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preconfigure.py
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preconfigure.py
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#!/usr/bin/env python
## \file configure.py
# \brief An extended configuration script.
# \author T. Albring
# \version 7.0.0 "Blackbird"
#
# SU2 Project Website: https://su2code.github.io
#
# The SU2 Project is maintained by the SU2 Foundation
# (http://su2foundation.org)
#
# Copyright 2012-2019, SU2 Contributors (cf. AUTHORS.md)
#
# SU2 is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# SU2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with SU2. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function, division, absolute_import
from optparse import OptionParser, BadOptionError
import sys,time, os, subprocess, os.path, glob, re, shutil, fileinput
from subprocess import call
# "Pass-through" option parsing -- an OptionParser that ignores
# unknown options and lets them pile up in the leftover argument
# list. Useful to pass unknown arguments to the automake configure.
class PassThroughOptionParser(OptionParser):
def _process_long_opt(self, rargs, values):
try:
OptionParser._process_long_opt(self, rargs, values)
except BadOptionError as err:
self.largs.append(err.opt_str)
def _process_short_opts(self, rargs, values):
try:
OptionParser._process_short_opts(self, rargs, values)
except BadOptionError as err:
self.largs.append(err.opt_str)
def main():
# Command Line Options
usage = './preconfigure.py [options]' \
'\nNote: Options not listed below are passed to the automake configure.' \
'\n Compiler flags must be set with \'export CFLAGS=...\' or \'export CXXFLAGS=...\' ' \
'\n before calling this script.'
parser = PassThroughOptionParser(usage = usage)
parser.add_option("--enable-direct-diff", action="store_true",
help="Enable direct differentiation mode support", dest="directdiff", default=False)
parser.add_option("--enable-autodiff", action="store_true",
help="Enable Automatic Differentiation support", dest="ad_support", default=False)
parser.add_option("--with-ad", action="store", type = "string", help="AD Tool, CODI/ADOLC", default="CODI", dest="adtool")
parser.add_option("--enable-mpi", action="store_true",
help="Enable mpi support", dest="mpi_enabled", default=False)
parser.add_option("--enable-PY_WRAPPER", action="store_true",
help="Enable Python wrapper compilation", dest="py_wrapper_enabled", default=False)
parser.add_option("--disable-tecio", action="store_true",
help="Disable Tecplot binary support", dest="tecio_disabled", default=False)
parser.add_option("--disable-normal", action="store_true",
help="Disable normal mode support", dest="normal_mode", default=False)
parser.add_option("-c" , "--check", action="store_true",
help="Check the source code for potential problems", dest="check", default=False)
parser.add_option("-r" , "--replace", action="store_true",
help="Do a search and replace of necessary symbols. Creates back up of source files.", dest="replace", default=False)
parser.add_option("-d" , "--delete", action="store_true",
help="Removes the back up files.", dest="remove", default=False)
parser.add_option("-v" , "--revert", action="store_true",
help="Revert files to original state.", dest="revert", default=False)
parser.add_option("-u", "--update", action="store_true",
help="Update and recompile submodules.", dest="update", default=False)
(options, args)=parser.parse_args()
options.adtool = options.adtool.upper()
if options.directdiff == False:
adtool_dd = ""
else:
adtool_dd = options.adtool
if options.ad_support == False:
adtool_da = ""
else:
adtool_da = options.adtool
conf_environ = os.environ
made_adolc = False
made_codi = False
header()
modes = {'SU2_BASE' : not options.normal_mode == True,
'SU2_DIRECTDIFF' : adtool_dd ,
'SU2_AD' : adtool_da }
# Create a dictionary from the arguments
argument_dict = dict(zip(args[::2],args[1::2]))
# Set the default installation path (if not set with --prefix)
argument_dict['--prefix'] = argument_dict.get('--prefix', os.getcwd().rstrip())
if not options.check:
if any([modes["SU2_AD"] == 'CODI', modes["SU2_DIRECTDIFF"] == 'CODI']):
conf_environ, made_codi = init_codi(argument_dict,modes,options.mpi_enabled, options.update)
configure(argument_dict,
conf_environ,
options.mpi_enabled,
options.py_wrapper_enabled,
options.tecio_disabled,
modes,
made_adolc,
made_codi)
if options.check:
prepare_source(options.replace, options.remove, options.revert)
def prepare_source(replace = False, remove = False, revert = False):
# Directories containing the source code
print('Preparing source code ...')
dir_list = [ "Common",
"SU2_CFD",
"SU2_DEF",
"SU2_DOT",
"SU2_GEO",
"SU2_SOL",
"SU2_MSH"]
file_list = ""
exclude_dic_lines = {}
exclude_dic_files = {}
exclude_file_name = 'preconf.exclude'
# # Build the dictionaries for line and file excludes that
# # are defined in the exlude file 'preconf.exclude'.
# # Syntax:
# # PathTo/File[:Line1,Line2,...]
# if os.path.exists(exclude_file_name):
# print 'Reading \'' + exclude_file_name + '\' ...'
# with open(exclude_file_name, 'r') as exclude:
# for line in exclude:
# exclude_line = line.split(':')
# exclude_file = exclude_line[0].rstrip()
# if len(exclude_line) > 1:
# exclude_lines = exclude_line[1].split(',')
# for index,item in enumerate(exclude_lines):
# exclude_lines[index] = int(item.rstrip())
# exclude_dic_lines[exclude_line[0].rstrip()] = exclude_lines
# else:
# exclude_dic_files[exclude_line[0].rstrip()] = [-1]
# else:
# print('Exclude file \'' + exclude_file_name + '\' not found. Checking all files.')
# Hardcoded files that will be skipped
exclude_dic_files = { 'Common/include/datatype_structure.hpp' : [-1],
'Common/include/datatype_structure.inl' : [-1],
'Common/include/mpi_structure.hpp' : [-1],
'Common/include/mpi_structure.inl' : [-1],
'Common/src/datatype_structure.cpp': [-1],
'Common/src/mpi_structure.cpp' : [-1] }
str_double = 'double'
regex_double = re.compile(r'(^|[^\w])('+str_double+')([^\w]|$)')
replacement_double = r'\1su2double\3'
simple_replacements = {'MPI_Reduce' : 'SU2_MPI::Reduce',
'MPI_Allreduce' : 'SU2_MPI::Allreduce',
'MPI_Gather' : 'SU2_MPI::Gather',
'MPI_Allgather' : 'SU2_MPI::Allgather',
'MPI_Isend' : 'SU2_MPI::Isend',
'MPI_Irecv' : 'SU2_MPI::Irecv',
'MPI_Send' : 'SU2_MPI::Send',
'MPI_Wait' : 'SU2_MPI::Wait',
'MPI_Waitall' : 'SU2_MPI::Waitall',
'MPI_Waitany' : 'SU2_MPI::Waitany',
'MPI_Bsend' : 'SU2_MPI::Bsend' ,
'MPI_Bcast' : 'SU2_MPI::Bcast',
'MPI_Sendrecv' : 'SU2_MPI::Sendrecv',
'MPI_Init' : 'SU2_MPI::Init',
'MPI_Recv' : 'SU2_MPI::Recv',
'MPI_Comm_size' : 'SU2_MPI::Comm_size',
'MPI_Comm_rank' : 'SU2_MPI::Comm_rank',
'MPI_Init' : 'SU2_MPI::Init',
'MPI_Barrier' : 'SU2_MPI::Barrier',
'MPI_Abort' : 'SU2_MPI::Abort',
'MPI_Request' : 'SU2_MPI::Request',
'MPI_Get_count' : 'SU2_MPI::Get_count',
'MPI_Finalize' : 'SU2_MPI::Finalize',
'MPI_Buffer_detach': 'SU2_MPI::Buffer_detach',
'MPI_Buffer_attach': 'SU2_MPI::Buffer_attach',
'MPI_Status' : 'SU2_MPI::Status',
'sprintf' : 'SPRINTF'}
regex_cast_1 = re.compile(r'(^|[^\w|^\\])(int)(\s*\()')
replacement_cast_1 = r'\1SU2_TYPE::Int\3'
regex_cast_2 = re.compile(r'\(int\)\s*')
logfile = open ('preconf.log','w')
backup_ext = '.orig'
print('Checking for problems...')
# Test each source file for the occurrence of missing replacements
# and print the respective lines.
for dir in dir_list:
file_list = glob.glob(dir+os.path.sep+'*[src,include]'+os.path.sep+'*[.cpp,.hpp,.inl]')
for file in file_list:
if not file in exclude_dic_files.keys():
if all([not replace, revert]):
# Check if back up file exists
if os.path.isfile(file + backup_ext):
os.remove(file);
shutil.copy(file + backup_ext, file)
else:
print('Cannot find backup file ' + file + backup_ext)
# Remove backup files if requested
if all([not replace, remove]):
if os.path.isfile(file + backup_ext):
print('Removing' + file + backup_ext)
os.remove(file + backup_ext)
if all([not remove, not revert]):
num_found = 0
found_line = ""
ignore_line = ""
new_line = ""
for line in fileinput.input(file, inplace = 1, backup = backup_ext):
new_line = line.rstrip('\n')
if any([re.findall(regex_double, line), find_all(line, simple_replacements), re.findall(regex_cast_1, line)]):
if not fileinput.lineno() in exclude_dic_lines.get(file,[]):
if replace:
new_line = replace_all(new_line, simple_replacements)
new_line = re.sub(regex_double, replacement_double, new_line)
new_line = re.sub(regex_cast_1, replacement_cast_1, new_line)
found_line = found_line + '\tLine ' + str(fileinput.lineno()) +': ' + line.rstrip() + '\n\t\t => ' + new_line.rstrip() + '\n'
else:
found_line = found_line + '\tLine ' + str(fileinput.lineno()) +': ' + line.rstrip() + '\n'
num_found = num_found + 1
else:
ignore_line = ignore_line + 'Ignoring line ' + str(fileinput.lineno()) + ' in ' + file + ' (' + line.rstrip() + ')\n'
print(new_line)
if num_found > 0:
if replace:
print('Solved ' + str(num_found) + ' potential problem(s) in ' + file + '.')
logfile.write('Solved ' + str(num_found) + ' potential problem(s) in ' + file + ':\n')
else:
print('Found ' + str(num_found) + ' potential problem(s) in ' + file + '.')
logfile.write('Found ' + str(num_found) + ' potential problem(s) in ' + file + ':\n')
logfile.write( found_line )
else:
os.remove(file + backup_ext)
if not ignore_line == "":
print(ignore_line.rstrip())
else:
print('Ignoring file ' + file)
print('\nPlease check preconf.log to get more information about potential problems.')
def replace_all(text, dic):
for i, j in dic.iteritems():
text = text.replace(i, j)
return text
def find_all(text, dic):
for i,j in dic.iteritems():
if not text.find(i) == -1:
return True
return False
def init_codi(argument_dict, modes, mpi_support = False, update = False):
modules_failed = True
# This information of the modules is used if projects was not cloned using git
# The sha tag must be maintained manually to point to the correct commit
sha_version_codi = 'bd4a639c2fe625a80946c8365bd2976a2868cf46'
github_repo_codi = 'https://github.com/scicompkl/CoDiPack'
sha_version_medi = '46a97e1d6e8fdd3cb42b06534cff6acad2a49693'
github_repo_medi = 'https://github.com/SciCompKL/MeDiPack'
medi_name = 'MeDiPack'
codi_name = 'CoDiPack'
alt_name_medi = 'externals/medi'
alt_name_codi = 'externals/codi'
# Some log and error files
log = open( 'preconf.log', 'w' )
err = open( 'preconf.err', 'w' )
pkg_environ = os.environ
codi_status = False
ampi_status = False
print("Checking the status of submodules")
print('=====================================================================')
# Remove modules if update is requested
if update:
if os.path.exists(alt_name_codi):
print('Removing ' + alt_name_codi)
shutil.rmtree(alt_name_codi)
if os.path.exists(alt_name_medi):
print('Removing ' + alt_name_medi)
shutil.rmtree(alt_name_medi)
submodule_check(codi_name, alt_name_codi, github_repo_codi, sha_version_codi, log, err, update)
if mpi_support:
submodule_check(medi_name, alt_name_medi, github_repo_medi, sha_version_medi, log, err, update)
return pkg_environ, True
def submodule_check(name, alt_name, github_rep, sha_tag, log, err, update = False):
try:
status = submodule_status(alt_name, update)
if status:
print('Found correct version of ' + name + ' in ' + alt_name + '.')
except RuntimeError:
if all([os.path.exists(alt_name), not os.path.exists(alt_name + '/' + sha_tag)]):
print('Found an old or unspecified version of ' + name + ' in ' + alt_name + '.\nUse -u to reset module.')
sys.exit()
if not os.path.exists(alt_name):
print('\ngit command failed (either git is not installed or this is not a git repository).')
print('\nUsing fall-back method to initialize submodule ' + name)
download_module(name, alt_name, github_rep, sha_tag, log, err)
else:
print('Found correct version of ' + name + ' in ' + alt_name + '.')
def submodule_status(path, update):
try:
status = check_output('git submodule status ' + path).decode()
except RuntimeError:
raise RuntimeError
status_indicator = status[0][0]
if status_indicator == '+':
sys.stderr.write('WARNING: the currently checked out submodule commit in ' + path + ' does not match the SHA-1 found in the index.\n')
sys.stderr.write('Use \'git submodule update --init '+ path + '\' to reset the module if necessary.\n')
return False
elif any([status_indicator == '-', update]):
print('Initialize submodule ' + path + ' using git ... ')
subprocess.check_call('git submodule update --init ' + path, shell = True)
return True
def download_module(name, alt_name, git_repo, commit_sha, logfile, errorfile):
print('\nInitializing ' + name + ' \'' + commit_sha + '\'')
print('=====================================================================')
# Download package
try:
print('Downloading module from ' + git_repo)
subprocess.check_call('wget -N ' + git_repo + '/archive/' + commit_sha + '.zip', stdout = logfile, stderr = errorfile, shell = True )
except subprocess.CalledProcessError:
print('Download of module ' + name + ' failed. See preconf.err for more information.')
print('To download it manually, perform the following steps:')
print('\t - Download the zip at \"' + git_repo + '/archive/' + commit_sha + '.zip\"')
print('\t - Extract the archive to externals/' + alt_name)
print('\t - Execute command \'touch externals/'+ alt_name + '/' + commit_sha + '\'')
print('\t - Run preconfigure.py again')
sys.exit()
# Extract zip archive
try:
print('Extracting archive ...')
subprocess.check_call('unzip -u ' + commit_sha + '.zip', stdout = logfile, stderr = errorfile, shell=True)
except subprocess.CalledProcessError:
print('Extraction of module ' + name + ' failed. See preconf.err for more information.')
sys.exit()
# Rename folder and create a file to identify the version
try:
print('Creating identifier ...')
subprocess.check_call('mv '+ name + '-' + commit_sha + ' ' + alt_name + ' && touch ' + alt_name + '/' + commit_sha, stdout = logfile, stderr = errorfile, shell = True)
except subprocess.CalledProcessError:
print('Renaming of module ' + name + ' failed. See preconf.err for more information.')
sys.exit()
# Remove archive
subprocess.check_call('rm ' + commit_sha + '.zip', shell=True)
def configure(argument_dict,
conf_environ,
mpi_support,
py_wrapper,
tecio,
modes,
made_adolc,
made_codi):
# Boostrap to generate Makefile.in
bootstrap_command = './bootstrap'
# Set the base command for running configure
configure_base = '../configure'
# Add the arguments to the configure command
for arg in argument_dict:
configure_base = configure_base + " " + arg + "=" + argument_dict[arg]
configure_mode = ''
if mpi_support:
configure_base = configure_base + ' --enable-mpi'
if py_wrapper:
configure_base = configure_base + ' --enable-PY_WRAPPER'
if tecio:
configure_base = configure_base + ' --disable-tecio'
build_dirs = ''
print( '\nPreparing build environment\n' \
'=====================================================================')
run_command(bootstrap_command, 'bootstrap.log', 'bootstrap.err', conf_environ)
# Create the commands for the different configurations and run configure
for key in modes:
if modes[key]:
print('\nRunning configure in folder ' + key + ' ', end = '')
if modes[key] == 'CODI':
if key == 'SU2_DIRECTDIFF':
configure_mode = '--enable-codi-forward'
if key == 'SU2_AD':
configure_mode = '--enable-codi-reverse'
print('using ' + modes[key])
elif modes[key] == 'ADOLC':
if key == 'SU2_DIRECTDIFF':
configure_mode = '--enable-adolc-forward'
if key == 'SU2_AD':
configure_mode = '--enable-adolc-reverse'
print('using ' + modes[key])
elif modes[key] == 'COMPLEX':
configure_mode = '--enable-complex'
print('using ' + modes[key])
else:
configure_mode = ''
print('')
print('=====================================================================')
log = os.getcwd().rstrip() + '/conf_'+ key+'.log'
err = os.getcwd().rstrip() + '/conf_'+ key+'.err'
if not os.path.exists(key):
os.mkdir(key)
os.chdir(key)
run_command(configure_base + ' ' + configure_mode, log, err, conf_environ)
os.chdir(os.pardir)
build_dirs += key + ' '
write_makefile(build_dirs)
print('\nPre-configuration Summary:\n' \
'=====================================================================\n'\
'\tConfiguration sets: '+ build_dirs + '\n')
print('\tUse "make <install>" to compile (and install) all configured binaries:\n')
if modes['SU2_BASE']:
print('\tSU2_CFD -> General solver for direct, cont. adjoint and linearized equations.\n' \
'\tSU2_DOT -> Gradient Projection Code.\n' \
'\tSU2_DEF -> Mesh Deformation Code.\n' \
'\tSU2_MSH -> Mesh Adaption Code.\n' \
'\tSU2_SOL -> Solution Export Code.\n' \
'\tSU2_GEO -> Geometry Definition Code.\n')
if modes['SU2_AD']:
print('\tSU2_CFD_AD -> Discrete Adjoint Solver and general AD support.')
print('\tSU2_DOT_AD -> Mesh sensitivity computation and general AD support.')
if modes['SU2_DIRECTDIFF']:
print('\tSU2_CFD_DIRECTDIFF -> Direct Differentation Mode.')
print('\n')
print('\tPlease be sure to add the $SU2_HOME and $SU2_RUN environment variables,\n' \
'\tand update your $PATH (and $PYTHONPATH if applicable) with $SU2_RUN.\n' \
'\n' \
'\tBased on the input to this configuration, add these lines to your .bashrc file: \n' \
'\n' \
'\texport SU2_RUN="'+argument_dict['--prefix']+'/bin"\n' \
'\texport SU2_HOME="'+os.getcwd().rstrip()+'"\n' \
'\texport PATH=$PATH:$SU2_RUN\n' \
'\texport PYTHONPATH=$PYTHONPATH:$SU2_RUN\n')
def run_command(command, log, err, env):
try:
logfile = open(log, 'w')
errfile = open(err, 'w')
print('Command: ' + command)
subprocess.check_call(command, env = env, stdout = logfile, stderr = errfile, shell=True)
print('Logfile written to ' + log)
logfile.close()
errfile.close()
except subprocess.CalledProcessError:
errfile = open(err, 'r')
print('\nThere was an error while running command \'' + command + '\'.')
print('=== Error Log ===')
print(errfile.read())
errfile.close()
sys.exit(1)
def check_output(cmd):
std, err = subprocess.Popen([cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell = True).communicate()
if err:
raise RuntimeError(err)
return std
def write_makefile(build_dirs):
print('\nCreating Makefile ...\n')
makefile = open('Makefile', 'w')
makefile.writelines(['# This file is auto-generated by preconfigure.py\n',
'SUBDIRS = '+ build_dirs + '\n',
'INSTALLDIRS = $(SUBDIRS:%=install-%)\n',
'CLEANDIRS = $(SUBDIRS:%=clean-%)\n',
'\n',
'subdirs: $(SUBDIRS)\n',
'\n',
'$(SUBDIRS):\n',
'\t$(MAKE) -C $@\n',
'\n',
'install: $(INSTALLDIRS)\n',
'$(INSTALLDIRS):\n',
'\t$(MAKE) -C $(@:install-%=%) install\n',
'\n',
'clean: $(CLEANDIRS)\n',
'$(CLEANDIRS):\n',
'\t$(MAKE) -C $(@:clean-%=%) clean\n',
'\n',
'.PHONY: subdirs $(SUBDIRS)\n',
'.PHONY: subdirs $(INSTALLDIRS)\n',
'.PHONY: subdirs $(CLEANDIRS)\n',
'.PHONY: install\n'])
makefile.close()
def header():
print('-------------------------------------------------------------------------\n'\
'| ___ _ _ ___ | \n'\
'| / __| | | |_ ) Release 6.2.0 \'Falcon\' | \n'\
'| \__ \ |_| |/ / | \n'\
'| |___/\___//___| Pre-configuration Script | \n'\
'| | \n'\
'------------------------------------------------------------------------- \n'\
'| The current SU2 release has been coordinated by the | \n'\
'| SU2 International Developers Society <www.su2devsociety.org> | \n'\
'| with selected contributions from the open-source community. | \n'\
'------------------------------------------------------------------------- \n'\
'| The main research teams contributing to the current release are: | \n'\
'| - Prof. Juan J. Alonso\'s group at Stanford University. | \n'\
'| - Prof. Piero Colonna\'s group at Delft University of Technology. | \n'\
'| - Prof. Nicolas R. Gauger\'s group at Kaiserslautern U. of Technology. | \n'\
'| - Prof. Alberto Guardone\'s group at Polytechnic University of Milan. | \n'\
'| - Prof. Rafael Palacios\' group at Imperial College London. | \n'\
'| - Prof. Vincent Terrapon\'s group at the University of Liege. | \n'\
'| - Prof. Edwin van der Weide\'s group at the University of Twente. | \n'\
'| - Lab. of New Concepts in Aeronautics at Tech. Inst. of Aeronautics. | \n'\
'------------------------------------------------------------------------- \n'\
'| Copyright 2012-2019, Francisco D. Palacios, Thomas D. Economon, | \n'\
'| Tim Albring, and the SU2 contributors. | \n'\
'| | \n'\
'| SU2 is free software; you can redistribute it and/or | \n'\
'| modify it under the terms of the GNU Lesser General Public | \n'\
'| License as published by the Free Software Foundation; either | \n'\
'| version 2.1 of the License, or (at your option) any later version. | \n'\
'| | \n'\
'| SU2 is distributed in the hope that it will be useful, | \n'\
'| but WITHOUT ANY WARRANTY; without even the implied warranty of | \n'\
'| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | \n'\
'| Lesser General Public License for more details. | \n'\
'| | \n'\
'| You should have received a copy of the GNU Lesser General Public | \n'\
'| License along with SU2. If not, see <http://www.gnu.org/licenses/>. | \n'\
'------------------------------------------------------------------------- \n')
# -------------------------------------------------------------------
# Run Main Program
# -------------------------------------------------------------------
# this is only accessed if running from command prompt
if __name__ == '__main__':
main()