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openifs_wu_submit.py
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#! /usr/bin/python3
# Script to submit OpenIFS workunits
# This script has been written by Andy Bowery (Oxford University, 2023)
if __name__ == "__main__":
import os, zipfile, shutil, datetime, calendar, math, MySQLdb, fcntl, hashlib, gzip
import json, argparse, subprocess, time, sys, xml.etree.ElementTree as ET
from email.mime.text import MIMEText
from subprocess import Popen, PIPE
from xml.dom import minidom
from shutil import copyfile
#-----------------Parse command line-----------------
# use argparse to read in the options from the shell command line
parser = argparse.ArgumentParser()
# app_name is either oifs_43r3, oifs_43r3_arm, oifs_43r3_bl or oifs_43r3_ps
parser.add_argument("--app_name",help="application name",default="oifs_43r3")
# submission_test is either true of false
parser.add_argument("--submission_test",help="submission script test",default="false")
options = parser.parse_args()
if (options.submission_test):
print("Running as a test\n")
if options.app_name not in ('oifs_43r3','oifs_43r3_arm','oifs_43r3_bl','oifs_43r3_ps'):
raise ValueError('Incorrect app_name')
print("Application name: "+options.app_name)
if options.submission_test not in ('true','false'):
raise ValueError('Submission script test must be either true or false')
#print("Submission script test: "+options.submission_test
#----------------------------------------------------
# Check if a lockfile is present from an ongoing submission
lockfile='/tmp/lockfile_workgen'
print("Waiting for lock...\n")
f=open(lockfile,'w')
fcntl.lockf(f,fcntl.LOCK_EX)
print("got lock\n")
# Set the regionid as global
regionid = 15
# Set the max_results_per_workunit
max_results_per_workunit = 3
# Set the flops factor (for the progress bar)
flops_factor = 12800000000000
#-----------------Parse the project config xml file-----------------
#xmldoc3 = minidom.parse(project_dir+'../../config.xml')
xmldoc3 = minidom.parse('../../config.xml')
configs = xmldoc3.getElementsByTagName('config')
if not(options.submission_test):
for config in configs:
db_host = str(config.getElementsByTagName('db_host')[0].childNodes[0].nodeValue)
db_user = str(config.getElementsByTagName('db_user')[0].childNodes[0].nodeValue)
db_passwd = str(config.getElementsByTagName('db_passwd')[0].childNodes[0].nodeValue)
primary_db = str(config.getElementsByTagName('db_name')[0].childNodes[0].nodeValue)
project_dir = '/storage/www/'+primary_db+'/'
input_directory = project_dir+'oifs_workgen/incoming_xmls'
ancil_file_location = '/storage/cpdn_ancil_files/oifs_ancil_files/'
else:
primary_db = ''
project_dir = './test_directory/'
input_directory = './test_directory/'
ancil_file_location = './test_directory/ancils/'
# Set batch id prefix, adding a 'd' if a dev batch
if primary_db == 'cpdnboinc_dev':
batch_prefix = 'd'
secondary_db = 'cpdnexpt_dev'
project_url = 'https://dev.cpdn.org/'
database_port = 33001
elif primary_db == 'cpdnboinc_alpha':
batch_prefix = 'a'
secondary_db = 'cpdnexpt_alpha'
project_url = 'https://alpha.cpdn.org/'
database_port = 33001
elif primary_db == 'cpdnboinc':
batch_prefix = ''
secondary_db = 'cpdnexpt'
project_url = 'https://www.cpdn.org/'
database_port = 3306
else:
batch_prefix = ''
secondary_db = ''
project_url = ''
database_port = ''
#------From database read appid, last workunitid and last batchid------
# If submission_test is not true, query the database
if not(options.submission_test):
# Open cursor and connection to primary_db
db = MySQLdb.connect(db_host,db_user,db_passwd,primary_db,port=database_port)
cursor = db.cursor()
# Find the appid
query = """select id from app where name = '%s'""" % (options.app_name)
cursor.execute(query)
appid = cursor.fetchone()[0]
print("appid: "+str(appid))
# Find the last workunit id
query = 'select max(id) from workunit'
cursor.execute(query)
last_wuid = cursor.fetchone()
# Close cursor and connection to primary_db
cursor.close()
db.close()
else:
appid = 1
# Catch the case of no workunits in the database
if (options.submission_test) or last_wuid[0] == None:
wuid = 0
else:
wuid = last_wuid[0]
print("Last workunit id: "+str(wuid))
# If submission_test is not true, query the database
if not(options.submission_test):
# Open cursor and connection to secondary_db
db = MySQLdb.connect(db_host,db_user,db_passwd,secondary_db,port=database_port)
cursor = db.cursor()
# Find the last batch id
query = 'select max(id) from cpdn_batch'
cursor.execute(query)
last_batchid = cursor.fetchone()
# Catch the case of no batches in the database
if (options.submission_test) or last_batchid[0] == None:
batch_count = 0
else:
batch_count = last_batchid[0]
print("Last batch id: "+str(batch_count))
#--------------------------------------------------------------------------
print("")
print("--------------------------------------")
print("Starting submission run: "+str(datetime.datetime.now()))
print("--------------------------------------")
print("")
# Make a temporary directory for reorganising the files required by the workunit
if not(options.submission_test):
if not os.path.isdir(project_dir+"temp_openifs_submission_files"):
os.mkdir(project_dir+"temp_openifs_submission_files")
#------------------Read the submission and config XMLs--------------------
# Iterate over the xmlfile in the input directory
for input_xmlfile in os.listdir(input_directory):
if input_xmlfile.endswith(".xml"):
print("--------------------------------------")
print("Processing input xmlfile: "+str(input_xmlfile))
print("")
# Parse the input xmlfile
xmldoc = minidom.parse(input_directory+"/"+input_xmlfile)
# Iterate over the batches in the xmlfile
batches = xmldoc.getElementsByTagName('batch')
for batch in batches:
batch_count = batch_count + 1
number_of_workunits = 0
# Check model_class and if it is not openifs then exit loop and move on to the next xml file
model_class = str(batch.getElementsByTagName('model_class')[0].childNodes[0].nodeValue)
print("model_class: "+model_class)
non_openifs_class = False
if model_class != 'openifs':
non_openifs_class = True
print("The model class of the XML is not openifs, so moving on to the next XML file\n")
batch_count = batch_count - 1
break
model_config = str(batch.getElementsByTagName('model_config')[0].childNodes[0].nodeValue)
print("model_config: "+model_config)
fullpos_namelist_file = str(batch.getElementsByTagName('fullpos_namelist')[0].childNodes[0].nodeValue)
if not(options.submission_test):
fullpos_namelist = ancil_file_location + 'fullpos_namelist/' + fullpos_namelist_file
else:
fullpos_namelist = './config/' + fullpos_namelist_file
print("fullpos_namelist: "+fullpos_namelist)
nthreads = str(batch.getElementsByTagName('num_threads')[0].childNodes[0].nodeValue)
print("num_threads: "+nthreads)
batch_infos = batch.getElementsByTagName('batch_info')
for batch_info in batch_infos:
batch_desc = str(batch_info.getElementsByTagName('desc')[0].childNodes[0].nodeValue)
batch_name = str(batch_info.getElementsByTagName('name')[0].childNodes[0].nodeValue)
batch_owner = str(batch_info.getElementsByTagName('owner')[0].childNodes[0].nodeValue)
project_name = str(batch_info.getElementsByTagName('proj')[0].childNodes[0].nodeValue)
tech_info = str(batch_info.getElementsByTagName('tech_info')[0].childNodes[0].nodeValue)
umid_end = str(batch_info.getElementsByTagName('umid_end')[0].childNodes[0].nodeValue)
umid_start = str(batch_info.getElementsByTagName('umid_start')[0].childNodes[0].nodeValue)
xml_batchid = str(batch_info.getElementsByTagName('batchid')[0].childNodes[0].nodeValue)
# Set batchid to batch_count
batchid = batch_count
# Check whether the XML is containing workunits to add to an existing batch
# First, check whether xml_batchid is a numerical value
if xml_batchid.isdigit():
# Second, check whether xml_batchid is contained in the cpdn_batch table
#print("xml_batchid: "+xml_batchid)
if not(options.submission_test):
query = """select 1 from cpdn_batch where id = '%s'""" % (xml_batchid)
cursor.execute(query)
# If xml_batchid contained in the cpdn_batch table then overwrite batchid with xml_batchid
if cursor.fetchone():
batchid = int(xml_batchid)
else:
batchid = 0
# Create the batch folder structure in the download directory
download_dir = project_dir + "download/"
if not(options.submission_test):
# If folders do not exist, create them
if not(os.path.exists(download_dir+'batch_'+batch_prefix+str(batchid)+'/')):
os.mkdir(download_dir+'batch_'+batch_prefix+str(batchid)+'/')
if not(os.path.exists(download_dir+'batch_'+batch_prefix+str(batchid)+'/workunits/')):
os.mkdir(download_dir+'batch_'+batch_prefix+str(batchid)+'/workunits/')
if not(os.path.exists(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/')):
os.mkdir(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/')
# Find the project id
if not(options.submission_test):
query = """select id from cpdn_project where name ='%s'""" %(project_name)
cursor.execute(query)
projectid = cursor.fetchone()[0]
else:
projectid = 0
print("batchid: "+batch_prefix+str(batchid))
print("batch_desc: "+batch_desc)
#print("batch_name: "+batch_name)
print("batch_owner: "+batch_owner)
print("project_name: "+project_name)
print("tech_info: "+tech_info)
#print("umid_start: "+umid_start)
#print("umid_end: "+umid_end)
#print("projectid: "+str(projectid))
# Parse the config xmlfile
if not(options.submission_test):
xmldoc2 = minidom.parse(project_dir+'oifs_workgen/config_dir/'+model_config)
else:
xmldoc2 = minidom.parse(project_dir+'config/'+model_config)
model_configs = xmldoc2.getElementsByTagName('model_config')
for model_config in model_configs:
horiz_resolution = str(model_config.getElementsByTagName('horiz_resolution')[0].childNodes[0].nodeValue)
vert_resolution = str(model_config.getElementsByTagName('vert_resolution')[0].childNodes[0].nodeValue)
grid_type = str(model_config.getElementsByTagName('grid_type')[0].childNodes[0].nodeValue)
timestep = str(model_config.getElementsByTagName('timestep')[0].childNodes[0].nodeValue)
timestep_units = str(model_config.getElementsByTagName('timestep_units')[0].childNodes[0].nodeValue)
upload_frequency = str(model_config.getElementsByTagName('upload_frequency')[0].childNodes[0].nodeValue)
namelist_template = str(model_config.getElementsByTagName('namelist_template_global')[0].childNodes[0].nodeValue)
wam_namelist_template = str(model_config.getElementsByTagName('wam_template_global')[0].childNodes[0].nodeValue)
#print("horiz_resolution: "+horiz_resolution)
#print("vert_resolution: "+vert_resolution)
#print("grid_type: "+grid_type)
#print("timestep: "+timestep)
#print("timestep_units: "+timestep_units)
#print("upload_frequency: "+upload_frequency)
print("namelist_template: "+namelist_template)
print("wam_namelist_template: "+wam_namelist_template)
first_wuid = wuid + 1
first_start_year = 9999
last_start_year = 0
# Iterate over the workunits in the xmlfile
workunits = batch.getElementsByTagName('workunit')
for workunit in workunits:
number_of_workunits = number_of_workunits+1
analysis_member_number = str(workunit.getElementsByTagName('analysis_member_number')[0].childNodes[0].nodeValue)
ensemble_member_number = str(workunit.getElementsByTagName('ensemble_member_number')[0].childNodes[0].nodeValue)
exptid = str(workunit.getElementsByTagName('exptid')[0].childNodes[0].nodeValue)
fclen = str(workunit.getElementsByTagName('fclen')[0].childNodes[0].nodeValue)
fclen_units = str(workunit.getElementsByTagName('fclen_units')[0].childNodes[0].nodeValue)
start_day = int(workunit.getElementsByTagName('start_day')[0].childNodes[0].nodeValue)
start_hour = int(workunit.getElementsByTagName('start_hour')[0].childNodes[0].nodeValue)
start_month = int(workunit.getElementsByTagName('start_month')[0].childNodes[0].nodeValue)
start_year = int(workunit.getElementsByTagName('start_year')[0].childNodes[0].nodeValue)
unique_member_id = str(workunit.getElementsByTagName('unique_member_id')[0].childNodes[0].nodeValue)
parameters = workunit.getElementsByTagName('parameters')
# If baroclinic wave simulation
if options.app_name == 'oifs_43r3_bl':
for parameter in parameters:
zn = str(parameter.getElementsByTagName('zn')[0].childNodes[0].nodeValue)
zb = str(parameter.getElementsByTagName('zb')[0].childNodes[0].nodeValue)
zt0 = str(parameter.getElementsByTagName('zt0')[0].childNodes[0].nodeValue)
zu0 = str(parameter.getElementsByTagName('zu0')[0].childNodes[0].nodeValue)
zrh0 = str(parameter.getElementsByTagName('zrh0')[0].childNodes[0].nodeValue)
zgamma = str(parameter.getElementsByTagName('zgamma')[0].childNodes[0].nodeValue)
zchar = str(parameter.getElementsByTagName('zchar')[0].childNodes[0].nodeValue)
# If perturbed surface
if options.app_name == 'oifs_43r3_ps':
for parameter in parameters:
zuncerta = str(parameter.getElementsByTagName('zuncerta')[0].childNodes[0].nodeValue)
zuncertb = str(parameter.getElementsByTagName('zuncertb')[0].childNodes[0].nodeValue)
zuncertc = str(parameter.getElementsByTagName('zuncertc')[0].childNodes[0].nodeValue)
zuncertd = str(parameter.getElementsByTagName('zuncertd')[0].childNodes[0].nodeValue)
zuncerte = str(parameter.getElementsByTagName('zuncerte')[0].childNodes[0].nodeValue)
# This section can be used to resubmit particular workunits from an XML file
# To use this, provide a file containing a list of umids that are contained within the XML
# This section will then check whether workunit is in the list and resubmit, and will exit loop if not listed
##umid_present = 0
##with open(project_dir+'oifs_workgen/src/FILE_OF_WORKUNITS_TO_RESEND', 'r') as umids_resubmit:
## for umid_line in umids_resubmit:
## if umid_line.rstrip() == str(unique_member_id):
## print("umid_present")
## umid_present = 1
##if umid_present == 0:
## continue
# Set the first_start_year
if start_year < first_start_year:
first_start_year = start_year
# Set the last_start_year
if start_year > last_start_year:
last_start_year = start_year
# Set the workunit id and file names
wuid = wuid + 1
last_wuid = wuid
ic_ancil_zip = "ic_ancil_"+str(wuid)+".zip"
ifsdata_zip = "ifsdata_"+str(wuid)+".zip"
climate_data_zip = "clim_data_"+str(wuid)+".zip"
# Check the grid_type is an acceptable value, one of:
# l_2 is linear grid, _2 is quadratic grid, _full is full grid, _3 is cubic grid, _4 is octahedral cubic grid
if grid_type not in ('l_2','_2','_full','_3','_4'):
raise ValueError('Invalid grid_type')
print("--------------------------------------")
print("wuid:" +str(wuid))
print("batchid: "+str(batchid))
print("analysis_member_number: "+analysis_member_number)
print("ensemble_member_number: "+ensemble_member_number)
#print("exptid: "+exptid)
#print("fclen: "+fclen)
#print("fclen_units: "+fclen_units)
#print("start_day: "+str(start_day))
#print("start_hour: "+str(start_hour))
#print("start_month: "+str(start_month))
#print("start_year: "+str(start_year))
#print("unique_member_id: "+unique_member_id)
# Set the start_date field
if str(start_year) is None or start_year <= 0:
start_date = '0000'
else:
start_date = str(start_year).zfill(4)
if str(start_month) is None or start_month <= 0:
start_date = start_date + '00'
elif start_month > 0 and start_month < 13:
start_date = start_date + str(start_month).zfill(2)
if str(start_day) is None or start_day <= 0:
start_date = start_date + '00'
elif start_day > 0 and start_day < 32:
start_date = start_date + str(start_day).zfill(2)
if str(start_hour) is None or start_hour <= 0:
start_date = start_date + '00'
elif start_hour > 0 and start_hour < 25:
start_date = start_date + str(start_hour).zfill(2)
#----------------------------Construct the ancillary files----------------------------
# Construct ic_ancil_location
if not(options.submission_test):
ic_ancil_location = ancil_file_location+"ic_ancil/"+str(exptid)+"/"+str(start_date)+"/"+str(analysis_member_number)+"/"
else:
ic_ancil_location = '../ancils/'
ic_ancils = workunit.getElementsByTagName('ic_ancil')
for ic_ancil in ic_ancils:
ic_ancil_zip_in = str(ic_ancil.getElementsByTagName('ic_ancil_zip')[0].childNodes[0].nodeValue)
# Test whether the ic_ancil_zip is present
try:
os.path.exists(ic_ancil_location+str(ic_ancil_zip_in))
except OSError:
print("The following file is not present in the oifs_ancil_files: "+ic_ancil_zip_in)
# Change to the download dir and create link to file
if not(options.submission_test):
os.chdir(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/')
args = ['ln','-s',ic_ancil_location+str(ic_ancil_zip_in),ic_ancil_zip]
p = subprocess.Popen(args)
p.wait()
else:
args = ['ln','-s','../ancils/'+str(ic_ancil_zip_in),project_dir+ic_ancil_zip]
#print(args)
p = subprocess.Popen(args)
p.wait()
ifsdatas = workunit.getElementsByTagName('ifsdata')
for ifsdata in ifsdatas:
GHG_zip = str(ifsdata.getElementsByTagName('GHG_zip')[0].childNodes[0].nodeValue)
radiation_zip = str(ifsdata.getElementsByTagName('other_radiation_zip')[0].childNodes[0].nodeValue)
SO4_zip = str(ifsdata.getElementsByTagName('SO4_zip')[0].childNodes[0].nodeValue)
# Copy each of the ifsdata zip files to the temp directory
if not(options.submission_test):
copyfile(ancil_file_location+"ifsdata/GHG_files/"+GHG_zip,project_dir+"temp_openifs_submission_files/"+GHG_zip)
copyfile(ancil_file_location+"ifsdata/other_radiation_files/"+radiation_zip,project_dir+"temp_openifs_submission_files/"+radiation_zip)
copyfile(ancil_file_location+"ifsdata/SO4_files/"+SO4_zip,project_dir+"temp_openifs_submission_files/"+SO4_zip)
else:
copyfile(ancil_file_location+GHG_zip,download_dir+GHG_zip)
copyfile(ancil_file_location+radiation_zip,download_dir+radiation_zip)
copyfile(ancil_file_location+SO4_zip,download_dir+SO4_zip)
# Unzip each of the ifsdata files in the temp directory
if not(options.submission_test):
zip_file = zipfile.ZipFile(project_dir+"temp_openifs_submission_files/"+GHG_zip,'r')
zip_file.extractall(project_dir+"temp_openifs_submission_files/")
zip_file.close()
zip_file = zipfile.ZipFile(project_dir+"temp_openifs_submission_files/"+radiation_zip,'r')
zip_file.extractall(project_dir+"temp_openifs_submission_files/")
zip_file.close()
zip_file = zipfile.ZipFile(project_dir+"temp_openifs_submission_files/"+SO4_zip,'r')
zip_file.extractall(project_dir+"temp_openifs_submission_files/")
zip_file.close()
else:
zip_file = zipfile.ZipFile(download_dir+GHG_zip,'r')
zip_file.extractall(download_dir)
zip_file.close()
zip_file = zipfile.ZipFile(download_dir+radiation_zip,'r')
zip_file.extractall(download_dir)
zip_file.close()
zip_file = zipfile.ZipFile(download_dir+SO4_zip,'r')
zip_file.extractall(download_dir)
zip_file.close()
# Remove the zip files
if not(options.submission_test):
os.remove(project_dir+"temp_openifs_submission_files/"+GHG_zip)
os.remove(project_dir+"temp_openifs_submission_files/"+radiation_zip)
os.remove(project_dir+"temp_openifs_submission_files/"+SO4_zip)
else:
os.remove(download_dir+GHG_zip)
os.remove(download_dir+radiation_zip)
os.remove(download_dir+SO4_zip)
# Zip together the ifsdata files
if not(options.submission_test):
shutil.make_archive(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/ifsdata_'+str(wuid), 'zip', project_dir+"temp_openifs_submission_files/")
else:
shutil.make_archive(project_dir+'/ifsdata_'+str(wuid), 'zip', download_dir)
shutil.move(project_dir+'/ifsdata_'+str(wuid)+'.zip',project_dir+'download/ifsdata_'+str(wuid)+'.zip')
shutil.move(project_dir+'/ic_ancil_'+str(wuid)+'.zip',project_dir+'download/ic_ancil_'+str(wuid)+'.zip')
# Change the working path
os.chdir(project_dir)
climate_datas = workunit.getElementsByTagName('climate_data')
for climate_data in climate_datas:
climate_data_zip_in = str(climate_data.getElementsByTagName('climate_data_zip')[0].childNodes[0].nodeValue)
# Test whether the climate_data_zip is present
if not(options.submission_test):
try:
os.path.exists(ancil_file_location+"climate_data/"+str(climate_data_zip_in))
except OSError:
print("The following file is not present in the oifs_ancil_files: "+str(climate_data_zip_in))
# Change to the download dir and create link to file
if not(options.submission_test):
os.chdir(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/')
args = ['ln','-s',ancil_file_location+"climate_data/"+str(climate_data_zip_in),climate_data_zip]
p = subprocess.Popen(args)
p.wait()
else:
args = ['ln','-s','../ancils/'+str(climate_data_zip_in),'./download/'+climate_data_zip]
#print(args)
p = subprocess.Popen(args)
p.wait()
#--------------------------Calculate model parameters required for submission----------------------------
# GC: Set the memory bound & estimated output instance filesizes
# These are taken from measurements by G.Carver and listed at:
# https://docs.google.com/document/d/1AxLzZ6-m2owRscf_9SCv2TwRAcMl1pzbxFfbm6qeSL4/edit?usp=sharing
# Add another 0.5Gb to task mem to allow for wrapper plus bit extra in case of leaks.
# Ordered by the 'N' number: N80 & up.
# gribfield_size is approximate as not all GRIB fields are packed to the same precision.
# Updated: Jan/23, add in size of model restarts which become significant with higher resolution
# and scale as square of resolution.
fields_per_output = 200 # assume scientist typically has this total no. of fields per output instance
# also assume output every day TODO: improve by reading NFRPOS from namelist
if int(horiz_resolution) == 63 and int(vert_resolution) == 91:
memory_bound = str(5370000000)
gribfield_size = 70.0 # approx value of single GRIB field output (Kb - converted below)
restart_size = 0.7 # approx value of single set of restart files (Gb).
elif int(horiz_resolution) == 159 and int(vert_resolution) == 60 and grid_type == 'l_2':
memory_bound = str(6010000000)
gribfield_size = 70.0
restart_size = 0.7
elif int(horiz_resolution) == 159 and int(vert_resolution) == 91 and grid_type == 'l_2':
memory_bound = str(8804000000)
gribfield_size = 70.0
restart_size = 1.0
elif int(horiz_resolution) == 95 and int(vert_resolution) == 91:
memory_bound = str(10844000000)
gribfield_size = 80.0
restart_size = 1.4
elif int(horiz_resolution) == 255 and int(vert_resolution) == 60:
memory_bound = str(13786000000)
gribfield_size = 90.0
restart_size = 2.0
elif int(horiz_resolution) == 255 and int(vert_resolution) == 91:
memory_bound = str(20400000000)
gribfield_size = 90.0
restart_size = 2.6
elif int(horiz_resolution) == 319 and int(vert_resolution) == 60:
memory_bound = str(21300000000)
gribfield_size = 170.0
restart_size = 3.2
elif int(horiz_resolution) == 319 and int(vert_resolution) == 91:
memory_bound = str(31675000000)
gribfield_size = 170.0
restart_size = 4.0
elif int(horiz_resolution) == 159 and int(vert_resolution) == 60 and grid_type == '_4':
memory_bound = str(17810000000)
gribfield_size = 130.0
restart_size = 3.2
elif int(horiz_resolution) == 159 and int(vert_resolution) == 91 and grid_type == '_4':
memory_bound = str(26300000000)
gribfield_size = 130.0
restart_size = 4.0
# Calculate the number of timesteps from the number of days of the simulation
if fclen_units == 'days':
num_timesteps = (int(fclen) * 86400)/int(timestep)
print("timestep: "+str(timestep))
print("num_timesteps: "+str(num_timesteps))
print("fclen: "+str(int(fclen)))
num_hours = int(fclen) * 24
num_days = fclen
# Throw an error if not cleanly divisible
#if not(isinstance(num_timesteps,int)):
if int(num_timesteps) != num_timesteps:
raise ValueError('Length of simulation (in days) does not divide equally by timestep')
# Set upload interval and number of uploads, upload_interval is the number of timesteps between uploads
if upload_frequency == 'daily':
upload_interval = num_timesteps / int(fclen)
elif upload_frequency == 'weekly':
upload_interval = (num_timesteps / int(fclen)) * 7
elif upload_frequency == 'monthly':
upload_interval = (num_timesteps / int(fclen)) * 30
elif upload_frequency == 'yearly':
upload_interval = (num_timesteps / int(fclen)) * 365
# Throw an error if not cleanly divisible
if int(upload_interval) != upload_interval:
raise ValueError('The number of time steps does not divide equally by the upload frequency')
# Set the name of the workunit (days)
workunit_name = str(options.app_name)+'_'+str(unique_member_id)+'_'+str(start_date)+'_'+str(num_days)+'_'+batch_prefix+str(batchid)+'_'+str(wuid)
elif fclen_units == 'hours':
num_timesteps = (int(fclen) * 3600)/int(timestep)
num_hours = int(fclen)
num_days = str('{0:.3f}'.format(int(fclen) * 0.041666667)) # Convert to days and round to three decimals figures
# print("num_days: "+num_days)
# print("fclen: "+fclen)
# Throw an error if not cleanly divisible
if not(isinstance(num_timesteps,int)):
raise ValueError('Length of simulation (in hours) does not divide equally by timestep')
# Set upload interval and number of uploads, upload_interval is the number of timesteps between uploads
if upload_frequency == 'hourly':
upload_interval = num_timesteps / int(fclen)
# Set the name of the workunit (hours)
workunit_name = str(options.app_name)+'_'+str(unique_member_id)+'_'+str(start_date)+'_0_'+batch_prefix+str(batchid)+'_'+str(wuid)
# Compute disk_bound assuming worse case where none of the trickles can be uploaded until run is complete
# i.e. estimate total size of model output assuming 1 output per model day.
# Add 'extra' to account for climate files, executables etc in workunit. TODO: This is resolution dependent!
# Allow space for several sets of restart files; some may be kept by the model during the run
extra_wu_gb = 5
total_wu_gb = extra_wu_gb + 3*restart_size + float(num_days) * fields_per_output * (gribfield_size/(1024*1024))
disk_bound_gb = math.ceil(total_wu_gb)
disk_bound = str(disk_bound_gb * 1024**3 )
number_of_uploads = int(math.ceil(float(num_timesteps) / float(upload_interval)))
print("upload_interval: "+str(upload_interval))
print("number_of_uploads: "+str(number_of_uploads))
print("disk_bound, disk_bound (Gb): "+disk_bound+", "+str(disk_bound_gb))
# Throw an error if not cleanly divisible
if not(isinstance(number_of_uploads,int)):
raise ValueError('The total number of timesteps does not divide equally by the upload interval')
# Set the fpops_est and fpops_bound for the workunit
fpops_est = str(flops_factor * int(float(num_days)))
fpops_bound = str(flops_factor * int(float(num_days)) * 10)
#print("fpops_est: "+fpops_est)
#print("fpops_bound: "+fpops_bound)
#----------------------Construct XML for entry into workunit table----------------------
upload_infos = batch.getElementsByTagName('upload_info')
for upload_info in upload_infos:
upload_handler = str(upload_info.getElementsByTagName('upload_handler')[0].childNodes[0].nodeValue)
result_template_prefix = str(upload_info.getElementsByTagName('result_template_prefix')[0].childNodes[0].nodeValue)
result_template = result_template_prefix+'_n'+str(number_of_uploads)+'.xml'
#print("upload_handler: "+upload_handler)
#print("result_template: "+project_dir+result_template)
# If result template does not exist, then create a new template
if not (os.path.exists(project_dir+result_template)) or (options.submission_test):
output_string="<output_template>\n"
for upload_iteration in range(number_of_uploads):
output_string=output_string+"<file_info>\n" +\
" <name><OUTFILE_"+str(upload_iteration)+"/>.zip</name>\n" +\
" <generated_locally/>\n" +\
" <upload_when_present/>\n" +\
" <max_nbytes>100000000000000</max_nbytes>\n" +\
" <url>"+upload_handler+"</url>\n" +\
"</file_info>\n"
output_string = output_string + "<result>\n"
for upload_iteration in range(number_of_uploads):
output_string=output_string+" <file_ref>\n" +\
" <file_name><OUTFILE_"+str(upload_iteration)+"/>.zip</file_name>\n" +\
" <open_name>upload_file_"+str(upload_iteration)+".zip</open_name>\n" +\
" </file_ref>\n"
output_string = output_string + "</result>\n" +\
"</output_template>"
if not(options.submission_test):
OUTPUT=open(project_dir+result_template,"w")
# Create the result_template
print >> OUTPUT, output_string
OUTPUT.close()
else:
print("result template = "+output_string)
# Set the server_cgi from the upload_handler string
server_cgi = upload_handler[:-19]
#-------------------------Construct namelist files----------------------------
if not(options.submission_test):
namelist_template_dir = project_dir+'oifs_workgen/namelist_template_files/'
else:
namelist_template_dir = './config/'
# Read in the namelist template file
with open(namelist_template_dir+namelist_template, 'r') as namelist_file :
template_file = []
for line in namelist_file:
# Replace the values
line = line.replace('_EXPTID',exptid)
line = line.replace('_UNIQUE_MEMBER_ID',unique_member_id)
line = line.replace('_IC_ANCIL_FILE',"ic_ancil_"+str(wuid))
line = line.replace('_IFSDATA_FILE',"ifsdata_"+str(wuid))
line = line.replace('_CLIMATE_DATA_FILE',"clim_data_"+str(wuid))
line = line.replace('_HORIZ_RESOLUTION',horiz_resolution)
line = line.replace('_VERT_RESOLUTION',vert_resolution)
line = line.replace('_GRID_TYPE',grid_type)
line = line.replace('_NUM_TIMESTEPS',str(num_timesteps))
line = line.replace('_TIMESTEP',timestep)
line = line.replace('_UPLOAD_INTERVAL',str(upload_interval))
line = line.replace('_ENSEMBLE_MEMBER_NUMBER',str(ensemble_member_number))
line = line.replace('_NUM_HOURS',str(num_hours))
# If baroclinic wave simulation
if options.app_name == 'oifs_43r3_bl':
line = line.replace('_ZN',zn)
line = line.replace('_ZB',zb)
line = line.replace('_ZT0',zt0)
line = line.replace('_ZU0',zu0)
line = line.replace('_ZRH0',zrh0)
line = line.replace('_ZGAMMA',zgamma)
line = line.replace('_ZCHAR',zchar)
# If perturbed surface
if options.app_name == 'oifs_43r3_ps':
line = line.replace('_ZUNCERTA',zuncerta)
line = line.replace('_ZUNCERTB',zuncertb)
line = line.replace('_ZUNCERTC',zuncertc)
line = line.replace('_ZUNCERTD',zuncertd)
line = line.replace('_ZUNCERTE',zuncerte)
# Remove commented lines
if not line.startswith('!!'):
template_file.append(line)
if not(options.submission_test):
# Run dos2unix on the fullpos namelist to eliminate Windows end-of-line characters
args = ['dos2unix',fullpos_namelist]
p = subprocess.Popen(args)
p.wait()
#print os.getcwd()
# Read in the fullpos_namelist
with open(fullpos_namelist) as namelist_file_2:
fullpos_file = []
for line in namelist_file_2:
if not line.startswith('!!'):
fullpos_file.append(line)
# Write out the workunit file, this is a combination of the fullpos and main namelists
with open('fort.4', 'w') as workunit_file:
workunit_file.writelines(fullpos_file)
workunit_file.writelines(template_file)
workunit_file.close()
# Read in the wam_namelist template file
with open(namelist_template_dir+wam_namelist_template, 'r') as wam_namelist_file :
wam_template_file = []
for line_2 in wam_namelist_file:
# Replace the values
line_2 = line_2.replace('_START_DATE',str(start_date))
line_2 = line_2.replace('_EXPTID',exptid)
wam_template_file.append(line_2)
# Write out the wam_namelist file
with open('wam_namelist', 'w') as wam_file:
wam_file.writelines(wam_template_file)
wam_file.close()
# Zip together the fort.4 and wam_namelist files
if not(options.submission_test):
zip_file = zipfile.ZipFile(download_dir+'batch_'+batch_prefix+str(batchid)+'/workunits/'+workunit_name+'.zip','w')
else:
zip_file = zipfile.ZipFile('./download/'+workunit_name+'.zip','w')
zip_file.write('fort.4')
zip_file.write('wam_namelist')
zip_file.close()
# Remove the copied wam_namelist file
if not(options.submission_test):
args = ['rm','-rf','wam_namelist']
p = subprocess.Popen(args)
p.wait()
# Remove the fort.4 file
if not(options.submission_test):
args = ['rm','-f','fort.4']
p = subprocess.Popen(args)
p.wait()
if not(options.submission_test):
# Test whether the workunit_name_zip is present
try:
os.path.exists(download_dir+'batch_'+batch_prefix+str(batchid)+'/workunits/'+workunit_name+'.zip')
except OSError:
print("The following file is not present in the download files: "+workunit_name+'.zip')
# Test whether the ifsdata_zip is present
try:
os.path.exists(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/'+ifsdata_zip)
except OSError:
print("The following file is not present in the download files: "+ifsdata_zip)
#----------------------Construct the XML for entry into the result table-------------------
# Construct the input template
input_string="<input_template>\n" +\
"<file_info>\n" +\
" <number>0</number>\n" +\
"</file_info>\n" +\
"<file_info>\n" +\
" <number>1</number>\n" +\
"</file_info>\n" +\
"<file_info>\n" +\
" <number>2</number>\n" +\
"</file_info>\n" +\
"<file_info>\n" +\
" <number>3</number>\n" +\
"</file_info>\n" +\
"<workunit>\n" +\
" <file_ref>\n" +\
" <file_number>0</file_number>\n" +\
" <open_name>"+workunit_name+".zip</open_name>\n" +\
" </file_ref>\n" +\
" <file_ref>\n" +\
" <file_number>1</file_number>\n" +\
" <open_name>"+str(ic_ancil_zip)+"</open_name>\n" +\
" </file_ref>\n" +\
" <file_ref>\n" +\
" <file_number>2</file_number>\n" +\
" <open_name>"+str(ifsdata_zip)+"</open_name>\n" +\
" </file_ref>\n" +\
" <file_ref>\n" +\
" <file_number>3</file_number>\n" +\
" <open_name>"+str(climate_data_zip)+"</open_name>\n" +\
" </file_ref>\n" +\
" <command_line> "+str(start_date)+" "+str(exptid)+" "+str(unique_member_id)+" "+batch_prefix+str(batchid)+" "+str(wuid)+" "+str(num_days)+" "+str(options.app_name)+" "+str(nthreads)+"</command_line>\n" +\
" <rsc_fpops_est>"+fpops_est+"</rsc_fpops_est>\n" +\
" <rsc_fpops_bound>"+fpops_est+"0</rsc_fpops_bound>\n" +\
" <rsc_memory_bound>"+memory_bound+"</rsc_memory_bound>\n" +\
" <rsc_disk_bound>"+disk_bound+"</rsc_disk_bound>\n" +\
" <delay_bound>2592000</delay_bound>\n" +\
" <min_quorum>1</min_quorum>\n" +\
" <target_nresults>1</target_nresults>\n" +\
" <max_error_results>"+str(max_results_per_workunit)+"</max_error_results>\n" +\
" <max_total_results>"+str(max_results_per_workunit)+"</max_total_results>\n" +\
" <max_success_results>1</max_success_results>\n" +\
"</workunit>\n"+\
"</input_template>"
if not(options.submission_test):
OUTPUT=open(project_dir+"templates/"+str(options.app_name)+"_in_"+str(wuid),"w")
# Make the input_template
print >> OUTPUT, input_string
OUTPUT.close()
else:
print("input template = "+input_string)
#------------------------Set file URLs and get file sizes-------------------------
# Change back to the project directory
if not(options.submission_test):
os.chdir(project_dir)
if not(options.submission_test):
workunit_url = project_url+'download/batch_'+batch_prefix+str(batchid)+'/workunits/'+workunit_name+'.zip'
else:
workunit_url = project_url+workunit_name+'.zip'
# Get the md5 checksum of the workunit zip file
if not(options.submission_test):
workunit_zip_cksum = hashlib.md5(open(download_dir+'batch_'+batch_prefix+str(batchid)+'/workunits/'+workunit_name+'.zip','rb').read()).hexdigest()
else:
workunit_zip_cksum = hashlib.md5(open('./download/'+workunit_name+'.zip','rb').read()).hexdigest()
print("workunit_zip_cksum = "+str(workunit_zip_cksum))
# Calculate the size of the workunit zip in bytes
if not(options.submission_test):
workunit_zip_size = os.path.getsize(download_dir+'batch_'+batch_prefix+str(batchid)+'/workunits/'+workunit_name+'.zip')
else:
workunit_zip_size = os.path.getsize('./download/'+workunit_name+'.zip')
print("workunit_zip_size = "+str(workunit_zip_size))
if not(options.submission_test):
ic_ancil_url = project_url+'download/batch_'+batch_prefix+str(batchid)+'/ancils/'+str(ic_ancil_zip)
else:
ic_ancil_url = project_url+str(ic_ancil_zip)
# Get the md5 checksum of the ic_ancil zip file
if not(options.submission_test):
ic_ancil_zip_cksum = hashlib.md5(open(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/'+str(ic_ancil_zip),'rb').read()).hexdigest()
else:
ic_ancil_zip_cksum = hashlib.md5(open('./download/'+str(ic_ancil_zip),'rb').read()).hexdigest()
print("ic_ancil_zip_cksum = "+str(ic_ancil_zip_cksum))
# Calculate the size of the ic_ancil zip in bytes
if not(options.submission_test):
ic_ancil_zip_size = os.path.getsize(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/'+str(ic_ancil_zip))
else:
ic_ancil_zip_size = os.path.getsize('./download/'+str(ic_ancil_zip))
print("ic_ancil_zip_size = "+str(ic_ancil_zip_size))
if not(options.submission_test):
ifsdata_url = project_url+'download/batch_'+batch_prefix+str(batchid)+'/ancils/'+str(ifsdata_zip)
else:
ifsdata_url = project_url+str(ifsdata_zip)
# Get the md5 checksum of the ifsdata zip file
if not(options.submission_test):
ifsdata_zip_cksum = hashlib.md5(open(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/'+str(ifsdata_zip),'rb').read()).hexdigest()
else:
ifsdata_zip_cksum = hashlib.md5(open('./download/'+str(ifsdata_zip),'rb').read()).hexdigest()
print("ifsdata_zip_cksum = "+str(ifsdata_zip_cksum))
# Calculate the size of the ifsdata zip in bytes
if not(options.submission_test):
ifsdata_zip_size = os.path.getsize(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/'+str(ifsdata_zip))
else:
ifsdata_zip_size = os.path.getsize('./download/'+str(ifsdata_zip))
print("ifsdata_zip_size = "+str(ifsdata_zip_size))
if not(options.submission_test):
climate_data_url = project_url+'download/batch_'+batch_prefix+str(batchid)+'/ancils/'+str(climate_data_zip)
else:
climate_data_url = project_url+str(climate_data_zip)
# Get the md5 checksum of the climate_data zip file
if not(options.submission_test):
climate_data_zip_cksum = hashlib.md5(open(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/'+str(climate_data_zip),'rb').read()).hexdigest()
else:
climate_data_zip_cksum = hashlib.md5(open('./download/'+str(climate_data_zip),'rb').read()).hexdigest()
print("climate_data_zip_cksum = "+str(climate_data_zip_cksum))
# Calculate the size of the climate_data zip in bytes
if not(options.submission_test):
climate_data_zip_size = os.path.getsize(download_dir+'batch_'+batch_prefix+str(batchid)+'/ancils/'+str(climate_data_zip))
else:
climate_data_zip_size = os.path.getsize('./download/'+str(climate_data_zip))
print("climate_data_zip_size = "+str(climate_data_zip_size))
#----------------------Create the workunit in the BOINC database-----------------------
# Run the create_work script to create the workunit
args = ["./bin/create_work","-appname",str(options.app_name),"-wu_name",str(workunit_name),"-wu_template",\
"templates/"+str(options.app_name)+"_in_"+str(wuid),"-result_template",result_template,\
"-remote_file",str(workunit_url),str(workunit_zip_size),str(workunit_zip_cksum),\
"-remote_file",str(ic_ancil_url),str(ic_ancil_zip_size),str(ic_ancil_zip_cksum),\
"-remote_file",str(ifsdata_url),str(ifsdata_zip_size),str(ifsdata_zip_cksum),\
"-remote_file",str(climate_data_url),str(climate_data_zip_size),str(climate_data_zip_cksum)]
time.sleep(2)
if not(options.submission_test):
p = subprocess.Popen(args)
p.wait()
else:
print(args)
#------------Enter workunit details into the cpdn_workunit and parameter tables------------
# Calculate the run_years
if fclen_units == 'days':
run_years = 0.00274 * int(fclen)
else:
run_years = 0
# Enter the details of the submitted workunit into the workunit_table
query = """insert into cpdn_workunit(wuid,cpdn_batch,umid,name,start_year,run_years,appid) \
values(%s,%s,'%s','%s',%s,%s,%s)""" \
%(wuid,batchid,unique_member_id,workunit_name,start_year,run_years,appid)
if not(options.submission_test):
cursor.execute(query)
db.commit()
else:
print(query)
# Enter the fullpos_namelist details of the submitted workunit into the parameter table
query = """insert into parameter(paramtypeid,charvalue,submodelid,workunitid) \
values(%s,'%s',%s,%s)""" \
%('159',fullpos_namelist_file,'0',wuid)
if not(options.submission_test):
cursor.execute(query)
db.commit()
else:
print(query)
# Enter the analysis_member_number details of the submitted workunit into the parameter table
query = """insert into parameter(paramtypeid,charvalue,submodelid,workunitid) \
values(%s,'%s',%s,%s)""" \
%('160',analysis_member_number,'0',wuid)
if not(options.submission_test):
cursor.execute(query)
db.commit()
else:
print(query)
# Enter the ensemble_member_number details of the submitted workunit into the parameter table
query = """insert into parameter(paramtypeid,charvalue,submodelid,workunitid) \
values(%s,'%s',%s,%s)""" \
%('161',ensemble_member_number,'0',wuid)
if not(options.submission_test):
cursor.execute(query)
db.commit()
else:
print(query)
# Enter the fclen details of the submitted workunit into the parameter table
query = """insert into parameter(paramtypeid,charvalue,submodelid,workunitid) \
values(%s,'%s',%s,%s)""" \
%('162',fclen,'0',wuid)
if not(options.submission_test):
cursor.execute(query)