#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#*******************************************************************************
# @Author: Leopold Haimberger (University of Vienna)
#
# @Date: November 2015
#
# @Change History:
#
# February 2018 - Anne Philipp (University of Vienna):
# - applied PEP8 style guide
# - added documentation
# - moved install_args_and_control in here
# - splitted code in smaller functions
# - delete fortran build files in here instead of compile job script
# - changed static path names to variables from config file
# - splitted install function into several smaller pieces
# - use of tarfile package in python
# June 2020 - Anne Philipp
# - renamed "convert" functions to "fortran" functions
# - reconfigured mk_tarball to select *.template files instead
# of *.nl and *.temp
# - added check for makefile settings
#
# @License:
# (C) Copyright 2014-2020.
# Anne Philipp, Leopold Haimberger
#
# SPDX-License-Identifier: CC-BY-4.0
#
# This work is licensed under the Creative Commons Attribution 4.0
# International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
#
# @Methods:
# main
# get_install_cmdline_args
# install_via_gateway
# check_install_conditions
# mk_tarball
# un_tarball
# mk_env_vars
# mk_compilejob
# mk_job_template
# del_fortran_build
# mk_fortran_build
#
#*******************************************************************************
'''This script installs the flex_extract program.
Depending on the selected installation environment (locally or on the
ECMWF server ecgate or cca) the program extracts the command line
arguments and the CONTROL file parameter and prepares the corresponding
environment.
The necessary files are collected in a tar ball and placed
at the target location. There, is is untared, the environment variables are
set, and the Fortran code is compiled.
If the ECMWF environment is selected, a job script is prepared and submitted
for the remaining configurations after putting the tar ball on the
target ECMWF server.
Type: install.py --help
to get information about command line parameters.
Read the documentation for usage instructions.
'''
# ------------------------------------------------------------------------------
# MODULES
# ------------------------------------------------------------------------------
from __future__ import print_function
import os
import sys
import subprocess
import tarfile
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
# software specific classes and modules from flex_extract
import _config
from Classes.ControlFile import ControlFile
from Classes.UioFiles import UioFiles
from Mods.tools import (make_dir, put_file_to_ecserver, submit_job_to_ecserver,
silent_remove, execute_subprocess, none_or_str)
# ------------------------------------------------------------------------------
# FUNCTIONS
# ------------------------------------------------------------------------------
[docs]def main():
'''Controls the installation process. Calls the installation function
if target is specified.
Parameters
----------
Return
------
'''
args = get_install_cmdline_args()
c = ControlFile(args.controlfile)
c.assign_args_to_control(args)
check_install_conditions(c)
if c.install_target.lower() != 'local': # ecgate or cca
install_via_gateway(c)
else: # local
install_local(c)
return
[docs]def get_install_cmdline_args():
'''Decomposes the command line arguments and assigns them to variables.
Apply default values for arguments not present.
Parameters
----------
Return
------
args : Namespace
Contains the commandline arguments from script/program call.
'''
parser = ArgumentParser(description='Install flex_extract software '
'locally or on ECMWF machines',
formatter_class=ArgumentDefaultsHelpFormatter)
parser.add_argument('--target', dest='install_target',
type=none_or_str, default=None,
help="Valid targets: local | ecgate | cca , \
the latter two are at ECMWF")
parser.add_argument("--makefile", dest="makefile",
type=none_or_str, default=None,
help='Name of makefile for compiling the '
'Fortran program')
parser.add_argument("--ecuid", dest="ecuid",
type=none_or_str, default=None,
help='User id at ECMWF')
parser.add_argument("--ecgid", dest="ecgid",
type=none_or_str, default=None,
help='Group id at ECMWF')
parser.add_argument("--gateway", dest="gateway",
type=none_or_str, default=None,
help='Name of the local gateway server')
parser.add_argument("--destination", dest="destination",
type=none_or_str, default=None,
help='ecaccess association, e.g. '
'myUser@genericSftp')
parser.add_argument("--installdir", dest="installdir",
type=none_or_str, default=None,
help='Root directory of the '
'flex_extract installation')
# arguments for job submission to ECMWF, only needed by submit.py
parser.add_argument("--job_template", dest='job_template',
type=none_or_str, default="job.template",
help='Rudimentary template file to create a batch '
'job template for submission to ECMWF servers')
parser.add_argument("--controlfile", dest="controlfile",
type=none_or_str, default='CONTROL_EA5',
help="A file that contains all CONTROL parameters.")
args = parser.parse_args()
return args
[docs]def install_via_gateway(c):
'''Prepare data transfer to remote gateway and submit a job script which will
install everything on the remote gateway.
Parameters
----------
c : ControlFile
Contains all the parameters of CONTROL file and
command line.
Return
------
'''
tarball_name = _config.FLEXEXTRACT_DIRNAME + '.tar'
tar_file = os.path.join(_config.PATH_FLEXEXTRACT_DIR, tarball_name)
mk_compilejob(c.makefile, c.ecuid, c.ecgid, c.installdir)
mk_job_template(c.ecuid, c.ecgid, c.installdir)
mk_env_vars(c.ecuid, c.ecgid, c.gateway, c.destination)
mk_tarball(tar_file, c.install_target)
put_file_to_ecserver(_config.PATH_FLEXEXTRACT_DIR, tarball_name,
c.install_target, c.ecuid, c.ecgid)
submit_job_to_ecserver(c.install_target,
os.path.join(_config.PATH_REL_JOBSCRIPTS,
_config.FILE_INSTALL_COMPILEJOB))
silent_remove(tar_file)
print('Job compilation script has been submitted to ecgate for ' +
'installation in ' + c.installdir +
'/' + _config.FLEXEXTRACT_DIRNAME)
print('You should get an email with subject "flexcompile" within ' +
'the next few minutes!')
return
[docs]def install_local(c):
'''Perform the actual installation on a local machine.
Parameters
----------
c : ControlFile
Contains all the parameters of CONTROL file and
command line.
Return
------
'''
tar_file = os.path.join(_config.PATH_FLEXEXTRACT_DIR,
_config.FLEXEXTRACT_DIRNAME + '.tar')
if c.installdir == _config.PATH_FLEXEXTRACT_DIR:
print('WARNING: installdir has not been specified')
print('flex_extract will be installed in here by compiling the ' +
'Fortran source in ' + _config.PATH_FORTRAN_SRC)
os.chdir(_config.PATH_FORTRAN_SRC)
else: # creates the target working directory for flex_extract
c.installdir = os.path.expandvars(os.path.expanduser(
c.installdir))
if os.path.abspath(_config.PATH_FLEXEXTRACT_DIR) != \
os.path.abspath(c.installdir):
mk_tarball(tar_file, c.install_target)
make_dir(os.path.join(c.installdir,
_config.FLEXEXTRACT_DIRNAME))
os.chdir(os.path.join(c.installdir,
_config.FLEXEXTRACT_DIRNAME))
un_tarball(tar_file)
os.chdir(os.path.join(c.installdir,
_config.FLEXEXTRACT_DIRNAME,
_config.PATH_REL_FORTRAN_SRC))
# Create Fortran executable
print('Install ' + _config.FLEXEXTRACT_DIRNAME + ' software at ' +
c.install_target + ' in directory ' +
os.path.abspath(c.installdir) + '\n')
del_fortran_build('.')
mk_fortran_build('.', c.makefile)
os.chdir(_config.PATH_FLEXEXTRACT_DIR)
if os.path.isfile(tar_file):
os.remove(tar_file)
return
[docs]def check_install_conditions(c):
'''Checks necessary attributes and conditions
for the installation, e.g. whether they exist and contain values.
Otherwise set default values.
Parameters
----------
c : ControlFile
Contains all the parameters of CONTROL file and
command line.
Return
------
'''
if c.install_target and \
c.install_target not in _config.INSTALL_TARGETS:
print('ERROR: unknown or missing installation target ')
print('target: ', c.install_target)
print('please specify correct installation target ' +
str(_config.INSTALL_TARGETS))
print('use -h or --help for help')
sys.exit(1)
if c.install_target and c.install_target != 'local':
if not c.ecgid or not c.ecuid:
print('Please enter your ECMWF user id and group id '
' with command line options --ecuid --ecgid')
print('Try "' + sys.argv[0].split('/')[-1] + \
' -h" to print usage information')
print('Please consult ecaccess documentation or ECMWF user '
'support for further details.\n')
sys.exit(1)
if not c.gateway or not c.destination:
print('WARNING: Parameters GATEWAY and DESTINATION were '
'not properly set for working on ECMWF server. \n'
'There will be no transfer of output files to the '
'local gateway server possible!')
if not c.installdir:
c.installdir = '${HOME}'
else: # local
if not c.installdir:
c.installdir = _config.PATH_FLEXEXTRACT_DIR
if not c.makefile:
print('WARNING: no makefile was specified.')
if c.install_target == 'local':
c.makefile = 'makefile_local_gfortran'
print('WARNING: default makefile selected: makefile_local_gfortan')
elif c.install_target == 'ecgate':
c.makefile = 'makefile_ecgate'
print('WARNING: default makefile selected: makefile_ecgate')
elif c.install_target == 'cca' or \
c.install_target == 'ccb':
c.makefile = 'makefile_cray'
print('WARNING: default makefile selected: makefile_cray')
else:
pass
return
[docs]def mk_tarball(tarball_path, target):
'''Creates a tarball with all necessary files which need to be sent to the
installation directory.
It does not matter whether this is local or remote.
Collects all Python files, the Fortran source and makefiles,
the ECMWF_ENV file, the CONTROL files as well as the
template files.
Parameters
----------
tarball_path : str
The complete path to the tar file which will contain all
relevant data for flex_extract.
target : str
The queue where the job is submitted to.
Return
------
'''
print('Create tarball ...')
# change to FLEXEXTRACT directory so that the tar can contain
# relative pathes to the files and directories
ecd = _config.PATH_FLEXEXTRACT_DIR + '/'
os.chdir(ecd)
# get lists of the files to be added to the tar file
if target == 'local':
ecmwf_env_file = []
runfile = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_RUN_DIR,
'run_local.sh').files]
else:
ecmwf_env_file = [_config.PATH_REL_ECMWF_ENV]
runfile = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_RUN_DIR,
'run.sh').files]
pyfiles = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_PYTHON_SRC, '*py').files]
pytestfiles = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_PYTHONTEST_SRC, '*py').files]
controlfiles = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_CONTROLFILES,
'CONTROL*').files]
testfiles = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_TEST+"/Installation", '*').files]
tempfiles = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_TEMPLATES, '*.template').files]
gribtable = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_TEMPLATES, '*grib*').files]
ffiles = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, '*.f90').files]
hfiles = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, '*.h').files]
makefiles = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_FORTRAN_SRC, 'makefile*').files]
jobdir = [os.path.relpath(x, ecd)
for x in UioFiles(_config.PATH_REL_JOBSCRIPTS, '*.md').files]
# concatenate single lists to one for a better looping
filelist = pyfiles + pytestfiles + controlfiles + tempfiles + \
ffiles + gribtable + hfiles + makefiles + ecmwf_env_file + \
runfile + jobdir + testfiles +\
['CODE_OF_CONDUCT.md', 'LICENSE.md', 'README.md']
# create installation tar-file
exclude_files = [".ksh", ".tar"]
try:
with tarfile.open(tarball_path, "w:gz") as tar_handle:
for filename in filelist:
tar_handle.add(filename, recursive=False,
filter=lambda tarinfo: None
if os.path.splitext(tarinfo.name)[1]
in exclude_files
else tarinfo)
except tarfile.TarError as e:
print('... ERROR: ' + str(e))
sys.exit('\n... error occured while trying to create the tar-file ' +
str(tarball_path))
return
[docs]def un_tarball(tarball_path):
'''Extracts the given tarball into current directory.
Parameters
----------
tarball_path : str
The complete path to the tar file which will contain all
relevant data for flex_extract.
Return
------
'''
print('Untar ...')
try:
with tarfile.open(tarball_path) as tar_handle:
tar_handle.extractall()
except tarfile.TarError as e:
sys.exit('\n... error occured while trying to read tar-file ' +
str(tarball_path))
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... error occured while trying to read tar-file ' +
str(tarball_path))
return
[docs]def mk_env_vars(ecuid, ecgid, gateway, destination):
'''Creates a file named ECMWF_ENV which contains the
necessary environmental variables at ECMWF servers.
It is based on the template ECMWF_ENV.template.
Parameters
----------
ecuid : str
The user id on ECMWF server.
ecgid : str
The group id on ECMWF server.
gateway : str
The gateway server the user is using.
destination : str
The remote destination which is used to transfer files
from ECMWF server to local gateway server.
Return
------
'''
from genshi.template.text import NewTextTemplate
from genshi.template import TemplateLoader
from genshi.template.eval import UndefinedError
try:
loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False)
ecmwfvars_template = loader.load(_config.TEMPFILE_USER_ENVVARS,
cls=NewTextTemplate)
stream = ecmwfvars_template.generate(user_name=ecuid,
user_group=ecgid,
gateway_name=gateway,
destination_name=destination
)
except UndefinedError as e:
print('... ERROR ' + str(e))
sys.exit('\n... error occured while trying to generate template ' +
_config.PATH_ECMWF_ENV)
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... error occured while trying to generate template ' +
_config.PATH_ECMWF_ENV)
try:
with open(_config.PATH_ECMWF_ENV, 'w') as f:
f.write(stream.render('text'))
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... error occured while trying to write ' +
_config.PATH_ECMWF_ENV)
return
[docs]def mk_compilejob(makefile, ecuid, ecgid, fp_root):
'''Modifies the original job template file so that it is specified
for the user and the environment were it will be applied. Result
is stored in a new file "job.temp" in the python directory.
Parameters
----------
makefile : str
Name of the makefile which should be used to compile the Fortran
program.
ecuid : str
The user id on ECMWF server.
ecgid : str
The group id on ECMWF server.
fp_root : str
Path to the root directory of FLEXPART environment or flex_extract
environment.
Return
------
'''
from genshi.template.text import NewTextTemplate
from genshi.template import TemplateLoader
from genshi.template.eval import UndefinedError
if fp_root == '../':
fp_root = '$HOME'
try:
loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False)
compile_template = loader.load(_config.TEMPFILE_INSTALL_COMPILEJOB,
cls=NewTextTemplate)
stream = compile_template.generate(
usergroup=ecgid,
username=ecuid,
version_number=_config._VERSION_STR,
fp_root_scripts=fp_root,
makefile=makefile,
fortran_program=_config.FORTRAN_EXECUTABLE
)
except UndefinedError as e:
print('... ERROR ' + str(e))
sys.exit('\n... error occured while trying to generate template ' +
_config.TEMPFILE_INSTALL_COMPILEJOB)
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... error occured while trying to generate template ' +
_config.TEMPFILE_INSTALL_COMPILEJOB)
try:
compilejob = os.path.join(_config.PATH_JOBSCRIPTS,
_config.FILE_INSTALL_COMPILEJOB)
with open(compilejob, 'w') as f:
f.write(stream.render('text'))
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... error occured while trying to write ' +
compilejob)
return
[docs]def mk_job_template(ecuid, ecgid, fp_root):
'''Modifies the original job template file so that it is specified
for the user and the environment were it will be applied. Result
is stored in a new file.
Parameters
----------
ecuid : str
The user id on ECMWF server.
ecgid : str
The group id on ECMWF server.
fp_root : str
Path to the root directory of FLEXPART environment or flex_extract
environment.
Return
------
'''
from genshi.template.text import NewTextTemplate
from genshi.template import TemplateLoader
from genshi.template.eval import UndefinedError
fp_root_path_to_python = os.path.join(fp_root,
_config.FLEXEXTRACT_DIRNAME,
_config.PATH_REL_PYTHON_SRC)
if '$' in fp_root_path_to_python:
ind = fp_root_path_to_python.index('$')
fp_root_path_to_python = fp_root_path_to_python[0:ind] + '$' + \
fp_root_path_to_python[ind:]
try:
loader = TemplateLoader(_config.PATH_TEMPLATES, auto_reload=False)
compile_template = loader.load(_config.TEMPFILE_INSTALL_JOB,
cls=NewTextTemplate)
stream = compile_template.generate(
usergroup=ecgid,
username=ecuid,
version_number=_config._VERSION_STR,
fp_root_path=fp_root_path_to_python,
)
except UndefinedError as e:
print('... ERROR ' + str(e))
sys.exit('\n... error occured while trying to generate template ' +
_config.TEMPFILE_INSTALL_JOB)
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... error occured while trying to generate template ' +
_config.TEMPFILE_INSTALL_JOB)
try:
tempjobfile = os.path.join(_config.PATH_TEMPLATES,
_config.TEMPFILE_JOB)
with open(tempjobfile, 'w') as f:
f.write(stream.render('text'))
except OSError as e:
print('... ERROR CODE: ' + str(e.errno))
print('... ERROR MESSAGE:\n \t ' + str(e.strerror))
sys.exit('\n... error occured while trying to write ' +
tempjobfile)
return
[docs]def del_fortran_build(src_path):
'''Clean up the Fortran source directory and remove all
build files (e.g. \*.o, \*.mod and FORTRAN EXECUTABLE)
Parameters
----------
src_path : str
Path to the fortran source directory.
Return
------
'''
modfiles = UioFiles(src_path, '*.mod')
objfiles = UioFiles(src_path, '*.o')
exefile = UioFiles(src_path, _config.FORTRAN_EXECUTABLE)
modfiles.delete_files()
objfiles.delete_files()
exefile.delete_files()
return
[docs]def mk_fortran_build(src_path, makefile):
'''Compiles the Fortran code and generates the executable.
Parameters
----------
src_path : str
Path to the fortran source directory.
makefile : str
The name of the makefile which should be used.
Return
------
'''
try:
print('Using makefile: ' + makefile)
p = subprocess.Popen(['make', '-f',
os.path.join(src_path, makefile)],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
bufsize=1)
pout, perr = p.communicate()
print(pout.decode())
if p.returncode != 0:
print(perr.decode())
print('Please edit ' + makefile +
' or try another makefile in the src directory.')
print('Most likely ECCODES_INCLUDE_DIR, ECCODES_LIB '
'and EMOSLIB must be adapted.')
print('Available makefiles:')
print(UioFiles(src_path, 'makefile*'))
sys.exit('Compilation failed!')
except ValueError as e:
print('ERROR: makefile call failed:')
print(e)
else:
execute_subprocess(['ls', '-l',
os.path.join(src_path, _config.FORTRAN_EXECUTABLE)],
error_msg='FORTRAN EXECUTABLE COULD NOT BE FOUND!')
return
if __name__ == "__main__":
main()