[d69b677] | 1 | #!/usr/bin/env python |
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[a4b6cef] | 2 | # |
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[d69b677] | 3 | # This software is licensed under the terms of the Apache Licence Version 2.0 |
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[a4b6cef] | 4 | # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. |
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| 5 | # |
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[d69b677] | 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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[a4b6cef] | 9 | # Extension November 2015 - Leopold Haimberger - University of Vienna for: |
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[d69b677] | 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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[a4b6cef] | 17 | # |
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[d69b677] | 18 | # |
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| 19 | # Further documentation may be obtained from www.flexpart.eu |
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[a4b6cef] | 20 | # |
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| 21 | # Requirements: |
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[d69b677] | 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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[a4b6cef] | 27 | # |
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[d69b677] | 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 | def main(): |
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[a4b6cef] | 48 | ''' |
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| 49 | ''' |
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| 50 | # calledfromdir = os.getcwd() |
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[d69b677] | 51 | os.chdir(localpythonpath) |
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[a4b6cef] | 52 | args, c = install_args_and_control() |
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[d69b677] | 53 | # if c.outputdir[0]!='/': |
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[a4b6cef] | 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 is not None: |
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| 57 | install_via_gateway(c, args.install_target) |
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[d69b677] | 58 | else: |
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[a4b6cef] | 59 | print('Please specify installation target (local|ecgate|cca)') |
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| 60 | print('use -h or --help for help') |
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[d69b677] | 61 | sys.exit() |
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[a4b6cef] | 62 | |
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| 63 | def install_via_gateway(c, target): |
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| 64 | |
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| 65 | ecd = c.ecmwfdatadir |
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| 66 | template = ecd + 'python/compilejob.temp' |
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| 67 | job = ecd + 'python/compilejob.ksh' |
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| 68 | fo = open(job, 'w') |
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| 69 | #AP could do with open(template) as f, open(job, 'w') as fo: |
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| 70 | #AP or nested with statements |
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[d69b677] | 71 | with open(template) as f: |
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[a4b6cef] | 72 | fdata = f.read().split('\n') |
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| 73 | for data in fdata: |
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| 74 | if 'MAKEFILE=' in data: |
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| 75 | if c.makefile is not None: |
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| 76 | data = 'export MAKEFILE=' + c.makefile |
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| 77 | if 'FLEXPART_ROOT_SCRIPTS=' in data: |
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| 78 | if c.flexpart_root_scripts != '../': |
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| 79 | data = 'export FLEXPART_ROOT_SCRIPTS=' + \ |
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| 80 | c.flexpart_root_scripts |
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| 81 | else: |
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| 82 | data='export FLEXPART_ROOT_SCRIPTS=$HOME' |
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| 83 | if target.lower() != 'local': |
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| 84 | if '--workdir' in data: |
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| 85 | data = '#SBATCH --workdir=/scratch/ms/' + c.ecgid + \ |
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| 86 | '/' + c.ecuid |
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| 87 | if '##PBS -o' in data: |
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| 88 | data = '##PBS -o /scratch/ms/' + c.ecgid + '/' + c.ecuid + \ |
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| 89 | 'flex_ecmwf.$Jobname.$Job_ID.out' |
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| 90 | if 'FLEXPART_ROOT_SCRIPTS=' in data: |
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| 91 | if c.ec_flexpart_root_scripts != '../': |
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| 92 | data = 'export FLEXPART_ROOT_SCRIPTS=' + \ |
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| 93 | c.ec_flexpart_root_scripts |
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| 94 | else: |
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| 95 | data = 'export FLEXPART_ROOT_SCRIPTS=$HOME' |
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| 96 | fo.write(data + '\n') |
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[d69b677] | 97 | f.close() |
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| 98 | fo.close() |
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[a4b6cef] | 99 | |
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| 100 | if target.lower() != 'local': |
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| 101 | template = ecd + 'python/job.temp.o' |
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| 102 | #AP hier eventuell Zeile für Zeile lesen und dann if Entscheidung |
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| 103 | with open(template) as f: |
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| 104 | fdata = f.read().split('\n') |
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| 105 | f.close() |
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| 106 | fo = open(template[:-2], 'w') |
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| 107 | for data in fdata: |
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| 108 | if '--workdir' in data: |
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| 109 | data = '#SBATCH --workdir=/scratch/ms/' + c.ecgid + \ |
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| 110 | '/' + c.ecuid |
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| 111 | if '##PBS -o' in data: |
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| 112 | data = '##PBS -o /scratch/ms/' + c.ecgid + '/' + \ |
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| 113 | c.ecuid + 'flex_ecmwf.$Jobname.$Job_ID.out' |
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| 114 | if 'export PATH=${PATH}:' in data: |
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| 115 | data += c.ec_flexpart_root_scripts + '/ECMWFDATA7.0/python' |
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| 116 | if 'cat>>' in data or 'cat >>' in data: |
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| 117 | i = data.index('>') |
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| 118 | fo.write(data[:i] + data[i+1:] + '\n') |
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| 119 | fo.write('GATEWAY ' + c.gateway + '\n') |
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| 120 | fo.write('DESTINATION ' + c.destination + '\n') |
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| 121 | fo.write('EOF\n') |
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| 122 | |
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| 123 | fo.write(data + '\n') |
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| 124 | fo.close() |
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| 125 | |
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| 126 | job = ecd + 'python/ECMWF_ENV' |
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| 127 | with open(job, 'w') as fo: |
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| 128 | fo.write('ECUID ' + c.ecuid + '\n') |
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| 129 | fo.write('ECGID ' + c.ecgid + '\n') |
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| 130 | fo.write('GATEWAY ' + c.gateway + '\n') |
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| 131 | fo.write('DESTINATION ' + c.destination + '\n') |
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| 132 | fo.close() |
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| 133 | |
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| 134 | |
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| 135 | |
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| 136 | if target.lower() == 'local': |
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[d69b677] | 137 | # compile CONVERT2 |
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[a4b6cef] | 138 | if c.flexpart_root_scripts is None or c.flexpart_root_scripts == '../': |
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| 139 | print('Warning: FLEXPART_ROOT_SCRIPTS has not been specified') |
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| 140 | print('Only CONVERT2 will be compiled in ' + ecd + '/../src') |
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| 141 | else: |
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| 142 | c.flexpart_root_scripts = os.path.expandvars(os.path.expanduser( |
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| 143 | c.flexpart_root_scripts)) |
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| 144 | if os.path.abspath(ecd) != os.path.abspath(c.flexpart_root_scripts): |
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| 145 | os.chdir('/') |
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| 146 | p = subprocess.check_call(['tar', '-cvf', |
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| 147 | ecd + '../ECMWFDATA7.0.tar', |
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| 148 | ecd + 'python', |
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| 149 | ecd + 'grib_templates', |
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| 150 | ecd + 'src']) |
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| 151 | try: |
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| 152 | os.makedirs(c.flexpart_root_scripts + '/ECMWFDATA7.0') |
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| 153 | except: |
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| 154 | pass |
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| 155 | os.chdir(c.flexpart_root_scripts + '/ECMWFDATA7.0') |
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| 156 | p = subprocess.check_call(['tar', '-xvf', |
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| 157 | ecd + '../ECMWFDATA7.0.tar']) |
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| 158 | os.chdir(c.flexpart_root_scripts + '/ECMWFDATA7.0/src') |
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| 159 | |
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| 160 | os.chdir('../src') |
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| 161 | print(('install ECMWFDATA7.0 software on ' + target + ' in directory ' |
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| 162 | + os.getcwd())) |
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| 163 | if c.makefile is None: |
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| 164 | makefile = 'Makefile.local.ifort' |
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| 165 | else: |
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| 166 | makefile = c.makefile |
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| 167 | flist = glob.glob('*.mod') + glob.glob('*.o') |
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| 168 | if flist: |
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| 169 | p = subprocess.check_call(['rm'] + flist) |
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[d69b677] | 170 | try: |
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[a4b6cef] | 171 | print(('Using makefile: ' + makefile)) |
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| 172 | p = subprocess.check_call(['make', '-f', makefile]) |
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| 173 | p = subprocess.check_call(['ls', '-l',' CONVERT2']) |
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| 174 | except: |
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| 175 | print('compile failed - please edit ' + makefile + |
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| 176 | ' or try another Makefile in the src directory.') |
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| 177 | print('most likely GRIB_API_INCLUDE_DIR, GRIB_API_LIB \ |
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| 178 | and EMOSLIB must be adapted.') |
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| 179 | print('Available Makefiles:') |
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| 180 | print(glob.glob('Makefile*')) |
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| 181 | |
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| 182 | elif target.lower() == 'ecgate': |
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[d69b677] | 183 | os.chdir('/') |
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[a4b6cef] | 184 | p = subprocess.check_call(['tar', '-cvf', |
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| 185 | ecd + '../ECMWFDATA7.0.tar', |
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| 186 | ecd + 'python', |
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| 187 | ecd + 'grib_templates', |
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| 188 | ecd + 'src']) |
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| 189 | try: |
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| 190 | p = subprocess.check_call(['ecaccess-file-put', |
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| 191 | ecd + '../ECMWFDATA7.0.tar', |
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| 192 | 'ecgate:/scratch/ms/' + c.ecgid + '/' + |
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| 193 | c.ecuid + '/ECMWFDATA7.0.tar']) |
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| 194 | except: |
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| 195 | print('ecaccess-file-put failed! Probably the eccert key has expired.') |
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| 196 | exit(1) |
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| 197 | p = subprocess.check_call(['ecaccess-job-submit', |
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| 198 | '-queueName', |
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| 199 | target, |
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| 200 | ecd + 'python/compilejob.ksh']) |
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| 201 | print('compilejob.ksh has been submitted to ecgate for \ |
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| 202 | installation in ' + c.ec_flexpart_root_scripts + |
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| 203 | '/ECMWFDATA7.0') |
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| 204 | print('You should get an email with subject flexcompile within \ |
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| 205 | the next few minutes') |
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| 206 | |
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| 207 | elif target.lower() == 'cca': |
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[d69b677] | 208 | os.chdir('/') |
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[a4b6cef] | 209 | p = subprocess.check_call(['tar', '-cvf', |
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| 210 | ecd + '../ECMWFDATA7.0.tar', |
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| 211 | ecd + 'python', |
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| 212 | ecd + 'grib_templates', |
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| 213 | ecd + 'src']) |
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| 214 | try: |
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| 215 | p = subprocess.check_call(['ecaccess-file-put', |
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| 216 | ecd + '../ECMWFDATA7.0.tar', |
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| 217 | 'cca:/scratch/ms/' + c.ecgid + '/' + |
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| 218 | c.ecuid + '/ECMWFDATA7.0.tar']) |
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| 219 | except: |
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| 220 | print('ecaccess-file-put failed! \ |
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| 221 | Probably the eccert key has expired.') |
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| 222 | exit(1) |
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| 223 | |
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| 224 | p=subprocess.check_call(['ecaccess-job-submit', |
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| 225 | '-queueName', |
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| 226 | target, |
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| 227 | ecd + 'python/compilejob.ksh'])) |
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| 228 | print('compilejob.ksh has been submitted to cca for installation in ' + |
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| 229 | c.ec_flexpart_root_scripts + '/ECMWFDATA7.0') |
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| 230 | print('You should get an email with subject flexcompile \ |
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| 231 | within the next few minutes') |
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[d69b677] | 232 | else: |
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[a4b6cef] | 233 | print('ERROR: unknown installation target ', target) |
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| 234 | print('Valid targets: ecgate, cca, local') |
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| 235 | |
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[d69b677] | 236 | return |
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| 237 | |
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[a4b6cef] | 238 | |
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[d69b677] | 239 | if __name__ == "__main__": |
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| 240 | main() |
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