#!/usr/bin/env python import argparse import threading from datamanager import DataManager from earthdiagnostics.ocean import Salinity, Circulation, Heat, General, Siasiesiv from utils import Utils from earthdiagnostics import cdftools, TempFile from autosubmit.date.chunk_date_lib import * from parser import Parser from autosubmit.config.log import Log import shutil import os class Diags: """ Launcher class for the diagnostics :param config_file: path to the configuration file :type config_file: str """ def __init__(self, config_file): Log.debug('Initialising Diags') self._read_config(config_file) self.datamanager = DataManager(self.institute, self.model, self.expid, self.data_dir, self.frequency, self.chunk_size, self.experiment_name) self.datamanager.add_startdate = self.add_startdate self.datamanager.add_name = self.add_name TempFile.scratch_folder = self.scratch_dir cdftools.path = self.cdftools_path self._create_dic_variables() Log.debug('Diags ready') def _create_dic_variables(self): self.dic_variables = dict() self.dic_variables['x'] = 'i' self.dic_variables['y'] = 'j' self.dic_variables['z'] = 'lev' self.dic_variables['nav_lon'] = 'lon' self.dic_variables['nav_lat'] = 'lat' self.dic_variables['nav_lev'] = 'lev' self.dic_variables['time_counter'] = 'time' self.dic_variables['t'] = 'time' def run(self): """ Run the diagnostics """ time = datetime.datetime.now() Log.info("Starting diagnostics at {0}", time) if not os.path.exists(self.scratch_dir): os.makedirs(self.scratch_dir) os.chdir(self.scratch_dir) self._prepare_mesh_files() self.datamanager.prepare_CMOR_files(self.startdates, self.members) # Run diagnostics Log.info('Running diagnostics') list_jobs = list() for fulldiag in self._get_commands(): Log.info("Running {0}", fulldiag) diag_options = fulldiag.split(',') if diag_options[0] == 'siasiesiv': list_jobs += Siasiesiv.generate_jobs(self.datamanager, self.startdates, self.members, self.chunks, diag_options) continue for startdate in self.startdates: for member in self.members: for chunk in range(1, self.chunks+1): self._execute_diagnostic(diag_options, startdate, member, chunk) Log.result('Finished {0}', fulldiag) numthreads = Utils.available_cpu_count() threads = list() for numthread in range(0, numthreads): t = threading.Thread(target=Diags._run_jobs, args=([list_jobs[numthread:len(list_jobs): numthreads]])) threads.append(t) t.start() for t in threads: t.join() TempFile.clean() finsih_time = datetime.datetime.now() Log.result("Diagnostics finished at {0}", finsih_time) Log.result("Time ellapsed: {0}", finsih_time - time) @staticmethod def _run_jobs(jobs): for job in jobs: job.compute() def _execute_diagnostic(self, diag_options, startdate, member, chunk): diag = diag_options[0] if diag == 'vertmeanmeters': variable = diag_options[1] depth_min = int(diag_options[2]) depth_max = int(diag_options[3]) depth = '{0}m-{1}m'.format(depth_min, depth_max) variables = (variable, '{0}mean{1}'.format(variable, depth)) for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): General.vertical_mean_meters(input_file, output_file, variable, depth_min, depth_max) elif diag == 'vertmean': variable = diag_options[1] lev_min = int(diag_options[2]) lev_max = int(diag_options[3]) lev = '{0}-{1}'.format(lev_min, lev_max) variables = (variable, '{0}mean{1}'.format(variable, lev)) for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): General.vertical_mean(input_file, output_file, variable, lev_min, lev_max) elif diag == 'convection': variables = ('mlotst', 'mlotstsites') for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Circulation.convection_sites(input_file, self.nemo_version, output_file) elif diag == 'psi': variables = ('uo', 'vo', 'vsftbarot') for [u_file, v_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Circulation.psi(u_file, v_file, output_file) elif diag == 'gyres': variables = ('vsftbarot', 'vsftbarotgyres') for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Circulation.gyres(str(input_file), self.nemo_version, str(output_file)) elif diag == 'ohc': basin = diag_options[1] mixed_layer = int(diag_options[2]) depth_min = int(diag_options[3]) depth_max = int(diag_options[4]) if mixed_layer == 1: mxl = 'mlotst' depth = '' elif mixed_layer == 0: mxl = '' depth = '{0}-{1}'.format(depth_min, depth_max) else: mxl = 'nomlotst' depth = '' variables = ('thetao', 'mlotst', 'ohcsum{0}{1}', 'ohcvmean{0}{1}'.format(mxl, depth)) for [input_file, mlotst_file, ohcsum_file, ohcvmean_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Heat.total(input_file, mlotst_file, ohcsum_file, ohcvmean_file, basin, mixed_layer, depth_min, depth_max) elif diag == 'ohclayer': depth_min = int(diag_options[1]) depth_max = int(diag_options[2]) depth = '{0}-{1}'.format(depth_min, depth_max) variables = ('thetao', 'ohc{0}'.format(depth)) for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Heat.layer(input_file, output_file, depth_min, depth_max) elif diag in ['moc', 'vsftmyz']: variables = ('vo', 'vsftmyz') for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Circulation.moc(input_file, output_file) elif diag in ['mocmax', 'vsftmyzmax']: if len(diag_options) != 5: Log.warning('vsftmyzmax requires 4 arguments. Skipping!') return lat_min = int(diag_options[1]) lat_max = int(diag_options[2]) lat = '{0}-{1}'.format(lat_min, lat_max) depth_min = int(diag_options[3]) depth_max = int(diag_options[4]) depth = '{0}-{1}'.format(depth_min, depth_max) variables = ('vsftmyz', 'vsftmyzmax') for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Circulation.max_moc(input_file, lat_min, lat_max, output_file.replace('vsftmyzmax', 'vsftmyzmax{0}-{1}'.format(lat, depth)), depth_min, depth_max) elif diag in ['mocarea', 'vsftmyzarea']: if len(diag_options) != 6: Log.warning('vsftmyzarea requires between 5 arguments. Skipping!') return lat_min = int(diag_options[1]) lat_max = int(diag_options[2]) lat = '{0}{1}'.format(Utils.get_cardinal_coordinate(lat_min, True), Utils.get_cardinal_coordinate(lat_max, True)) depth_min = int(diag_options[3]) depth_max = int(diag_options[4]) depth = '{0}-{1}'.format(depth_min, depth_max) basin = diag_options[5] variables = ('vsftmyz', 'vsftmyz{0}{1}{2}'.format(lat, depth, basin)) for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Circulation.area_moc(input_file, lat_min, lat_max, output_file, depth_min, depth_max, basin) elif diag == 'mlotsthc': variables = ('thetao', 'mlotst', 'ohcvertsummlotst') for [input_file, mlotst_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Heat.mixed_layer_content(input_file, mlotst_file, output_file) elif diag == 'mlotstsc': variables = ('so', 'mlotst', 'scvertsummlotst') for [input_file, mlotst_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): Salinity.mixed_layer_content(input_file, mlotst_file, output_file) elif diag == 'interp3d': variable = diag_options[1] if len(diag_options) == 3: domain = diag_options[2] if domain == 'seaice': domain = 'seaIce' else: domain = 'ocean' input_files = self.datamanager.get_files(startdate, member, chunk, domain, [variable]) output_files = self.datamanager.get_files(startdate, member, chunk, domain, [variable], 'regular') for x in range(0, len(input_files[0])): General.interpolate(input_files[0][x], output_files[0][x], variable, self.nemo_version) elif diag == 'cutsection': variable = diag_options[1] zonal = diag_options[2] == 'z' value = int(diag_options[3]) coordinate = Utils.get_cardinal_coordinate(value, zonal) variables = (variable, '{0}{1}'.format(variable, coordinate)) for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables, 'regular'): General.cut_section(input_file, output_file, variable, zonal, value) elif diag == 'avgsection': variable = diag_options[1] lon_min = int(diag_options[2]) lon_max = int(diag_options[3]) lat_min = int(diag_options[4]) lat_max = int(diag_options[5]) output_name = '{0}{1}{2}{3}{4}'.format(variable, Utils.get_cardinal_coordinate(lon_min, False), Utils.get_cardinal_coordinate(lon_max, False), Utils.get_cardinal_coordinate(lat_min, True), Utils.get_cardinal_coordinate(lat_max, True)) variables = (variable, output_name) for [input_file, output_file] in self.datamanager.get_files(startdate, member, chunk, 'ocean', variables): General.avgsection(input_file, output_file, lon_min, lon_max, lat_min, lat_max) else: Log.warning('Diagnostic {0} not available', diag) return def _get_commands(self): Log.debug('Preparing command list') commands = self.diags.split() for alias, added_commands in self._aliases.items(): if alias in commands: Log.debug('Changing alias {0} for {1}', alias, ' '.join(added_commands)) commands.remove(alias) for add_command in added_commands: commands.append(add_command) Log.debug('Command list ready ') return commands def _prepare_mesh_files(self): Log.info('Copying mesh files') self._copy_file(os.path.join(self.con_files, 'mesh_mask_nemo.{0}.nc'.format(self.nemo_version)), 'mesh_hgr.nc') self._link_file('mesh_hgr.nc', 'mesh_zgr.nc') self._link_file('mesh_hgr.nc', 'mask.nc') self._copy_file(os.path.join(self.con_files, 'new_maskglo.{0}.nc'.format(self.nemo_version)), 'new_maskglo.nc') self._copy_file(os.path.join(self.con_files, 'mask.regions.{0}.nc'.format(self.nemo_version)), 'mask_regions.nc') self._copy_file(os.path.join(self.con_files, 'mask.regions.3d.{0}.nc'.format(self.nemo_version)), 'mask_regions.3d.nc') Log.result('Mesh files ready!') def _copy_file(self, source, destiny): if not os.path.exists(source): Log.user_warning('File {0} is not available for {1}', destiny, self.nemo_version) return if os.path.exists(destiny): if os.stat(source).st_size == os.stat(destiny).st_size: Log.info('File {0} already exists', destiny) return Log.info('Creating file {0}', destiny) shutil.copy(source, destiny) Log.info('File {0} ready', destiny) Utils.rename_variables('mesh_hgr.nc', self.dic_variables, False, True) def _link_file(self, source, destiny): if not os.path.exists(source): Log.user_warning('File {0} is not available for {1}', destiny, self.nemo_version) if os.path.exists(destiny): if os.stat(source).st_size == os.stat(destiny).st_size: Log.info('File {0} already exists', destiny) return else: os.remove(destiny) os.symlink(source, destiny) Log.info('File {0} ready', destiny) def _read_config(self, config_file): self.parser = Parser() self.parser.optionxform = str self.parser.read(config_file) # Read diags config self.scratch_dir = self.parser.get_option('DIAGNOSTICS', 'SCRATCH_DIR') self.data_dir = self.parser.get_option('DIAGNOSTICS', 'DATA_DIR') self.con_files = self.parser.get_option('DIAGNOSTICS', 'CON_FILES') self.diags = self.parser.get_option('DIAGNOSTICS', 'DIAGS').lower() self.frequency = self.parser.get_option('DIAGNOSTICS', 'FREQUENCY') self.cdftools_path = self.parser.get_option('DIAGNOSTICS', 'CDFTOOLS_PATH') # Read experiment config self.institute = self.parser.get_option('EXPERIMENT', 'INSTITUTE') self.expid = self.parser.get_option('EXPERIMENT', 'EXPID') self.experiment_name = self.parser.get_option('EXPERIMENT', 'NAME') self.members = list() for member in self.parser.get_option('EXPERIMENT', 'MEMBERS').split(): self.members.append(int(member)) self.startdates = self.parser.get_option('EXPERIMENT', 'STARTDATES').split() self.chunk_size = self.parser.get_int_option('EXPERIMENT', 'CHUNK_SIZE') self.chunks = self.parser.get_int_option('EXPERIMENT', 'CHUNKS') self.model = self.parser.get_option('EXPERIMENT', 'MODEL') self.nemo_version = self.parser.get_option('EXPERIMENT', 'NEMO_VERSION') self.add_name = self.parser.get_bool_option('CMOR', 'ADD_NAME') self.add_startdate = self.parser.get_bool_option('CMOR', 'ADD_STARTDATE') # Read aliases self._aliases = dict() if self.parser.has_section('ALIAS'): for option in self.parser.options('ALIAS'): self._aliases[option.lower()] = self.parser.get_option('ALIAS', option).lower().split() self.scratch_dir = os.path.join(self.scratch_dir, 'diags', self.expid) if not os.path.exists(self.scratch_dir): os.makedirs(self.scratch_dir) os.chdir(self.scratch_dir) def main(): parser = argparse.ArgumentParser(description='Main executable for Earth Diagnostics.') parser.add_argument('-v', '--version', action='version', version='0.1', help="returns Earth Diagnostics's version number and exit") parser.add_argument('-lf', '--logfile', choices=('EVERYTHING', 'DEBUG', 'INFO', 'RESULT', 'USER_WARNING', 'WARNING', 'ERROR', 'CRITICAL', 'NO_LOG'), default='DEBUG', type=str, help="sets file's log level.") parser.add_argument('-lc', '--logconsole', choices=('EVERYTHING', 'DEBUG', 'INFO', 'RESULT', 'USER_WARNING', 'WARNING', 'ERROR', 'CRITICAL', 'NO_LOG'), default='INFO', type=str, help="sets console's log level") parser.add_argument('-f', '--configfile', default='diags.conf', type=str) args = parser.parse_args() Log.set_console_level(args.logconsole) Log.set_file_level(args.logfile) diags = Diags(args.configfile) diags.run() TempFile.clean() if __name__ == "__main__": main()