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How to use spawning method in locust
Best Python code snippet using locust
run_svim.py
Source:run_svim.py 
1#!/usr/bin/env python2from __future__ import print_function3print(1)4import matplotlib5matplotlib.use('TkAgg')6print(2)7import time8from datetime import datetime, date, time, timedelta9from dateutil.relativedelta import relativedelta10import numpy as np11print(3)12from opendrift.readers import reader_basemap_landmask13from opendrift.readers import reader_ROMS_native14from kino.pelagicplankton import PelagicPlanktonDrift15from opendrift.readers import reader_netCDF_CF_generic16import logging17import gdal18import os19#from netCDF4 import Dataset, datetime, date2num,num2date20print(4)21from numpy.random import RandomState22import matplotlib.pyplot as plt23try:24 import ogr25 import osr26except Exception as e:27 print (e)28 raise ValueError('OGR library is needed to read shapefiles.')29print(5)30def setupSeed(hoursBetweenTimestepInROMSFiles,startTime,endTime,startSpawningTime,endSpawningTime,releaseParticles):31 ##################################################32 # Create seed variation as function of day33 ##################################################34 # Make datetime array from start to end at 3 hour interval35 difference=endTime-startTime36 hoursOfSimulation=divmod(difference.total_seconds(), 3600)37 difference=endSpawningTime-startSpawningTime38 hoursOfSpawning=divmod(difference.total_seconds(), 3600)39 timeStepsSimulation=int(int(hoursOfSimulation[0])/hoursBetweenTimestepInROMSFiles)40 41 print ("\nsvim TIME EVOLUTION:")42 print ("=>SIMULATION: Drift simulation will run for %s simulation hours" %(timeStepsSimulation))43 print ("=>SPAWNING: Simulated spawning will run for %s simulation hours\n initiated on %s and ending on %s"%(timeStepsSimulation,startSpawningTime,endSpawningTime))44 interval = timedelta(hours=24)45 hoursPerSpawning=divmod(interval.total_seconds(), 3600) #hours per spawning event46 timeStepsSpawning=int(int(hoursOfSpawning[0])/int(hoursPerSpawning[0])) #number of spawning timesteps47 spawningTimes = [startSpawningTime + interval*n for n in range(timeStepsSpawning)] #times of spawning48 # Define number of particles released per spawning day, summing to ~releaseParticles and following a gaussian curve49 mu, sigma = 1, 0.25 # mean and standard deviation of the gaussian curve 50 prng = RandomState(1) # random number generator (specify number to ensure the same sequence each time)51 s = prng.normal(mu, sigma, timeStepsSpawning) # random distribution52 num=(s*releaseParticles/timeStepsSpawning).astype(int) # number of particles released per spawning event as releaseParticles/timeStepsSpawning, weighted by random distribution53 num=np.sort(num) #sort particles in increasing order 54 num=np.concatenate((num[len(num)%2::2],num[::-2]),axis=0) #release the highest number of particles at the midpoint of the spawning period55 56 print ("SPAWNING: Simulated spawning will release %s eggs"%(np.sum(num)))57 return num, spawningTimes58print(6)59def createOutputFilenames(startTime,endTime,verticalBehavior,spawning_ground):60 startDate=''61 if startTime.day<10:62 startDate+='0%s'%(startTime.day)63 else:64 startDate+='%s'%(startTime.day)65 if startTime.month<10:66 startDate+='0%s'%(startTime.month)67 else:68 startDate+='%s'%(startTime.month)69 startDate+='%s'%(startTime.year)70 endDate=''71 if endTime.day<10:72 endDate+='0%s'%(endTime.day)73 else:74 endDate+='%s'%(endTime.day)75 if endTime.month<10:76 endDate+='0%s'%(endTime.month)77 else:78 endDate+='%s'%(endTime.month)79 endDate+='%s'%(endTime.year)80 81 # File naming82 if verticalBehavior:83 outputFilename='results_stock_recruitment/opendrift_%s_%s_to_%s_vertical.nc'%(spawning_ground,startDate,endDate)84 animationFilename='figures/animation_%s_%s_to_%s_vertical.mp4'%(spawning_ground,startDate,endDate)85 plotFilename='figures/plot_%s_%s_to_%s_vertical.png'%(spawning_ground,startDate,endDate)86 else:87 outputFilename='results_stock_recruitment/opendrift_%s_%s_to_%s_novertical.nc'%(spawning_ground,startDate,endDate)88 animationFilename='figures/animation_%s_%s_to_%s_novertical.mp4'%(spawning_ground,startDate,endDate)89 plotFilename='figures/plot_%s_%s_to_%s_novertical.png'%(spawning_ground,startDate,endDate)90 if not os.path.exists('figures'):91 os.makedirs('figures')92 if not os.path.exists('results'):93 os.makedirs('results')94 return outputFilename, animationFilename, plotFilename95print(7)96 97def createAndRunSimulation(lowDepth,highDepth,endTime,shapefile,outputFilename,animationFilename,plotFilename,releaseParticles,pattern_svim,verticalBehavior,spawning_ground):98 # Setup a new simulation99 o = PelagicPlanktonDrift(loglevel=0) # Set loglevel to 0 for debug information100 #o.max_speed = 10101 #######################102 # Preparing readers103 #######################104 reader_basemap = reader_basemap_landmask.Reader(105 llcrnrlon=-7, llcrnrlat=50,106 urcrnrlon=15, urcrnrlat=65,107 resolution='i', projection='merc')108 109 o.add_reader([reader_basemap]) #Note: Include because of issue with linearNDfast110 o.set_config('general:basemap_resolution', 'i')111 reader_svim = reader_ROMS_native.Reader(pattern_svim)#SVIM reader used to cover area outside svim reader112 o.add_reader([reader_svim]) #FORCE loaded for wind information113 114 num, spawningTimes = setupSeed(hoursBetweenTimestepInROMSFiles,startTime,endTime,startSpawningTime,endSpawningTime,releaseParticles)115 116 #######################117 #Adjusting configuration118 #######################119 if verticalBehavior:120 o.set_config('processes:turbulentmixing', True)121 else:122 o.set_config('processes:turbulentmixing', False)123 o.set_config('turbulentmixing:diffusivitymodel','windspeed_Sundby1983')124 o.set_config('turbulentmixing:timestep', 4) # seconds125 o.set_config('turbulentmixing:verticalresolution', 2) # default is 1 meter, but since we have longer timestep we justify it126 if verticalBehavior:127 o.set_config('processes:verticaladvection', False)128 else:129 o.set_config('processes:verticaladvection', False)130 o.set_config('turbulentmixing:TSprofiles', False)131 #o.set_config('turbulentmixing:max_iterations', 400) #200 used in ms version132 o.set_config('drift:scheme', 'euler')133 o.set_config('general:coastline_action', 'previous') #Prevent stranding, jump back to previous position134 135 #######################136 # IBM configuration 137 #######################138 o.set_config('biology:constantIngestion', 0.75)139 o.set_config('biology:activemetabOn', 1)140 o.set_config('biology:cod', True)141 o.set_config('biology:haddock', False)142 o.set_config('biology:attenuationCoefficient',0.18)143 if verticalBehavior:144 o.set_config('biology:fractionOfTimestepSwimming',0.15) # Pause-swim behavior145 else:146 o.set_config('biology:fractionOfTimestepSwimming',0.00) # Pause-swim behavior147 o.set_config('biology:lowerStomachLim',0.3) #Min. stomach fullness needed to actively swim down148 149 150 #######################151 # Seed particles152 #######################153 #Fixed distribution in depth:154 def eq_div(N, i):155 return [] if i <= 0 else [N / i + 1] * (N % i) + [N / i] * (i - N % i)156 z_levels=range(lowDepth,highDepth+1,10) #levels of depth distribution157 for i, nums in enumerate(num):158 if nums <= 0:159 continue160 z_dist=eq_div(nums,len(z_levels)) #number of particles per level (approx. equal)161 print ("Running i=%s num=%s for spawning ground=%s"%(i,nums,spawning_ground))162 print ("Depths ",np.repeat(z_levels,z_dist))163 o.seed_from_shapefile(shapefile, nums, layername=None,featurenum=[1], z=np.repeat(z_levels,z_dist), time=spawningTimes[i])164 print ("Elements scheduled for %s : %s"%(spawning_ground,o.elements_scheduled))165 #########################166 # Run the model167 #########################168 o.run(end_time=endTime, time_step=timedelta(hours=1),time_step_output=timedelta(hours=12), 169 outfile=outputFilename,export_variables=['lon', 'lat', 'z','sea_water_temperature','length','weight','survival','sea_floor_depth_below_sea_level']) 170 print (o)171 #o.animation(background=['x_sea_water_velocity', 'y_sea_water_velocity'],filename=animationFilename)172print(8)173#########################174# SETUP175#########################176spawning_ground='viking'177lowDepth, highDepth = -50, 0 # in negative meters178verticalBehavior=False179for year in range(2010, 2011):180 print(year)181#Spawning period and number of particles per spawning ground:182 if spawning_ground=='south':183 startTime=datetime(year-1,12,15,1,00,00) 184 endTime=datetime(year,8,15,1,00,00) 185 startSpawningTime=startTime186 endSpawningTime=datetime(year,4,15,1,00,00)187 releaseParticles=32400 # Total number of particles to release (result with be approximately this number)188 elif spawning_ground=='northwest':189 startTime=datetime(year,1,1,1,00,00) 190 endTime=datetime(year,9,29,1,00,00) 191 startSpawningTime=startTime192 endSpawningTime=datetime(year,5,1,1,00,00)193 releaseParticles=22950194 elif spawning_ground=='viking':195 startTime=datetime(year,2,1,1,00,00) 196 endTime=datetime(year,9,29,1,00,00) 197 startSpawningTime=startTime198 endSpawningTime=datetime(year,5,15,1,00,00)199 releaseParticles=27000200 else:201 print ("spawning_ground is not correctly defined")202#Find forcing files needed based on months:203 startDay = datetime(startTime.year,startTime.month,1)204 endDay = datetime(endTime.year,endTime.month,1)205 month_range = [startDay]206 while startDay<endDay:207 startDay = startDay + relativedelta(months=1)208 month_range.append(startDay)209 pattern_svim=[]210 for i in month_range:211 x='/Volumes/Untitled/ROMS_files/SVIM_compressed/'+str(i.year)+'/'+'ocean_avg_'+str(i.year)+str(i.month).zfill(2)+'01.nc4'212 pattern_svim.append(x)213 hoursBetweenTimestepInROMSFiles=24214 shapefile='/Volumes/Untitled/Sustain/Spawning_grounds/Shapefiles_Gio_KINO/'+str(spawning_ground)+'.shp'215 print ("=> Using shapefile %s"%(shapefile))216 outputFilename, animationFilename, plotFilename = createOutputFilenames(startTime,endTime,verticalBehavior,spawning_ground)217 print ("Result files will be stored as:\nnetCDF=> %s\nmp4=> %s"%(outputFilename,animationFilename))218 ...
runspawningserver.py
Source:runspawningserver.py
1#!/usr/bin/env python2# Licensed to Cloudera, Inc. under one3# or more contributor license agreements. See the NOTICE file4# distributed with this work for additional information5# regarding copyright ownership. Cloudera, Inc. licenses this file6# to you under the Apache License, Version 2.0 (the7# "License"); you may not use this file except in compliance8# with the License. You may obtain a copy of the License at9#10# http://www.apache.org/licenses/LICENSE-2.011#12# Unless required by applicable law or agreed to in writing, software13# distributed under the License is distributed on an "AS IS" BASIS,14# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.15# See the License for the specific language governing permissions and16# limitations under the License.17import desktop.lib.eventlet_util18import logging19import os20import sys21from django.core.management.base import BaseCommand22from desktop import conf23import spawning.spawning_controller24from desktop.lib.daemon_utils import drop_privileges_if_necessary25from django.utils.translation import ugettext as _26SPAWNING_SERVER_HELP = r"""27 Run Hue using the Spawning WSGI server in asynchronous mode.28"""29SPAWNING_SERVER_OPTIONS = {30 'access_log_file': os.devnull,31 'backdoor': None,32 'chuid': None,33 'coverage': None,34 'daemonize': None,35 'deadman_timeout': 1,36 'factory': 'spawning.django_factory.config_factory',37 'host': conf.HTTP_HOST.get(),38 'max_age': None,39 'max_memory': 0,40 'no_keepalive': None,41 'pidfile': None,42 'port': conf.HTTP_PORT.get(),43 'processes': 1,44 'reload': None,45 'restart_args': None,46 'server_user': conf.SERVER_USER.get(),47 'server_group': conf.SERVER_GROUP.get(),48 'ssl_certificate': conf.SSL_CERTIFICATE.get(),49 'ssl_private_key': conf.SSL_PRIVATE_KEY.get(),50 'status_host': '',51 'status_port': 0,52 'stderr': None,53 'stdout': None,54 'sysinfo': None,55 'threads': 0,56 'verbose': None,57 'watch': None58}59LOG = logging.getLogger(__name__)60class Command(BaseCommand):61 help = _("Spawning Server for Hue.")62 def handle(self, *args, **options):63 from django.conf import settings64 from django.utils import translation65 if not conf.ENABLE_SERVER.get():66 LOG.info("Hue is configured to not start its own web server.")67 sys.exit(0)68 # Activate the current language, because it won't get activated later.69 try:70 translation.activate(settings.LANGUAGE_CODE)71 except AttributeError:72 pass73 runspawningserver()74 def usage(self, subcommand):75 return SPAWNING_SERVER_HELP76def runspawningserver():77 try:78 sock = spawning.spawning_controller.bind_socket(SPAWNING_SERVER_OPTIONS)79 except Exception, ex:80 LOG.error('Could not bind port %s: %s. Exiting' % (str(SPAWNING_SERVER_OPTIONS['port']), ex,))81 return82 drop_privileges_if_necessary(SPAWNING_SERVER_OPTIONS)83 factory = SPAWNING_SERVER_OPTIONS['factory']84 pos_args = ['desktop.settings']85 argv_str_format = '--factory=%s %s --port %s -s %d -t %d'86 argv_str = argv_str_format % (SPAWNING_SERVER_OPTIONS['factory'],87 pos_args[0],88 SPAWNING_SERVER_OPTIONS['port'],89 SPAWNING_SERVER_OPTIONS['processes'],90 SPAWNING_SERVER_OPTIONS['threads'])91 factory_args = {92 'access_log_file': SPAWNING_SERVER_OPTIONS['access_log_file'],93 'args': pos_args,94 'argv_str': argv_str,95 'coverage': SPAWNING_SERVER_OPTIONS['coverage'],96 'deadman_timeout': SPAWNING_SERVER_OPTIONS['deadman_timeout'],97 'host': SPAWNING_SERVER_OPTIONS['host'],98 'max_age' : SPAWNING_SERVER_OPTIONS['max_age'],99 'no_keepalive' : SPAWNING_SERVER_OPTIONS['no_keepalive'],100 'num_processes': SPAWNING_SERVER_OPTIONS['processes'],101 'pidfile': SPAWNING_SERVER_OPTIONS['pidfile'],102 'port': SPAWNING_SERVER_OPTIONS['port'],103 'reload': SPAWNING_SERVER_OPTIONS['reload'],104 'ssl_certificate': SPAWNING_SERVER_OPTIONS['ssl_certificate'],105 'ssl_private_key': SPAWNING_SERVER_OPTIONS['ssl_private_key'],106 'status_host': SPAWNING_SERVER_OPTIONS['status_host'] or SPAWNING_SERVER_OPTIONS['host'],107 'status_port': SPAWNING_SERVER_OPTIONS['status_port'],108 'sysinfo': SPAWNING_SERVER_OPTIONS['sysinfo'],109 'threadpool_workers': SPAWNING_SERVER_OPTIONS['threads'],110 'verbose': SPAWNING_SERVER_OPTIONS['verbose'],111 'watch': SPAWNING_SERVER_OPTIONS['watch']112 }113 os.environ['HUE_SPAWNING'] = 'yes'114 spawning.spawning_controller.start_controller(sock, factory, factory_args)115if __name__ == '__main__':...
spawningTypes.py
Source:spawningTypes.py
1from AdaptivePELE.constants import blockNames2class SPAWNING_TYPES:3 sameWeight, inverselyProportional, epsilon, simulatedAnnealing, FAST, variableEpsilon, UCB, independent, REAP, null, independentMetric, ProbabilityMSMCalculator, MetastabilityMSMCalculator, UncertaintyMSMCalculator, IndependentMSMCalculator = list(range(15))4SPAWNING_TYPE_TO_STRING_DICTIONARY = {5 SPAWNING_TYPES.independent: blockNames.StringSpawningTypes.independent,6 SPAWNING_TYPES.sameWeight: blockNames.StringSpawningTypes.sameWeight,7 SPAWNING_TYPES.inverselyProportional: blockNames.StringSpawningTypes.inverselyProportional,8 SPAWNING_TYPES.epsilon: blockNames.StringSpawningTypes.epsilon,9 SPAWNING_TYPES.FAST: blockNames.StringSpawningTypes.fast,10 SPAWNING_TYPES.variableEpsilon: blockNames.StringSpawningTypes.variableEpsilon,11 SPAWNING_TYPES.simulatedAnnealing: blockNames.StringSpawningTypes.simulatedAnnealing,12 SPAWNING_TYPES.UCB: blockNames.StringSpawningTypes.UCB,13 SPAWNING_TYPES.REAP: blockNames.StringSpawningTypes.REAP,14 SPAWNING_TYPES.null: blockNames.StringSpawningTypes.null,15 SPAWNING_TYPES.independentMetric: blockNames.StringSpawningTypes.independentMetric,16 SPAWNING_TYPES.ProbabilityMSMCalculator: blockNames.StringSpawningTypes.ProbabilityMSMCalculator,17 SPAWNING_TYPES.MetastabilityMSMCalculator: blockNames.StringSpawningTypes.MetastabilityMSMCalculator,18 SPAWNING_TYPES.UncertaintyMSMCalculator: blockNames.StringSpawningTypes.UncertaintyMSMCalculator,19 SPAWNING_TYPES.IndependentMSMCalculator: blockNames.StringSpawningTypes.IndependentMSMCalculator20}21MSMSpawning = set([blockNames.StringSpawningTypes.ProbabilityMSMCalculator, blockNames.StringSpawningTypes.MetastabilityMSMCalculator, blockNames.StringSpawningTypes.UncertaintyMSMCalculator, blockNames.StringSpawningTypes.IndependentMSMCalculator])22class EPSILON_VARIATION_TYPES:23 linearVariation, contactsVariation = list(range(2))24EPSILON_VARIATION_TYPE_TO_STRING_DICTIONARY = {25 EPSILON_VARIATION_TYPES.linearVariation: blockNames.VariableEpsilonTypes.linearVariation,26 EPSILON_VARIATION_TYPES.contactsVariation: blockNames.VariableEpsilonTypes.contactsVariation,27}...
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