysisTask in analyses.values():
if analysisTask._runStatus.value == AnalysisTask.BLOCKED:
prereqs = analysisTask.runAfterTasks + analysisTask.subtasks
prereqStatus = [prereq._runStatus.value for prereq in prereqs]
if any([runStatus == AnalysisTask.FAIL for runStatus in
prereqStatus]):
# a prerequisite failed so this task cannot succeed
analysisTask._runStatus.value = AnalysisTask.FAIL
if all([runStatus == AnalysisTask.SUCCESS for runStatus in
prereqStatus]):
# no unfinished prerequisites so we can run this task
analysisTask._runStatus.value = AnalysisTask.READY
unfinishedCount = 0
for analysisTask in analyses.values():
if analysisTask._runStatus.value not in [AnalysisTask.SUCCESS,
AnalysisTask.FAIL]:
unfinishedCount += 1
if unfinishedCount <= 0:
# we're done
break
# launch new tasks
for key, analysisTask in analyses.items():
if analysisTask._runStatus.value == AnalysisTask.READY:
if isParallel:
print('Running {}'.format(analysisTask.printTaskName))
analysisTask._runStatus.value = AnalysisTask.RUNNING
analysisTask.start()
runningTasks[key] = analysisTask
if len(runningTasks.keys()) >= taskCount:
break
else:
analysisTask.run(writeLogFile=False)
if isParallel:
# wait for a task to finish
analysisTask = wait_for_task(runningTasks)
key = (analysisTask.taskName, analysisTask.subtaskName)
runningTasks.pop(key)
taskTitle = analysisTask.printTaskName
if analysisTask._runStatus.value == AnalysisTask.SUCCESS:
print(" Task {} has finished successfully.".format(
taskTitle))
elif analysisTask._runStatus.value == AnalysisTask.FAIL:
print("ERROR in task {}. See log file {} for details".format(
taskTitle, analysisTask._logFileName))
tasksWithErrors.append(taskTitle)
else:
print("Unexpected status from in task {}. This may be a "
"bug.".format(taskTitle))
else:
if analysisTask._runStatus.value == AnalysisTask.FAIL:
sys.exit(1)
if not isParallel and config.getboolean('plot', 'displayToScreen'):
import matplotlib.pyplot as plt
plt.show()
# raise the last exception so the process exits with an error
errorCount = len(tasksWithErrors)
if errorCount == 1:
print("There were errors in task {}".format(tasksWithErrors[0]))
sys.exit(1)
elif errorCount > 0:
print("There were errors in {} tasks: {}".format(
errorCount, ', '.join(tasksWithErrors)))
sys.exit(1)
# }}}
[docs]def wait_for_task(runningTasks, timeout=0.1): # {{{
"""
Build a list of analysis modules based on the 'generate' config option.
New tasks should be added here, following the approach used for existing
analysis tasks.
Parameters
----------
runningTasks : dict of ``AnalysisTasks``
The tasks that are currently running, with task names as keys
Returns
-------
analysisTask : ``AnalysisTasks``
A task that finished
"""
# Authors
# -------
# Xylar Asay-Davis
# necessary to have a timeout so we can kill the whole thing
# with a keyboard interrupt
while True:
for analysisTask in runningTasks.values():
analysisTask.join(timeout=timeout)
if not analysisTask.is_alive():
return analysisTask # }}}
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument("--setup_only", dest="setup_only", action='store_true',
help="If only the setup phase, not the run or HTML "
"generation phases, should be executed.")
parser.add_argument("--html_only", dest="html_only", action='store_true',
help="If only the setup and HTML generation phases, "
"not the run phase, should be executed.")
parser.add_argument("-g", "--generate", dest="generate",
help="A list of analysis modules to generate "
"(nearly identical generate option in config file).",
metavar="ANALYSIS1[,ANALYSIS2,ANALYSIS3,...]")
parser.add_argument("-l", "--list", dest="list", action='store_true',
help="List the available analysis tasks")
parser.add_argument("-p", "--purge", dest="purge", action='store_true',
help="Purge the analysis by deleting the output"
"directory before running")
parser.add_argument('configFiles', metavar='CONFIG',
type=str, nargs='*', help='config file')
args = parser.parse_args()
for configFile in args.configFiles:
if not os.path.exists(configFile):
raise OSError('Config file {} not found.'.format(configFile))
# add config.default to cover default not included in the config files
# provided on the command line
if pkg_resources.resource_exists('mpas_analysis', 'config.default'):
defaultConfig = pkg_resources.resource_filename('mpas_analysis',
'config.default')
configFiles = [defaultConfig] + args.configFiles
else:
print('WARNING: Did not find config.default. Assuming other config '
'file(s) contain a\n'
'full set of configuration options.')
defaultConfig = None
configFiles = args.configFiles
config = MpasAnalysisConfigParser()
config.read(configFiles)
if args.list:
analyses = build_analysis_list(config, refConfig=None)
for analysisTask in analyses:
print('task: {}'.format(analysisTask.taskName))
print(' component: {}'.format(analysisTask.componentName)),
print(' tags: {}'.format(', '.join(analysisTask.tags)))
sys.exit(0)
if config.has_option('runs', 'referenceRunConfigFile'):
refConfigFile = config.get('runs', 'referenceRunConfigFile')
if not os.path.exists(refConfigFile):
raise OSError('A reference config file {} was specified but the '
'file does not exist'.format(refConfigFile))
refConfigFiles = [refConfigFile]
if defaultConfig is not None:
refConfigFiles = [defaultConfig] + refConfigFiles
refConfig = MpasAnalysisConfigParser()
refConfig.read(refConfigFiles)
# replace the log directory so log files get written to this run's
# log directory, not the reference run's
logsDirectory = build_config_full_path(config, 'output',
'logsSubdirectory')
refConfig.set('output', 'logsSubdirectory', logsDirectory)
print('Comparing to reference run {} rather than observations. \n'
'Make sure that MPAS-Analysis has been run previously with the '
'ref config file.'.format(refConfig.get('runs', 'mainRunName')))
else:
refConfig = None
if args.purge:
outputDirectory = config.get('output', 'baseDirectory')
if not os.path.exists(outputDirectory):
print('Output directory {} does not exist.\n'
'No purge necessary.'.format(outputDirectory))
else:
print('Deleting contents of {}'.format(outputDirectory))
shutil.rmtree(outputDirectory)
if args.generate:
update_generate(config, args.generate)
if refConfig is not None:
# we want to use the "generate" option from the current run, not
# the reference config file
refConfig.set('output', 'generate', config.get('output', 'generate'))
logsDirectory = build_config_full_path(config, 'output',
'logsSubdirectory')
make_directories(logsDirectory)
analyses = build_analysis_list(config, refConfig)
analyses = determine_analyses_to_generate(analyses)
if not args.setup_only and not args.html_only:
run_analysis(config, analyses)
if not args.setup_only:
generate_html(config, analyses, refConfig)
# vim: foldmethod=marker ai ts=4 sts=4 et sw=4 ft=python