| 1 | #!/usr/bin/env python |
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| 2 | # |
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| 3 | # This software is licensed under the terms of the Apache Licence Version 2.0 |
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| 4 | # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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| 5 | # |
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| 6 | # Functionality provided: Prepare input 3D-wind fields in hybrid coordinates + surface fields for FLEXPART runs |
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| 7 | # |
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| 8 | # Creation: October 2014 - Anne Fouilloux - University of Oslo |
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| 9 | # Extension November 2015 - Leopold Haimberger - University of Vienna for: |
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| 10 | # - using the WebAPI also for general MARS retrievals |
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| 11 | # - job submission on ecgate and cca |
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| 12 | # - job templates suitable for twice daily operational dissemination |
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| 13 | # - dividing retrievals of longer periods into digestable chunks |
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| 14 | # - retrieve also longer term forecasts, not only analyses and short term forecast data |
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| 15 | # - conversion into GRIB2 |
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| 16 | # - conversion into .fp format for faster execution of FLEXPART |
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| 17 | # |
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| 18 | # |
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| 19 | # Further documentation may be obtained from www.flexpart.eu |
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| 20 | # |
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| 21 | # Requirements: |
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| 22 | # in addition to a standard python 2.6 or 2.7 installation the following packages need to be installed |
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| 23 | # ECMWF WebMARS, gribAPI with python enabled, emoslib, ecaccess web toolkit, all available from https://software.ecmwf.int/ |
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| 24 | # dateutils |
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| 25 | # matplotlib (optional, for debugging) |
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| 26 | # |
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| 27 | # |
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| 28 | import calendar |
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| 29 | import shutil |
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| 30 | import datetime |
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| 31 | import time |
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| 32 | import os,sys,glob |
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| 33 | import subprocess |
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| 34 | import inspect |
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| 35 | # add path to submit.py to pythonpath so that python finds its buddies |
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| 36 | localpythonpath=os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) |
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| 37 | sys.path.append(localpythonpath) |
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| 38 | from UIOTools import UIOFiles |
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| 39 | from string import strip |
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| 40 | from argparse import ArgumentParser,ArgumentDefaultsHelpFormatter |
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| 41 | from GribTools import GribTools |
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| 42 | from FlexpartTools import EIFlexpart, Control, install_args_and_control |
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| 43 | from getMARSdata import getMARSdata |
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| 44 | from prepareFLEXPART import prepareFLEXPART |
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| 45 | |
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| 46 | |
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| 47 | |
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| 48 | def main(): |
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| 49 | |
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| 50 | calledfromdir=os.getcwd() |
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| 51 | os.chdir(localpythonpath) |
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| 52 | args,c=install_args_and_control() |
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| 53 | # if c.outputdir[0]!='/': |
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| 54 | # c.outputdir=os.path.join(calledfromdir,c.outputdir) |
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| 55 | # c.inputdir=c.outputdir |
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| 56 | if args.install_target!=None: |
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| 57 | install_via_gateway(c,args.install_target) |
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| 58 | |
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| 59 | else: |
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| 60 | print 'Please specify installation target (local|ecgate|cca)' |
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| 61 | print 'use -h or --help for help' |
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| 62 | sys.exit() |
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| 63 | |
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| 64 | def install_via_gateway(c,target): |
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| 65 | |
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| 66 | ecd=c.flexextractdir |
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| 67 | template=ecd+'python/compilejob.temp' |
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| 68 | job=ecd+'python/compilejob.ksh' |
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| 69 | fo=open(job,'w') |
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| 70 | with open(template) as f: |
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| 71 | fdata = f.read().split('\n') |
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| 72 | for data in fdata: |
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| 73 | if 'MAKEFILE=' in data: |
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| 74 | if c.makefile is not None: |
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| 75 | data='export MAKEFILE='+c.makefile |
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| 76 | if 'FLEXPART_ROOT_SCRIPTS=' in data: |
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| 77 | if c.flexpart_root_scripts!='../': |
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| 78 | data='export FLEXPART_ROOT_SCRIPTS='+c.flexpart_root_scripts |
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| 79 | else: |
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| 80 | data='export FLEXPART_ROOT_SCRIPTS=$HOME' |
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| 81 | if target.lower()!='local': |
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| 82 | if '--workdir' in data: |
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| 83 | data='#SBATCH --workdir=/scratch/ms/'+c.ecgid+'/'+c.ecuid |
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| 84 | if '##PBS -o' in data: |
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| 85 | data='##PBS -o /scratch/ms/'+c.ecgid+'/'+c.ecuid+'flex_ecmwf.$Jobname.$Job_ID.out' |
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| 86 | if 'FLEXPART_ROOT_SCRIPTS=' in data: |
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| 87 | if c.ec_flexpart_root_scripts!='../': |
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| 88 | data='export FLEXPART_ROOT_SCRIPTS='+c.ec_flexpart_root_scripts |
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| 89 | else: |
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| 90 | data='export FLEXPART_ROOT_SCRIPTS=$HOME' |
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| 91 | |
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| 92 | fo.write(data+'\n') |
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| 93 | f.close() |
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| 94 | fo.close() |
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| 95 | |
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| 96 | if target.lower()!='local': |
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| 97 | template=ecd+'python/job.temp.o' |
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| 98 | with open(template) as f: |
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| 99 | fdata = f.read().split('\n') |
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| 100 | f.close() |
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| 101 | fo=open(template[:-2],'w') |
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| 102 | for data in fdata: |
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| 103 | if '--workdir' in data: |
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| 104 | data='#SBATCH --workdir=/scratch/ms/'+c.ecgid+'/'+c.ecuid |
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| 105 | if '##PBS -o' in data: |
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| 106 | data='##PBS -o /scratch/ms/'+c.ecgid+'/'+c.ecuid+'flex_ecmwf.$Jobname.$Job_ID.out' |
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| 107 | if 'export PATH=${PATH}:' in data: |
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| 108 | data+=c.ec_flexpart_root_scripts+'/flex_extract_v7.0.4/python' |
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| 109 | |
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| 110 | if 'cat>>' in data or 'cat >>' in data: |
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| 111 | i=data.index('>') |
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| 112 | fo.write(data[:i]+data[i+1:]+'\n') |
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| 113 | fo.write('GATEWAY '+c.gateway+'\n') |
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| 114 | fo.write('DESTINATION '+c.destination+'\n') |
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| 115 | fo.write('EOF\n') |
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| 116 | |
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| 117 | fo.write(data+'\n') |
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| 118 | fo.close() |
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| 119 | |
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| 120 | job=ecd+'python/ECMWF_ENV' |
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| 121 | fo=open(job,'w') |
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| 122 | fo.write('ECUID '+c.ecuid+'\n') |
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| 123 | fo.write('ECGID '+c.ecgid+'\n') |
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| 124 | fo.write('GATEWAY '+c.gateway+'\n') |
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| 125 | fo.write('DESTINATION '+c.destination+'\n') |
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| 126 | fo.close() |
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| 127 | |
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| 128 | |
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| 129 | |
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| 130 | if target.lower()=='local': |
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| 131 | # compile CONVERT2 |
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| 132 | if c.flexpart_root_scripts==None or c.flexpart_root_scripts=='../': |
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| 133 | print 'Warning: FLEXPART_ROOT_SCRIPTS has not been specified' |
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| 134 | print 'Only CONVERT2 will be compiled in '+ecd+'/../src' |
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| 135 | else: |
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| 136 | c.flexpart_root_scripts=os.path.expandvars(os.path.expanduser(c.flexpart_root_scripts)) |
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| 137 | if os.path.abspath(ecd)!=os.path.abspath(c.flexpart_root_scripts): |
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| 138 | os.chdir('/') |
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| 139 | p=subprocess.check_call(['tar','-cvf',ecd+'../flex_extract_v7.0.4.tar',ecd+'python',ecd+'grib_templates',ecd+'src']) |
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| 140 | try: |
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| 141 | os.makedirs(c.flexpart_root_scripts+'/flex_extract_v7.0.4') |
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| 142 | except: |
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| 143 | pass |
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| 144 | os.chdir(c.flexpart_root_scripts+'/flex_extract_v7.0.4') |
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| 145 | p=subprocess.check_call(['tar','-xvf',ecd+'../flex_extract_v7.0.4.tar']) |
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| 146 | os.chdir(c.flexpart_root_scripts+'/flex_extract_v7.0.4/src') |
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| 147 | |
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| 148 | os.chdir('../src') |
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| 149 | print 'install flex_extract_v7.0.4 software on '+target+' in directory '+os.getcwd() |
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| 150 | if c.makefile==None: |
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| 151 | makefile='Makefile.local.ifort' |
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| 152 | else: |
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| 153 | makefile=c.makefile |
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| 154 | flist=glob.glob('*.mod')+glob.glob('*.o') |
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| 155 | if flist: |
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| 156 | p=subprocess.check_call(['rm']+flist) |
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| 157 | try: |
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| 158 | print 'Using makefile: '+makefile |
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| 159 | p=subprocess.check_call(['make','-f',makefile]) |
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| 160 | p=subprocess.check_call(['ls','-l','CONVERT2']) |
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| 161 | except: |
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| 162 | print 'compile failed - please edit '+makefile+' or try another Makefile in the src directory.' |
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| 163 | print 'most likely GRIB_API_INCLUDE_DIR, GRIB_API_LIB and EMOSLIB must be adapted.' |
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| 164 | print 'Available Makefiles:' |
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| 165 | print glob.glob('Makefile*') |
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| 166 | |
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| 167 | elif target.lower()=='ecgate': |
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| 168 | os.chdir('/') |
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| 169 | p=subprocess.check_call(['tar','-cvf',ecd+'../flex_extract_v7.0.4.tar',ecd+'python',ecd+'grib_templates',ecd+'src']) |
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| 170 | try: |
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| 171 | p=subprocess.check_call(['ecaccess-file-put',ecd+'../flex_extract_v7.0.4.tar','ecgate:/home/ms/'+c.ecgid+'/'+c.ecuid+'/flex_extract_v7.0.4.tar']) |
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| 172 | except: |
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| 173 | print 'ecaccess-file-put failed! Probably the eccert key has expired.' |
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| 174 | exit(1) |
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| 175 | p=subprocess.check_call(['ecaccess-job-submit','-queueName',target,ecd+'python/compilejob.ksh']) |
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| 176 | print 'compilejob.ksh has been submitted to ecgate for installation in '+c.ec_flexpart_root_scripts+'/flex_extract_v7.0.4' |
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| 177 | print 'You should get an email with subject flexcompile within the next few minutes' |
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| 178 | elif target.lower()=='cca': |
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| 179 | os.chdir('/') |
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| 180 | p=subprocess.check_call(['tar','-cvf',ecd+'../flex_extract_v7.0.4.tar',ecd+'python',ecd+'grib_templates',ecd+'src']) |
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| 181 | try: |
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| 182 | p=subprocess.check_call(['ecaccess-file-put',ecd+'../flex_extract_v7.0.4.tar','cca:/home/ms/'+c.ecgid+'/'+c.ecuid+'/flex_extract_v7.0.4.tar']) |
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| 183 | except: |
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| 184 | print 'ecaccess-file-put failed! Probably the eccert key has expired.' |
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| 185 | exit(1) |
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| 186 | |
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| 187 | p=subprocess.check_call(['ecaccess-job-submit','-queueName',target,ecd+'python/compilejob.ksh']) |
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| 188 | print 'compilejob.ksh has been submitted to cca for installation in '+c.ec_flexpart_root_scripts+'/flex_extract_v7.0.4' |
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| 189 | print 'You should get an email with subject flexcompile within the next few minutes' |
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| 190 | else: |
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| 191 | print 'ERROR: unknown installation target ',target |
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| 192 | print 'Valid targets: ecgate, cca, local' |
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| 193 | return |
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| 194 | |
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| 195 | |
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| 196 | if __name__ == "__main__": |
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| 197 | main() |
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