def install_step(self):
"""Install CUDA using Perl install script."""
# define how to run the installer
# script has /usr/bin/perl hardcoded, but we want to have control over which perl is being used
if LooseVersion(self.version) <= LooseVersion("5"):
install_interpreter = "perl"
install_script = "install-linux.pl"
self.cfg.update('installopts', '--prefix=%s' % self.installdir)
elif LooseVersion(self.version) > LooseVersion("5") and LooseVersion(self.version) < LooseVersion("10.1"):
install_interpreter = "perl"
install_script = "cuda-installer.pl"
# note: also including samples (via "-samplespath=%(installdir)s -samples") would require libglut
self.cfg.update('installopts', "-verbose -silent -toolkitpath=%s -toolkit" % self.installdir)
else:
install_interpreter = ""
install_script = "./cuda-installer"
# note: also including samples (via "-samplespath=%(installdir)s -samples") would require libglut
self.cfg.update('installopts', "--silent --toolkit --toolkitpath=%s --defaultroot=%s" % (
self.installdir, self.installdir))
cmd = "%(preinstallopts)s %(interpreter)s %(script)s %(installopts)s" % {
'preinstallopts': self.cfg['preinstallopts'],
'interpreter': install_interpreter,
'script': install_script,
'installopts': self.cfg['installopts']
}
# prepare for running install script autonomously
qanda = {}
stdqa = {
# this question is only asked if CUDA tools are already available system-wide
r"Would you like to remove all CUDA files under .*? (yes/no/abort): ": "no",
}
noqanda = [
r"^Configuring",
r"Installation Complete",
r"Verifying archive integrity.*",
r"^Uncompressing NVIDIA CUDA",
r".* -> .*",
]
# patch install script to handle Q&A autonomously
if install_interpreter == "perl":
patch_perl_script_autoflush(os.path.join(self.builddir, install_script))
# make sure $DISPLAY is not defined, which may lead to (weird) problems
# this is workaround for not being able to specify --nox11 to the Perl install scripts
if 'DISPLAY' in os.environ:
os.environ.pop('DISPLAY')
# overriding maxhits default value to 300 (300s wait for nothing to change in the output without seeing a known
# question)
run_cmd_qa(cmd, qanda, std_qa=stdqa, no_qa=noqanda, log_all=True, simple=True, maxhits=300)
# check if there are patches to apply
if len(self.src) > 1:
for patch in self.src[1:]:
self.log.debug("Running patch %s", patch['name'])
run_cmd("/bin/sh " + patch['path'] + " --accept-eula --silent --installdir=" + self.installdir)
def install_step(self):
"""Install CUDA using Perl install script."""
# define how to run the installer
# script has /usr/bin/perl hardcoded, but we want to have control over which perl is being used
if LooseVersion(self.version) <= LooseVersion("5"):
install_script = "install-linux.pl"
install_script_path = os.path.join(self.builddir, install_script)
cmd = "perl ./%s --prefix=%s" % (install_script, self.installdir)
else:
# the following would require to include "osdependencies = 'libglut'" because of samples
# installparams = "-samplespath=%(x)s/samples/ -toolkitpath=%(x)s -samples -toolkit" % {'x': self.installdir}
install_script = "cuda-installer.pl"
installparams = "-toolkitpath=%s -toolkit" % self.installdir
cmd = "perl ./%s -verbose -silent %s" % (install_script, installparams)
# prepare for running install script autonomously
qanda = {}
stdqa = {
# this question is only asked if CUDA tools are already available system-wide
r"Would you like to remove all CUDA files under .*? (yes/no/abort): ": "no",
}
noqanda = [r"Installation Complete"]
# patch install script to handle Q&A autonomously
patch_perl_script_autoflush(os.path.join(self.builddir, install_script))
# make sure $DISPLAY is not defined, which may lead to (weird) problems
# this is workaround for not being able to specify --nox11 to the Perl install scripts
if 'DISPLAY' in os.environ:
os.environ.pop('DISPLAY')
run_cmd_qa(cmd, qanda, std_qa=stdqa, no_qa=noqanda, log_all=True, simple=True)
def install_step(self):
"""Install CUDA using Perl install script."""
# define how to run the installer
# script has /usr/bin/perl hardcoded, but we want to have control over which perl is being used
if LooseVersion(self.version) <= LooseVersion("5"):
install_interpreter = "perl"
install_script = "install-linux.pl"
self.cfg.update('installopts', '--prefix=%s' % self.installdir)
elif LooseVersion(self.version) > LooseVersion("5") and LooseVersion(self.version) < LooseVersion("10.1"):
install_interpreter = "perl"
install_script = "cuda-installer.pl"
# note: also including samples (via "-samplespath=%(installdir)s -samples") would require libglut
self.cfg.update('installopts', "-verbose -silent -toolkitpath=%s -toolkit" % self.installdir)
else:
install_interpreter = ""
install_script = "./cuda-installer"
# note: also including samples (via "-samplespath=%(installdir)s -samples") would require libglut
self.cfg.update('installopts', "--silent --toolkit --toolkitpath=%s --defaultroot=%s" % (
self.installdir, self.installdir))
cmd = "%(preinstallopts)s %(interpreter)s %(script)s %(installopts)s" % {
'preinstallopts': self.cfg['preinstallopts'],
'interpreter': install_interpreter,
'script': install_script,
'installopts': self.cfg['installopts']
}
# prepare for running install script autonomously
qanda = {}
stdqa = {
# this question is only asked if CUDA tools are already available system-wide
r"Would you like to remove all CUDA files under .*? (yes/no/abort): ": "no",
}
noqanda = [
r"^Configuring",
r"Installation Complete",
r"Verifying archive integrity.*",
r"^Uncompressing NVIDIA CUDA",
r".* -> .*",
]
# patch install script to handle Q&A autonomously
if install_interpreter == "perl":
patch_perl_script_autoflush(os.path.join(self.builddir, install_script))
# make sure $DISPLAY is not defined, which may lead to (weird) problems
# this is workaround for not being able to specify --nox11 to the Perl install scripts
if 'DISPLAY' in os.environ:
os.environ.pop('DISPLAY')
# overriding maxhits default value to 300 (300s wait for nothing to change in the output without seeing a known
# question)
run_cmd_qa(cmd, qanda, std_qa=stdqa, no_qa=noqanda, log_all=True, simple=True, maxhits=300)
# check if there are patches to apply
if len(self.src) > 1:
for patch in self.src[1:]:
self.log.debug("Running patch %s", patch['name'])
run_cmd("/bin/sh " + patch['path'] + " --accept-eula --silent --installdir=" + self.installdir)
def install_step(self):
run_cmd("mkdir -p " + self.installdir)
# define how to run the installer
if LooseVersion(self.version) <= LooseVersion("5"):
install_script = os.path.join(self.builddir, "install-linux.pl")
cmd = install_script + " --prefix=" + self.installdir
else:
# the following would require to include "osdependencies = 'libglut'" because of -samples
# installparams = "-samplespath=%s/samples/ -toolkitpath=%s -samples -toolkit" % (self.installdir, self.installdir))
installparams = "-toolkitpath=%s -toolkit" % self.installdir
install_script = os.path.join(self.builddir, "cuda-installer.pl")
cmd = install_script + " -verbose -silent " + installparams
qanda = {}
stdqa = {
"Would you like to remove all CUDA files under .*? (yes/no/abort): ": "no",
}
noqanda = [r"Installation Complete"]
# patch install script to handle Q&A autonomously
patch_perl_script_autoflush(install_script)
run_cmd_qa(cmd, qanda, std_qa=stdqa, no_qa=noqanda, log_all=True, simple=True)
# FIXME (kehoste): what is this about? why chmod the installdir?!?
try:
os.chmod(self.installdir, stat.S_IRWXU | stat.S_IXOTH | stat.S_IXGRP | stat.S_IROTH | stat.S_IRGRP)
except OSError, err:
self.log.exception("Can't set permissions on %s: %s" % (self.installdir, err))
def install_step(self):
"""Custom install procedure for RepeatMasker."""
super(EB_RepeatMasker, self).install_step()
# check for required dependencies
perl_root = get_software_root('Perl')
if perl_root:
perl = os.path.join(perl_root, 'bin', 'perl')
else:
raise EasyBuildError("Missing required dependency: Perl")
trf_root = get_software_root('TRF')
if trf_root:
trf = os.path.join(trf_root, 'trf')
else:
raise EasyBuildError("Missing required dependency: TRF")
# determine which search engine to use
# see also http://www.repeatmasker.org/RMDownload.html
cand_search_engines = ['CrossMatch', 'RMBlast', 'WUBlast', 'HMMER']
search_engine = None
for dep in cand_search_engines:
if get_software_root(dep):
if search_engine is None:
search_engine = dep
else:
raise EasyBuildError("Found multiple candidate search engines: %s and %s", search_engine, dep)
if search_engine is None:
raise EasyBuildError("No search engine found, one of these must be included as dependency: %s",
' '.join(cand_search_engines))
change_dir(self.installdir)
patch_perl_script_autoflush('configure')
search_engine_map = {
'CrossMatch': '1',
'RMBlast': '2',
'WUBlast': '3',
'HMMER': '4',
}
search_engine_bindir = os.path.join(get_software_root(search_engine), 'bin')
cmd = "perl ./configure"
qa = {
'<PRESS ENTER TO CONTINUE>': '',
# select search engine
'Enter Selection:': search_engine_map[search_engine],
}
std_qa = {
r'\*\*PERL PROGRAM\*\*\n([^*]*\n)+Enter path.*': perl,
r'\*\*REPEATMASKER INSTALLATION DIRECTORY\*\*\n([^*]*\n)+Enter path.*': self.installdir,
r'\*\*TRF PROGRAM\*\*\n([^*]*\n)+Enter path.*': trf,
# search engine installation path (location of /bin subdirectory)
# also enter 'Y' to confirm + '5' ("Done") to complete selection process for search engine
r'\*\*.* INSTALLATION PATH\*\*\n([^*]*\n)+Enter path.*': search_engine_bindir + '\nY\n5',
}
run_cmd_qa(cmd, qa, std_qa=std_qa, log_all=True, simple=True, log_ok=True)
def install_step(self):
"""Install CUDA using Perl install script."""
# define how to run the installer
# script has /usr/bin/perl hardcoded, but we want to have control over which perl is being used
if LooseVersion(self.version) <= LooseVersion("5"):
install_script = "install-linux.pl"
install_script_path = os.path.join(self.builddir, install_script)
cmd = "perl ./%s --prefix=%s %s" % (
install_script, self.installdir, self.cfg['installopts'])
else:
# the following would require to include "osdependencies = 'libglut'" because of samples
# installparams = "-samplespath=%(x)s/samples/ -toolkitpath=%(x)s -samples -toolkit" % {'x': self.installdir}
install_script = "cuda-installer.pl"
installparams = "-toolkitpath=%s -toolkit" % self.installdir
cmd = "perl ./%s -verbose -silent %s %s" % (
install_script, installparams, self.cfg['installopts'])
# prepare for running install script autonomously
qanda = {}
stdqa = {
# this question is only asked if CUDA tools are already available system-wide
r"Would you like to remove all CUDA files under .*? (yes/no/abort): ":
"no",
}
noqanda = [
r"^Configuring",
r"Installation Complete",
r"Verifying archive integrity.*",
r"^Uncompressing NVIDIA CUDA",
r".* -> .*",
]
# patch install script to handle Q&A autonomously
patch_perl_script_autoflush(os.path.join(self.builddir,
install_script))
# make sure $DISPLAY is not defined, which may lead to (weird) problems
# this is workaround for not being able to specify --nox11 to the Perl install scripts
if 'DISPLAY' in os.environ:
os.environ.pop('DISPLAY')
#overriding maxhits default value to 300 (300s wait for nothing to change in the output without seeing a known question)
run_cmd_qa(cmd,
qanda,
std_qa=stdqa,
no_qa=noqanda,
log_all=True,
simple=True,
maxhits=300)
def test_patch_perl_script_autoflush(self):
"""Test patching Perl script for autoflush."""
fh, fp = tempfile.mkstemp()
os.close(fh)
perl_lines = ["$!/usr/bin/perl", "use strict;", "print hello", "", "print hello again"]
perltxt = "\n".join(perl_lines)
ft.write_file(fp, perltxt)
ft.patch_perl_script_autoflush(fp)
txt = ft.read_file(fp)
self.assertTrue(len(txt.split("\n")) == len(perl_lines) + 4)
self.assertTrue(txt.startswith(perl_lines[0] + "\n\nuse IO::Handle qw();\nSTDOUT->autoflush(1);"))
for line in perl_lines[1:]:
self.assertTrue(line in txt)
os.remove(fp)
os.remove("%s.eb.orig" % fp)
def install_step(self):
run_cmd("mkdir -p " + self.installdir)
# define how to run the installer
if LooseVersion(self.version) <= LooseVersion("5"):
install_script = os.path.join(self.builddir, "install-linux.pl")
cmd = install_script + " --prefix=" + self.installdir
else:
# the following would require to include "osdependencies = 'libglut'" because of -samples
# installparams = "-samplespath=%s/samples/ -toolkitpath=%s -samples -toolkit" % (self.installdir, self.installdir))
installparams = "-toolkitpath=%s -toolkit" % self.installdir
install_script = os.path.join(self.builddir, "cuda-installer.pl")
cmd = install_script + " -verbose -silent " + installparams
qanda = {}
stdqa = {
"Would you like to remove all CUDA files under .*? (yes/no/abort): ":
"no",
}
noqanda = [r"Installation Complete"]
# patch install script to handle Q&A autonomously
patch_perl_script_autoflush(install_script)
run_cmd_qa(cmd,
qanda,
std_qa=stdqa,
no_qa=noqanda,
log_all=True,
simple=True)
# FIXME (kehoste): what is this about? why chmod the installdir?!?
try:
os.chmod(
self.installdir, stat.S_IRWXU | stat.S_IXOTH | stat.S_IXGRP
| stat.S_IROTH | stat.S_IRGRP)
except OSError, err:
self.log.exception("Can't set permissions on %s: %s" %
(self.installdir, err))
def test_patch_perl_script_autoflush(self):
"""Test patching Perl script for autoflush."""
fh, fp = tempfile.mkstemp()
os.close(fh)
perl_lines = [
"$!/usr/bin/perl",
"use strict;",
"print hello",
"",
"print hello again",
]
perltxt = '\n'.join(perl_lines)
ft.write_file(fp, perltxt)
ft.patch_perl_script_autoflush(fp)
txt = ft.read_file(fp)
self.assertTrue(len(txt.split('\n')) == len(perl_lines) + 4)
self.assertTrue(txt.startswith(perl_lines[0] + "\n\nuse IO::Handle qw();\nSTDOUT->autoflush(1);"))
for line in perl_lines[1:]:
self.assertTrue(line in txt)
os.remove(fp)
os.remove("%s.eb.orig" % fp)
else:
self.log.error("JasPer module not loaded?")
# patch ungrib Makefile so that JasPer is found
fn = os.path.join("ungrib", "src", "Makefile")
jasperlibs = "%s -ljasper %s -lpng" % (jasperlib, libpnglib)
try:
for line in fileinput.input(fn, inplace=1, backup='.orig.JasPer'):
line = re.sub(r"^(\s*-L\.\s*-l\$\(LIBTARGET\))(\s*;.*)$", r"\1 %s\2" % jasperlibs, line)
line = re.sub(r"^(\s*\$\(COMPRESSION_LIBS\))(\s*;.*)$", r"\1 %s\2" % jasperlibs, line)
sys.stdout.write(line)
except IOError, err:
self.log.error("Failed to patch %s: %s" % (fn, err))
# patch arch/Config.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join("arch", "Config.pl"))
# configure
# determine build type option to look for
self.comp_fam = self.toolchain.comp_family()
build_type_option = None
if LooseVersion(self.version) >= LooseVersion("3.4"):
knownbuildtypes = {
'smpar': 'serial',
'dmpar': 'dmpar'
}
if self.comp_fam == toolchain.INTELCOMP: #@UndefinedVariable
def install_step(self):
"""Custom install procedure for RepeatModeler."""
super(EB_RepeatModeler, self).install_step()
# Required dependencies, and bin path relative to software root
required_deps = {
'CD-HIT': 'bin',
'Kent_tools': 'bin',
'Perl': os.path.join('bin', 'perl'),
'RECON': 'bin',
'RepeatMasker': '',
'RepeatScout': '',
'TRF': os.path.join('bin', 'trf'),
}
# Search engines, and bin path relative to software root
search_engines = {
'ABBlast': 'bin',
'RMBlast': 'bin',
'WUBlast': 'bin',
}
# Optional dependencies for LTR pipeline, and bin path relative to software root
optional_LTR_deps = {
'GenomeTools': 'bin',
'LTR_retriever': '',
'MAFFT': 'bin',
'TWL-NINJA': 'bin',
}
for dep, path in required_deps.items():
required_deps[dep] = get_dep_path(dep, path, log=self.log, optional=False)
for dep, path in search_engines.items():
search_engines[dep] = get_dep_path(dep, path, log=self.log, optional=True)
for dep, path in optional_LTR_deps.items():
optional_LTR_deps[dep] = get_dep_path(dep, path, log=self.log, optional=True)
# Check at least one search engine is present, and not both ABBlast/WUBlast
if not any(search_engines.values()):
raise EasyBuildError("At least one search engine must be specified: RMBlast, ABBlast, WUBlast")
elif search_engines['ABBlast'] and search_engines['WUBlast']:
raise EasyBuildError("Cannot specify both ABBlast and WUBlast")
# Check if all LTR Pipeline dependencies present
if all(optional_LTR_deps.values()):
self.log.info("All LTR pipeline dependencies found, enabling LTR support")
with_LTR = 'y'
else:
self.log.info("Not all LTR pipeline dependencies found, disabling LTR support")
with_LTR = 'n'
# Map search engine to configuration option
search_engine_map = {
'ABBlast': '2',
'RMBlast': '1',
'WUBlast': '2',
}
# List of search engines to use (mapped)
mapped_engines = [search_engine_map[k] for k, v in search_engines.items() if v] + ['3']
change_dir(self.installdir)
# Fix perl shebang in configure script (#!/usr/local/bin/perl)
orig_fix_perl_shebang_for = self.cfg['fix_perl_shebang_for']
self.cfg['fix_perl_shebang_for'] = [os.path.join(self.installdir, 'configure')]
self.fix_shebang()
self.cfg['fix_perl_shebang_for'] = orig_fix_perl_shebang_for
patch_perl_script_autoflush('configure')
qa = {
'<PRESS ENTER TO CONTINUE>': '',
}
std_qa = {
r'\*\*PERL INSTALLATION PATH\*\*\n\n[^*]*\n+Enter path.*:\s*': required_deps['Perl'],
r'UCSCTOOLS_DIR.*:\s*': required_deps['Kent_tools'],
r'LTR_RETRIEVER_DIR.*:\s*': optional_LTR_deps['LTR_retriever'],
r'RMBLAST_DIR.*:\s*': search_engines['RMBlast'],
r'ABBLAST_DIR.*:\s*': search_engines['ABBlast'] or search_engines['WUBlast'],
# Configure first engine
r'.*(\[ Un\-configured \]\n.*){2}\n.*\n+Enter Selection\:\s*': mapped_engines[0],
# Configure second engine if multiple specified, otherwise skip
r'.*(\[ Un\-configured \]\n.*\[ Configured \]|\[ Configured \]\n.*\[ Un-configured \])'
r'\n\n.*\n+Enter Selection\:\s*': mapped_engines[1],
# All engines configured
r'.*(\[ Configured \]\n.*){2}\n.*\n+Enter Selection\:\s*': '3',
# LTR
r'LTR.*\[optional](.*\n)*of analysis \[y] or n\?\:\s*': with_LTR,
}
cmdopts = ' ' + ' '.join([
'-trf_prgm "%(TRF)s"',
'-repeatmasker_dir "%(RepeatMasker)s"',
'-rscout_dir "%(RepeatScout)s"',
'-recon_dir "%(RECON)s"',
'-ucsctools_dir "%(Kent_tools)s"',
'-cdhit_dir "%(CD-HIT)s"',
]) % required_deps
if with_LTR:
cmdopts += ' ' + ' '.join([
'-mafft_dir "%(MAFFT)s"',
'-genometools_dir "%(GenomeTools)s"',
'-ltr_retriever_dir "%(LTR_retriever)s"',
'-ninja_dir "%(TWL-NINJA)s"',
]) % optional_LTR_deps
cmd = "perl ./configure" + cmdopts
run_cmd_qa(cmd, qa, std_qa=std_qa, log_all=True, simple=True, log_ok=True, maxhits=100)
def configure_step(self):
"""Configure build:
- set some magic environment variables
- run configure script
- adjust configure.wrf file if needed
"""
wrfdir = os.path.join(self.builddir, self.wrfsubdir)
# define $NETCDF* for netCDF dependency (used when creating WRF module file)
set_netcdf_env_vars(self.log)
# HDF5 (optional) dependency
hdf5 = get_software_root('HDF5')
if hdf5:
env.setvar('HDF5', hdf5)
# check if this is parallel HDF5
phdf5_bins = ['h5pcc', 'ph5diff']
parallel_hdf5 = True
for f in phdf5_bins:
if not os.path.exists(os.path.join(hdf5, 'bin', f)):
parallel_hdf5 = False
break
if parallel_hdf5:
env.setvar('PHDF5', hdf5)
else:
self.log.info(
"Parallel HDF5 module not loaded, assuming that's OK...")
else:
self.log.info("HDF5 module not loaded, assuming that's OK...")
# Parallel netCDF (optional) dependency
pnetcdf = get_software_root('PnetCDF')
if pnetcdf:
env.setvar('PNETCDF', pnetcdf)
# JasPer dependency check + setting env vars
jasper = get_software_root('JasPer')
if jasper:
jasperlibdir = os.path.join(jasper, "lib")
env.setvar('JASPERINC', os.path.join(jasper, "include"))
env.setvar('JASPERLIB', jasperlibdir)
else:
if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
raise EasyBuildError(
"JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?"
)
else:
self.log.info(
"JasPer module not loaded, assuming that's OK...")
# enable support for large file support in netCDF
env.setvar('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
if LooseVersion(self.version) < LooseVersion('4.0'):
patch_perl_script_autoflush(
os.path.join(wrfdir, "arch", "Config_new.pl"))
# determine build type option to look for
build_type_option = None
self.comp_fam = self.toolchain.comp_family()
if self.comp_fam == toolchain.INTELCOMP: # @UndefinedVariable
if LooseVersion(self.version) >= LooseVersion('3.7'):
build_type_option = "INTEL\ \(ifort\/icc\)"
else:
build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"
elif self.comp_fam == toolchain.GCC: # @UndefinedVariable
if LooseVersion(self.version) >= LooseVersion('3.7'):
build_type_option = "GNU\ \(gfortran\/gcc\)"
else:
build_type_option = "x86_64 Linux, gfortran compiler with gcc"
else:
raise EasyBuildError(
"Don't know how to figure out build type to select.")
# fetch selected build type (and make sure it makes sense)
known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
self.parallel_build_types = ["dmpar", "dm+sm"]
bt = self.cfg['buildtype']
if bt not in known_build_types:
raise EasyBuildError(
"Unknown build type: '%s'. Supported build types: %s", bt,
known_build_types)
# Escape the "+" in "dm+sm" since it's being used in a regexp below.
bt = bt.replace('+', r'\+')
# fetch option number based on build type option and selected build type
if LooseVersion(self.version) >= LooseVersion('3.7'):
# the two relevant lines in the configure output for WRF 3.8 are:
# 13. (serial) 14. (smpar) 15. (dmpar) 16. (dm+sm) INTEL (ifort/icc)
# 32. (serial) 33. (smpar) 34. (dmpar) 35. (dm+sm) GNU (gfortran/gcc)
build_type_question = "\s*(?P<nr>[0-9]+)\.\ \(%s\).*%s" % (
bt, build_type_option)
else:
# the relevant lines in the configure output for WRF 3.6 are:
# 13. Linux x86_64 i486 i586 i686, ifort compiler with icc (serial)
# 14. Linux x86_64 i486 i586 i686, ifort compiler with icc (smpar)
# 15. Linux x86_64 i486 i586 i686, ifort compiler with icc (dmpar)
# 16. Linux x86_64 i486 i586 i686, ifort compiler with icc (dm+sm)
# 32. x86_64 Linux, gfortran compiler with gcc (serial)
# 33. x86_64 Linux, gfortran compiler with gcc (smpar)
# 34. x86_64 Linux, gfortran compiler with gcc (dmpar)
# 35. x86_64 Linux, gfortran compiler with gcc (dm+sm)
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (
build_type_option, bt)
# run configure script
cmd = "./configure"
qa = {
# named group in match will be used to construct answer
"Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:":
"1",
"Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:":
"0"
}
no_qa = [
"testing for fseeko and fseeko64",
r"If you wish to change the default options, edit the file:[\s\n]*arch/configure_new.defaults"
]
std_qa = {
# named group in match will be used to construct answer
r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question:
"%(nr)s",
}
run_cmd_qa(cmd,
qa,
no_qa=no_qa,
std_qa=std_qa,
log_all=True,
simple=True)
cfgfile = 'configure.wrf'
# make sure correct compilers are being used
comps = {
'SCC': os.getenv('CC'),
'SFC': os.getenv('F90'),
'CCOMP': os.getenv('CC'),
'DM_FC': os.getenv('MPIF90'),
'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
}
regex_subs = [(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v)
for (k, v) in comps.items()]
apply_regex_substitutions(cfgfile, regex_subs)
# rewrite optimization options if desired
if self.cfg['rewriteopts']:
# replace default -O3 option in configure.wrf with CFLAGS/FFLAGS from environment
self.log.info("Rewriting optimization options in %s" % cfgfile)
# set extra flags for Intel compilers
# see http://software.intel.com/en-us/forums/showthread.php?t=72109&p=1#146748
if self.comp_fam == toolchain.INTELCOMP: # @UndefinedVariable
# -O3 -heap-arrays is required to resolve compilation error
for envvar in ['CFLAGS', 'FFLAGS']:
val = os.getenv(envvar)
if '-O3' in val:
env.setvar(envvar, '%s -heap-arrays' % val)
self.log.info("Updated %s to '%s'" %
(envvar, os.getenv(envvar)))
# replace -O3 with desired optimization options
regex_subs = [
(r"^(FCOPTIM.*)(\s-O3)(\s.*)$",
r"\1 %s \3" % os.getenv('FFLAGS')),
(r"^(CFLAGS_LOCAL.*)(\s-O3)(\s.*)$",
r"\1 %s \3" % os.getenv('CFLAGS')),
]
apply_regex_substitutions(cfgfile, regex_subs)
def configure_step(self):
"""Configure build:
- set some magic environment variables
- run configure script
- adjust configure.wrf file if needed
"""
# define $NETCDF* for netCDF dependency (used when creating WRF module file)
set_netcdf_env_vars(self.log)
# HDF5 (optional) dependency
hdf5 = get_software_root('HDF5')
if hdf5:
# check if this is parallel HDF5
phdf5_bins = ['h5pcc', 'ph5diff']
parallel_hdf5 = True
for f in phdf5_bins:
if not os.path.exists(os.path.join(hdf5, 'bin', f)):
parallel_hdf5 = False
break
if not (hdf5 or parallel_hdf5):
raise EasyBuildError("Parallel HDF5 module not loaded?")
else:
env.setvar('PHDF5', hdf5)
else:
self.log.info("HDF5 module not loaded, assuming that's OK...")
# JasPer dependency check + setting env vars
jasper = get_software_root('JasPer')
if jasper:
jasperlibdir = os.path.join(jasper, "lib")
env.setvar('JASPERINC', os.path.join(jasper, "include"))
env.setvar('JASPERLIB', jasperlibdir)
else:
if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
raise EasyBuildError("JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?")
else:
self.log.info("JasPer module not loaded, assuming that's OK...")
# enable support for large file support in netCDF
env.setvar('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join("arch", "Config_new.pl"))
# determine build type option to look for
build_type_option = None
self.comp_fam = self.toolchain.comp_family()
if self.comp_fam == toolchain.INTELCOMP: #@UndefinedVariable
if LooseVersion(self.version) >= LooseVersion('3.7'):
build_type_option = "INTEL\ \(ifort\/icc\)"
else:
build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"
elif self.comp_fam == toolchain.GCC: #@UndefinedVariable
if LooseVersion(self.version) >= LooseVersion('3.7'):
build_type_option = "GNU\ \(gfortran\/gcc\)"
else:
build_type_option = "x86_64 Linux, gfortran compiler with gcc"
else:
raise EasyBuildError("Don't know how to figure out build type to select.")
# fetch selected build type (and make sure it makes sense)
known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
self.parallel_build_types = ["dmpar", "smpar", "dm+sm"]
bt = self.cfg['buildtype']
if not bt in known_build_types:
raise EasyBuildError("Unknown build type: '%s'. Supported build types: %s", bt, known_build_types)
# fetch option number based on build type option and selected build type
if LooseVersion(self.version) >= LooseVersion('3.7'):
# the two relevant lines in the configure output for WRF 3.8 are:
# 13. (serial) 14. (smpar) 15. (dmpar) 16. (dm+sm) INTEL (ifort/icc)
# 32. (serial) 33. (smpar) 34. (dmpar) 35. (dm+sm) GNU (gfortran/gcc)
build_type_question = "\s*(?P<nr>[0-9]+)\.\ \(%s\).*%s" % (bt, build_type_option)
else:
# the relevant lines in the configure output for WRF 3.6 are:
# 13. Linux x86_64 i486 i586 i686, ifort compiler with icc (serial)
# 14. Linux x86_64 i486 i586 i686, ifort compiler with icc (smpar)
# 15. Linux x86_64 i486 i586 i686, ifort compiler with icc (dmpar)
# 16. Linux x86_64 i486 i586 i686, ifort compiler with icc (dm+sm)
# 32. x86_64 Linux, gfortran compiler with gcc (serial)
# 33. x86_64 Linux, gfortran compiler with gcc (smpar)
# 34. x86_64 Linux, gfortran compiler with gcc (dmpar)
# 35. x86_64 Linux, gfortran compiler with gcc (dm+sm)
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (build_type_option, bt)
# run configure script
cmd = "./configure"
qa = {
# named group in match will be used to construct answer
"Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:": "1",
"Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:": "0"
}
no_qa = [
"testing for fseeko and fseeko64",
r"If you wish to change the default options, edit the file:[\s\n]*arch/configure_new.defaults"
]
std_qa = {
# named group in match will be used to construct answer
r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question: "%(nr)s",
}
run_cmd_qa(cmd, qa, no_qa=no_qa, std_qa=std_qa, log_all=True, simple=True)
cfgfile = 'configure.wrf'
# make sure correct compilers are being used
comps = {
'SCC': os.getenv('CC'),
'SFC': os.getenv('F90'),
'CCOMP': os.getenv('CC'),
'DM_FC': os.getenv('MPIF90'),
'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
}
regex_subs = [(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v) for (k, v) in comps.items()]
apply_regex_substitutions(cfgfile, regex_subs)
# rewrite optimization options if desired
if self.cfg['rewriteopts']:
# replace default -O3 option in configure.wrf with CFLAGS/FFLAGS from environment
self.log.info("Rewriting optimization options in %s" % cfgfile)
# set extra flags for Intel compilers
# see http://software.intel.com/en-us/forums/showthread.php?t=72109&p=1#146748
if self.comp_fam == toolchain.INTELCOMP: #@UndefinedVariable
# -O3 -heap-arrays is required to resolve compilation error
for envvar in ['CFLAGS', 'FFLAGS']:
val = os.getenv(envvar)
if '-O3' in val:
env.setvar(envvar, '%s -heap-arrays' % val)
self.log.info("Updated %s to '%s'" % (envvar, os.getenv(envvar)))
# replace -O3 with desired optimization options
regex_subs = [
(r"^(FCOPTIM.*)(\s-O3)(\s.*)$", r"\1 %s \3" % os.getenv('FFLAGS')),
(r"^(CFLAGS_LOCAL.*)(\s-O3)(\s.*)$", r"\1 %s \3" % os.getenv('CFLAGS')),
]
apply_regex_substitutions(cfgfile, regex_subs)
def configure_step(self):
"""Configure build:
- set some magic environment variables
- run configure script
- adjust configure.wrf file if needed
"""
# netCDF dependency
set_netcdf_env_vars(self.log)
self.netcdf_mod_cmds = get_netcdf_module_set_cmds(self.log)
# HDF5 (optional) dependency
hdf5 = get_software_root('HDF5')
if hdf5:
# check if this is parallel HDF5
phdf5_bins = ['h5pcc', 'ph5diff']
parallel_hdf5 = True
for f in phdf5_bins:
if not os.path.exists(os.path.join(hdf5, 'bin', f)):
parallel_hdf5 = False
break
if not (hdf5 or parallel_hdf5):
self.log.error("Parallel HDF5 module not loaded?")
else:
env.setvar('PHDF5', hdf5)
else:
self.log.info("HDF5 module not loaded, assuming that's OK...")
# JasPer dependency check + setting env vars
jasper = get_software_root('JasPer')
if jasper:
jasperlibdir = os.path.join(jasper, "lib")
env.setvar('JASPERINC', os.path.join(jasper, "include"))
env.setvar('JASPERLIB', jasperlibdir)
else:
if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
self.log.error(
"JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?"
)
else:
self.log.info(
"JasPer module not loaded, assuming that's OK...")
# enable support for large file support in netCDF
env.setvar('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join("arch", "Config_new.pl"))
# determine build type option to look for
build_type_option = None
self.comp_fam = self.toolchain.comp_family()
if self.comp_fam == toolchain.INTELCOMP: #@UndefinedVariable
build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"
elif self.comp_fam == toolchain.GCC: #@UndefinedVariable
build_type_option = "x86_64 Linux, gfortran compiler with gcc"
else:
self.log.error(
"Don't know how to figure out build type to select.")
# fetch selected build type (and make sure it makes sense)
known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
self.parallel_build_types = ["dmpar", "smpar", "dm+sm"]
bt = self.cfg['buildtype']
if not bt in known_build_types:
self.log.error(
"Unknown build type: '%s'. Supported build types: %s" %
(bt, known_build_types))
# fetch option number based on build type option and selected build type
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (
build_type_option, bt)
# run configure script
cmd = "./configure"
qa = {
# named group in match will be used to construct answer
"Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:":
"1",
"Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:":
"0"
}
no_qa = [
"testing for fseeko and fseeko64",
r"If you wish to change the default options, edit the file:[\s\n]*arch/configure_new.defaults"
]
std_qa = {
# named group in match will be used to construct answer
r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question:
"%(nr)s",
}
run_cmd_qa(cmd,
qa,
no_qa=no_qa,
std_qa=std_qa,
log_all=True,
simple=True)
cfgfile = 'configure.wrf'
# make sure correct compilers are being used
comps = {
'SCC': os.getenv('CC'),
'SFC': os.getenv('F90'),
'CCOMP': os.getenv('CC'),
'DM_FC': os.getenv('MPIF90'),
'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
}
for line in fileinput.input(cfgfile, inplace=1, backup='.orig.comps'):
for (k, v) in comps.items():
line = re.sub(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v, line)
sys.stdout.write(line)
# rewrite optimization options if desired
if self.cfg['rewriteopts']:
# replace default -O3 option in configure.wrf with CFLAGS/FFLAGS from environment
self.log.info("Rewriting optimization options in %s" % cfgfile)
# set extra flags for Intel compilers
# see http://software.intel.com/en-us/forums/showthread.php?t=72109&p=1#146748
if self.comp_fam == toolchain.INTELCOMP: #@UndefinedVariable
# -O3 -heap-arrays is required to resolve compilation error
for envvar in ['CFLAGS', 'FFLAGS']:
val = os.getenv(envvar)
if '-O3' in val:
env.setvar(envvar, '%s -heap-arrays' % val)
self.log.info("Updated %s to '%s'" %
(envvar, os.getenv(envvar)))
# replace -O3 with desired optimization options
for line in fileinput.input(cfgfile,
inplace=1,
backup='.orig.rewriteopts'):
line = re.sub(r"^(FCOPTIM.*)(\s-O3)(\s.*)$",
r"\1 %s \3" % os.getenv('FFLAGS'), line)
line = re.sub(r"^(CFLAGS_LOCAL.*)(\s-O3)(\s.*)$",
r"\1 %s \3" % os.getenv('CFLAGS'), line)
sys.stdout.write(line)
def install_step(self):
"""Custom install procedure for RepeatMasker."""
super(EB_RepeatMasker, self).install_step()
# check for required dependencies
perl_root = get_software_root('Perl')
if perl_root:
perl = os.path.join(perl_root, 'bin', 'perl')
else:
raise EasyBuildError("Missing required dependency: Perl")
trf_root = get_software_root('TRF')
if trf_root:
trf = os.path.join(trf_root, 'trf')
else:
raise EasyBuildError("Missing required dependency: TRF")
# determine which search engine to use
# see also http://www.repeatmasker.org/RMDownload.html
cand_search_engines = ['CrossMatch', 'RMBlast', 'WUBlast', 'HMMER']
search_engine = None
for dep in cand_search_engines:
if get_software_root(dep):
if search_engine is None:
search_engine = dep
else:
raise EasyBuildError(
"Found multiple candidate search engines: %s and %s",
search_engine, dep)
if search_engine is None:
raise EasyBuildError(
"No search engine found, one of these must be included as dependency: %s",
' '.join(cand_search_engines))
change_dir(self.installdir)
patch_perl_script_autoflush('configure')
search_engine_map = {
'CrossMatch': '1',
'RMBlast': '2',
'WUBlast': '3',
'HMMER': '4',
}
search_engine_bindir = os.path.join(get_software_root(search_engine),
'bin')
cmd = "perl ./configure"
qa = {
'<PRESS ENTER TO CONTINUE>': '',
# select search engine
'Enter Selection:': search_engine_map[search_engine],
}
std_qa = {
r'\*\*PERL PROGRAM\*\*\n([^*]*\n)+Enter path.*':
perl,
r'\*\*REPEATMASKER INSTALLATION DIRECTORY\*\*\n([^*]*\n)+Enter path.*':
self.installdir,
r'\*\*TRF PROGRAM\*\*\n([^*]*\n)+Enter path.*':
trf,
# search engine installation path (location of /bin subdirectory)
# also enter 'Y' to confirm + '5' ("Done") to complete selection process for search engine
r'\*\*.* INSTALLATION PATH\*\*\n([^*]*\n)+Enter path.*':
search_engine_bindir + '\nY\n5',
}
run_cmd_qa(cmd,
qa,
std_qa=std_qa,
log_all=True,
simple=True,
log_ok=True)
def configure(self):
"""Configure build:
- set some magic environment variables
- run configure script
- adjust configure.wrf file if needed
"""
# netCDF dependency
set_netcdf_env_vars(self.log)
# HDF5 (optional) dependency
hdf5 = get_software_root('HDF5')
if hdf5:
# check if this is parallel HDF5
phdf5_bins = ['h5pcc','ph5diff']
parallel_hdf5 = True
for f in phdf5_bins:
if not os.path.exists(os.path.join(hdf5, 'bin', f)):
parallel_hdf5 = False
break
if not (hdf5 or parallel_hdf5):
self.log.error("Parallel HDF5 module not loaded?")
else:
env.set('PHDF5', hdf5)
else:
self.log.info("HDF5 module not loaded, assuming that's OK...")
# JasPer dependency check + setting env vars
jasper = get_software_root('JasPer')
jasperlibdir = os.path.join(jasper, "lib")
if jasper:
env.set('JASPERINC', os.path.join(jasper, "include"))
env.set('JASPERLIB', jasperlibdir)
else:
if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
self.log.error("JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?")
else:
self.log.info("JasPer module not loaded, assuming that's OK...")
# enable support for large file support in netCDF
env.set('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join("arch", "Config_new.pl"))
# determine build type option to look for
build_type_option = None
self.comp_fam = self.toolkit().comp_family()
if self.comp_fam == toolkit.INTEL:
build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"
elif self.comp_fam == toolkit.GCC:
build_type_option = "x86_64 Linux, gfortran compiler with gcc"
else:
self.log.error("Don't know how to figure out build type to select.")
# fetch selected build type (and make sure it makes sense)
known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
self.parallel_build_types = ["dmpar","smpar","dm+sm"]
bt = self.getcfg('buildtype')
if not bt in known_build_types:
self.log.error("Unknown build type: '%s'. Supported build types: %s" % (bt, known_build_types))
# fetch option number based on build type option and selected build type
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (build_type_option, bt)
# run configure script
cmd = "./configure"
qa = {
# named group in match will be used to construct answer
"Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:": "1",
"Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:": "0"
}
no_qa = []
std_qa = {
# named group in match will be used to construct answer
r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question: "%(nr)s",
}
run_cmd_qa(cmd, qa, no_qa=no_qa, std_qa=std_qa, log_all=True, simple=True)
cfgfile= 'configure.wrf'
# make sure correct compilers are being used
comps = {
'SCC': os.getenv('CC'),
'SFC': os.getenv('F90'),
'CCOMP': os.getenv('CC'),
'DM_FC': os.getenv('MPIF90'),
'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
}
for line in fileinput.input(cfgfile, inplace=1, backup='.orig.comps'):
for (k, v) in comps.items():
line = re.sub(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v, line)
sys.stdout.write(line)
# rewrite optimization options if desired
if self.getcfg('rewriteopts'):
# replace default -O3 option in configure.wrf with CFLAGS/FFLAGS from environment
self.log.info("Rewriting optimization options in %s" % cfgfile)
# set extra flags for Intel compilers
# see http://software.intel.com/en-us/forums/showthread.php?t=72109&p=1#146748
if self.comp_fam == toolkit.INTEL:
# -O3 -heap-arrays is required to resolve compilation error
for envvar in ['CFLAGS', 'FFLAGS']:
val = os.getenv(envvar)
if '-O3' in val:
env.set(envvar, '%s -heap-arrays' % val)
self.log.info("Updated %s to '%s'" % (envvar, os.getenv(envvar)))
# replace -O3 with desired optimization options
for line in fileinput.input(cfgfile, inplace=1, backup='.orig.rewriteopts'):
line = re.sub(r"^(FCOPTIM.*)(\s-O3)(\s.*)$", r"\1 %s \3" % os.getenv('FFLAGS'), line)
line = re.sub(r"^(CFLAGS_LOCAL.*)(\s-O3)(\s.*)$", r"\1 %s \3" % os.getenv('CFLAGS'), line)
sys.stdout.write(line)
def configure_step(self):
"""Configure build:
- set some magic environment variables
- run configure script
- adjust configure.wrf file if needed
"""
# define $NETCDF* for netCDF dependency (used when creating WRF module file)
set_netcdf_env_vars(self.log)
# HDF5 (optional) dependency
hdf5 = get_software_root('HDF5')
if hdf5:
# check if this is parallel HDF5
phdf5_bins = ['h5pcc', 'ph5diff']
parallel_hdf5 = True
for f in phdf5_bins:
if not os.path.exists(os.path.join(hdf5, 'bin', f)):
parallel_hdf5 = False
break
if not (hdf5 or parallel_hdf5):
raise EasyBuildError("Parallel HDF5 module not loaded?")
else:
env.setvar('PHDF5', hdf5)
else:
self.log.info("HDF5 module not loaded, assuming that's OK...")
# JasPer dependency check + setting env vars
jasper = get_software_root('JasPer')
if jasper:
jasperlibdir = os.path.join(jasper, "lib")
env.setvar('JASPERINC', os.path.join(jasper, "include"))
env.setvar('JASPERLIB', jasperlibdir)
else:
if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
raise EasyBuildError("JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?")
else:
self.log.info("JasPer module not loaded, assuming that's OK...")
# enable support for large file support in netCDF
env.setvar('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join("arch", "Config_new.pl"))
# determine build type option to look for
build_type_option = None
self.comp_fam = self.toolchain.comp_family()
if self.comp_fam == toolchain.INTELCOMP: #@UndefinedVariable
if LooseVersion(self.version) >= LooseVersion('3.7'):
build_type_option = "INTEL\ \(ifort\/icc\)"
else:
build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"
elif self.comp_fam == toolchain.GCC: #@UndefinedVariable
if LooseVersion(self.version) >= LooseVersion('3.7'):
build_type_option = "GNU\ \(gfortran\/gcc\)"
else:
build_type_option = "x86_64 Linux, gfortran compiler with gcc"
else:
raise EasyBuildError("Don't know how to figure out build type to select.")
# fetch selected build type (and make sure it makes sense)
known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
self.parallel_build_types = ["dmpar", "smpar", "dm+sm"]
bt = self.cfg['buildtype']
if not bt in known_build_types:
raise EasyBuildError("Unknown build type: '%s'. Supported build types: %s", bt, known_build_types)
# fetch option number based on build type option and selected build type
if LooseVersion(self.version) >= LooseVersion('3.7'):
# the two relevant lines in the configure output for WRF 3.8 are:
# 13. (serial) 14. (smpar) 15. (dmpar) 16. (dm+sm) INTEL (ifort/icc)
# 32. (serial) 33. (smpar) 34. (dmpar) 35. (dm+sm) GNU (gfortran/gcc)
build_type_question = "\s*(?P<nr>[0-9]+)\.\ \(%s\).*%s" % (bt, build_type_option)
else:
# the relevant lines in the configure output for WRF 3.6 are:
# 13. Linux x86_64 i486 i586 i686, ifort compiler with icc (serial)
# 14. Linux x86_64 i486 i586 i686, ifort compiler with icc (smpar)
# 15. Linux x86_64 i486 i586 i686, ifort compiler with icc (dmpar)
# 16. Linux x86_64 i486 i586 i686, ifort compiler with icc (dm+sm)
# 32. x86_64 Linux, gfortran compiler with gcc (serial)
# 33. x86_64 Linux, gfortran compiler with gcc (smpar)
# 34. x86_64 Linux, gfortran compiler with gcc (dmpar)
# 35. x86_64 Linux, gfortran compiler with gcc (dm+sm)
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (build_type_option, bt)
# run configure script
cmd = "./configure"
qa = {
# named group in match will be used to construct answer
"Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:": "1",
"Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:": "0"
}
no_qa = [
"testing for fseeko and fseeko64",
r"If you wish to change the default options, edit the file:[\s
]*arch/configure_new.defaults"
]
def configure_step(self):
"""Custom configuration procedure for WRF-Fire."""
comp_fam = self.toolchain.comp_family()
# define $NETCDF* for netCDF dependency
netcdf_fortran = get_software_root('netCDF-Fortran')
if netcdf_fortran:
env.setvar('NETCDF', netcdf_fortran)
else:
raise EasyBuildError("Required dependendy netCDF-Fortran is missing")
# define $PHDF5 for parallel HDF5 dependency
hdf5 = get_software_root('HDF5')
if hdf5 and os.path.exists(os.path.join(hdf5, 'bin', 'h5pcc')):
env.setvar('PHDF5', hdf5)
# first, configure WRF part
change_dir(os.path.join(self.cfg['start_dir'], 'WRFV3'))
# instruct WRF-Fire to create netCDF v4 output files
env.setvar('WRFIO_NETCDF4_FILE_SUPPORT', '1')
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join('arch', 'Config_new.pl'))
# determine build type option to look for
known_build_type_options = {
toolchain.INTELCOMP: "Linux x86_64 i486 i586 i686, ifort compiler with icc",
toolchain.GCC: "x86_64 Linux, gfortran compiler with gcc",
toolchain.PGI: "Linux x86_64, PGI compiler with pgcc",
}
build_type_option = known_build_type_options.get(comp_fam)
if build_type_option is None:
raise EasyBuildError("Don't know which WPS configure option to select for compiler family %s", comp_fam)
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (build_type_option, self.cfg['buildtype'])
qa = {
"Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:": '1',
}
std_qa = {
# named group in match will be used to construct answer
r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question: '%(nr)s',
}
run_cmd_qa('./configure', qa, std_qa=std_qa, log_all=True, simple=True)
cpp_flag = None
if comp_fam == toolchain.INTELCOMP:
cpp_flag = '-fpp'
elif comp_fam == toolchain.GCC:
cpp_flag = '-cpp'
else:
raise EasyBuildError("Don't know which flag to use to specify that Fortran files were preprocessed")
# patch configure.wrf to get things right
comps = {
'CFLAGS_LOCAL': os.getenv('CFLAGS'),
'DM_FC': os.getenv('MPIF90'),
'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
'FCOPTIM': os.getenv('FFLAGS'),
# specify that Fortran files have been preprocessed with cpp,
# see http://forum.wrfforum.com/viewtopic.php?f=5&t=6086
'FORMAT_FIXED': "-FI %s" % cpp_flag,
'FORMAT_FREE': "-FR %s" % cpp_flag,
}
regex_subs = [(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v) for (k, v) in comps.items()]
apply_regex_substitutions('configure.wrf', regex_subs)
# also configure WPS part
change_dir(os.path.join(self.cfg['start_dir'], 'WPS'))
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join('arch', 'Config.pl'))
# determine build type option to look for
known_build_type_options = {
toolchain.INTELCOMP: "PC Linux x86_64, Intel compiler",
toolchain.GCC: "PC Linux x86_64, g95 compiler",
toolchain.PGI: "PC Linux x86_64 (IA64 and Opteron), PGI compiler 5.2 or higher",
}
build_type_option = known_build_type_options.get(comp_fam)
if build_type_option is None:
raise EasyBuildError("Don't know which WPS configure option to select for compiler family %s", comp_fam)
known_wps_build_types = {
'dmpar': 'DM parallel',
'smpar': 'serial',
}
wps_build_type = known_wps_build_types.get(self.cfg['buildtype'])
if wps_build_type is None:
raise EasyBuildError("Don't know which WPS build type to pick for '%s'", self.cfg['builddtype'])
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s.*%s(?!NO GRIB2)" % (build_type_option, wps_build_type)
std_qa = {
# named group in match will be used to construct answer
r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question: '%(nr)s',
}
run_cmd_qa('./configure', {}, std_qa=std_qa, log_all=True, simple=True)
# patch configure.wps to get things right
comps = {
'CC': '%s %s' % (os.getenv('MPICC'), os.getenv('CFLAGS')),
'FC': '%s %s' % (os.getenv('MPIF90'), os.getenv('F90FLAGS'))
}
regex_subs = [(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v) for (k, v) in comps.items()]
# specify that Fortran90 files have been preprocessed with cpp
regex_subs.extend([
(r"^(F77FLAGS\s*=\s*)", r"\1 %s " % cpp_flag),
(r"^(FFLAGS\s*=\s*)", r"\1 %s " % cpp_flag),
])
apply_regex_substitutions('configure.wps', regex_subs)
def configure_step(self):
"""Configure build:
- set required environment variables (for netCDF, JasPer)
- patch compile script and ungrib Makefile for non-default install paths of WRF and JasPer
- run configure script and figure how to select desired build option
- patch configure.wps file afterwards to fix 'serial compiler' setting
"""
# netCDF dependency check + setting env vars (NETCDF, NETCDFF)
set_netcdf_env_vars(self.log)
# WRF dependency check
wrf = get_software_root('WRF')
if wrf:
wrfdir = os.path.join(wrf,
det_wrf_subdir(get_software_version('WRF')))
else:
raise EasyBuildError("WRF module not loaded?")
self.compile_script = 'compile'
if LooseVersion(self.version) >= LooseVersion('4.0.3'):
# specify install location of WRF via $WRF_DIR (supported since WPS 4.0.3)
# see https://github.com/wrf-model/WPS/pull/102
env.setvar('WRF_DIR', wrfdir)
else:
# patch compile script so that WRF is found
regex_subs = [(r"^(\s*set\s*WRF_DIR_PRE\s*=\s*)\${DEV_TOP}(.*)$",
r"\1%s\2" % wrfdir)]
apply_regex_substitutions(self.compile_script, regex_subs)
# libpng dependency check
libpng = get_software_root('libpng')
zlib = get_software_root('zlib')
if libpng:
paths = [libpng]
if zlib:
paths.insert(0, zlib)
libpnginc = ' '.join(
['-I%s' % os.path.join(path, 'include') for path in paths])
libpnglib = ' '.join(
['-L%s' % os.path.join(path, 'lib') for path in paths])
else:
# define these as empty, assume that libpng will be available via OS (e.g. due to --filter-deps=libpng)
libpnglib = ""
libpnginc = ""
# JasPer dependency check + setting env vars
jasper = get_software_root('JasPer')
if jasper:
env.setvar('JASPERINC', os.path.join(jasper, "include"))
jasperlibdir = os.path.join(jasper, "lib")
env.setvar('JASPERLIB', jasperlibdir)
jasperlib = "-L%s" % jasperlibdir
else:
raise EasyBuildError("JasPer module not loaded?")
# patch ungrib Makefile so that JasPer is found
jasperlibs = "%s -ljasper %s -lpng" % (jasperlib, libpnglib)
regex_subs = [
(r"^(\s*-L\.\s*-l\$\(LIBTARGET\))(\s*;.*)$",
r"\1 %s\2" % jasperlibs),
(r"^(\s*\$\(COMPRESSION_LIBS\))(\s*;.*)$",
r"\1 %s\2" % jasperlibs),
]
apply_regex_substitutions(os.path.join('ungrib', 'src', 'Makefile'),
regex_subs)
# patch arch/Config.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join("arch", "Config.pl"))
# configure
# determine build type option to look for
self.comp_fam = self.toolchain.comp_family()
build_type_option = None
if LooseVersion(self.version) >= LooseVersion("3.4"):
knownbuildtypes = {'smpar': 'serial', 'dmpar': 'dmpar'}
if self.comp_fam == toolchain.INTELCOMP: # @UndefinedVariable
build_type_option = " Linux x86_64, Intel compiler"
elif self.comp_fam == toolchain.GCC: # @UndefinedVariable
if LooseVersion(self.version) >= LooseVersion("3.6"):
build_type_option = "Linux x86_64, gfortran"
else:
build_type_option = "Linux x86_64 g95"
else:
raise EasyBuildError(
"Don't know how to figure out build type to select.")
else:
knownbuildtypes = {'smpar': 'serial', 'dmpar': 'DM parallel'}
if self.comp_fam == toolchain.INTELCOMP: # @UndefinedVariable
build_type_option = "PC Linux x86_64, Intel compiler"
elif self.comp_fam == toolchain.GCC: # @UndefinedVariable
build_type_option = "PC Linux x86_64, gfortran compiler,"
knownbuildtypes['dmpar'] = knownbuildtypes['dmpar'].upper()
else:
raise EasyBuildError(
"Don't know how to figure out build type to select.")
# check and fetch selected build type
bt = self.cfg['buildtype']
if bt not in knownbuildtypes.keys():
raise EasyBuildError(
"Unknown build type: '%s'. Supported build types: %s", bt,
knownbuildtypes.keys())
# fetch option number based on build type option and selected build type
build_type_question = r"\s*(?P<nr>[0-9]+).\s*%s\s*\(?%s\)?\s*\n" % (
build_type_option, knownbuildtypes[bt])
cmd = ' '.join(
[self.cfg['preconfigopts'], './configure', self.cfg['configopts']])
qa = {}
no_qa = [".*compiler is.*"]
std_qa = {
# named group in match will be used to construct answer
r"%s(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question:
"%(nr)s",
}
run_cmd_qa(cmd,
qa,
no_qa=no_qa,
std_qa=std_qa,
log_all=True,
simple=True)
# make sure correct compilers and compiler flags are being used
comps = {
'SCC': "%s -I$(JASPERINC) %s" % (os.getenv('CC'), libpnginc),
'SFC': os.getenv('F90'),
'DM_FC': os.getenv('MPIF90'),
'DM_CC': os.getenv('MPICC'),
'FC': os.getenv('MPIF90'),
'CC': os.getenv('MPICC'),
}
if self.toolchain.options.get('openmp', None):
comps.update({
'LDFLAGS':
'%s %s' %
(self.toolchain.get_flag('openmp'), os.environ['LDFLAGS'])
})
regex_subs = [(r"^(%s\s*=\s*).*$" % key, r"\1 %s" % val)
for (key, val) in comps.items()]
apply_regex_substitutions('configure.wps', regex_subs)
def install_step(self):
"""Install CUDA using Perl install script."""
# define how to run the installer
# script has /usr/bin/perl hardcoded, but we want to have control over which perl is being used
if LooseVersion(self.version) <= LooseVersion("5"):
install_interpreter = "perl"
install_script = "install-linux.pl"
self.cfg.update('installopts', '--prefix=%s' % self.installdir)
elif LooseVersion(self.version) > LooseVersion("5") and LooseVersion(self.version) < LooseVersion("10.1"):
install_interpreter = "perl"
install_script = "cuda-installer.pl"
# note: samples are installed by default
self.cfg.update('installopts', "-verbose -silent -toolkitpath=%s -toolkit" % self.installdir)
else:
install_interpreter = ""
install_script = "./cuda-installer"
# samples are installed in two places with identical copies:
# self.installdir/samples and $HOME/NVIDIA_CUDA-11.2_Samples
# changing the second location (the one under $HOME) to a scratch location using
# --samples --samplespath=self.builddir
# avoids the duplicate and pollution of the home directory of the installer.
self.cfg.update('installopts',
"--silent --samples --samplespath=%s --toolkit --toolkitpath=%s --defaultroot=%s" % (
self.builddir, self.installdir, self.installdir))
# When eb is called via sudo -u someuser -i eb ..., the installer may try to chown samples to the
# original user using the SUDO_USER environment variable, which fails
if "SUDO_USER" in os.environ:
self.log.info("SUDO_USER was defined as '%s', need to unset it to avoid problems..." %
os.environ["SUDO_USER"])
del os.environ["SUDO_USER"]
if LooseVersion("10.0") < LooseVersion(self.version) < LooseVersion("10.2") and get_cpu_architecture() == POWER:
# Workaround for
# https://devtalk.nvidia.com/default/topic/1063995/cuda-setup-and-installation/cuda-10-1-243-10-1-update-2-ppc64le-run-file-installation-issue/
install_script = " && ".join([
"mkdir -p %(installdir)s/targets/ppc64le-linux/include",
"([ -e %(installdir)s/include ] || ln -s targets/ppc64le-linux/include %(installdir)s/include)",
"cp -r %(builddir)s/builds/cublas/src %(installdir)s/.",
install_script
]) % {
'installdir': self.installdir,
'builddir': self.builddir
}
# Use C locale to avoid localized questions and crash on CUDA 10.1
self.cfg.update('preinstallopts', "export LANG=C && ")
cmd = "%(preinstallopts)s %(interpreter)s %(script)s %(installopts)s" % {
'preinstallopts': self.cfg['preinstallopts'],
'interpreter': install_interpreter,
'script': install_script,
'installopts': self.cfg['installopts']
}
# prepare for running install script autonomously
qanda = {}
stdqa = {
# this question is only asked if CUDA tools are already available system-wide
r"Would you like to remove all CUDA files under .*? (yes/no/abort): ": "no",
}
noqanda = [
r"^Configuring",
r"Installation Complete",
r"Verifying archive integrity.*",
r"^Uncompressing NVIDIA CUDA",
r".* -> .*",
]
# patch install script to handle Q&A autonomously
if install_interpreter == "perl":
patch_perl_script_autoflush(os.path.join(self.builddir, install_script))
p5lib = os.getenv('PERL5LIB', '')
if p5lib == '':
p5lib = self.builddir
else:
p5lib = os.pathsep.join([self.builddir, p5lib])
env.setvar('PERL5LIB', p5lib)
# make sure $DISPLAY is not defined, which may lead to (weird) problems
# this is workaround for not being able to specify --nox11 to the Perl install scripts
if 'DISPLAY' in os.environ:
os.environ.pop('DISPLAY')
# cuda-installer creates /tmp/cuda-installer.log (ignoring TMPDIR)
# Try to remove it before running the installer.
# This will fail with a usable error if it can't be removed
# instead of segfaulting in the cuda-installer.
remove_file('/tmp/cuda-installer.log')
# overriding maxhits default value to 1000 (seconds to wait for nothing to change in the output
# without seeing a known question)
run_cmd_qa(cmd, qanda, std_qa=stdqa, no_qa=noqanda, log_all=True, simple=True, maxhits=1000)
# Remove the cuda-installer log file
remove_file('/tmp/cuda-installer.log')
# check if there are patches to apply
if len(self.src) > 1:
for patch in self.src[1:]:
self.log.debug("Running patch %s", patch['name'])
run_cmd("/bin/sh " + patch['path'] + " --accept-eula --silent --installdir=" + self.installdir)
def configure_step(self):
"""Configure build:
- set required environment variables (for netCDF, JasPer)
- patch compile script and ungrib Makefile for non-default install paths of WRF and JasPer
- run configure script and figure how to select desired build option
- patch configure.wps file afterwards to fix 'serial compiler' setting
"""
# netCDF dependency check + setting env vars (NETCDF, NETCDFF)
set_netcdf_env_vars(self.log)
# WRF dependency check
wrf = get_software_root('WRF')
if wrf:
wrfdir = os.path.join(wrf, det_wrf_subdir(get_software_version('WRF')))
else:
raise EasyBuildError("WRF module not loaded?")
# patch compile script so that WRF is found
self.compile_script = "compile"
regex_subs = [(r"^(\s*set\s*WRF_DIR_PRE\s*=\s*)\${DEV_TOP}(.*)$", r"\1%s\2" % wrfdir)]
apply_regex_substitutions(self.compile_script, regex_subs)
# libpng dependency check
libpng = get_software_root('libpng')
zlib = get_software_root('zlib')
if libpng:
paths = [libpng]
if zlib:
paths.insert(0, zlib)
libpnginc = ' '.join(['-I%s' % os.path.join(path, 'include') for path in paths])
libpnglib = ' '.join(['-L%s' % os.path.join(path, 'lib') for path in paths])
else:
# define these as empty, assume that libpng will be available via OS (e.g. due to --filter-deps=libpng)
libpnglib = ""
libpnginc = ""
# JasPer dependency check + setting env vars
jasper = get_software_root('JasPer')
if jasper:
env.setvar('JASPERINC', os.path.join(jasper, "include"))
jasperlibdir = os.path.join(jasper, "lib")
env.setvar('JASPERLIB', jasperlibdir)
jasperlib = "-L%s" % jasperlibdir
else:
raise EasyBuildError("JasPer module not loaded?")
# patch ungrib Makefile so that JasPer is found
jasperlibs = "%s -ljasper %s -lpng" % (jasperlib, libpnglib)
regex_subs = [
(r"^(\s*-L\.\s*-l\$\(LIBTARGET\))(\s*;.*)$", r"\1 %s\2" % jasperlibs),
(r"^(\s*\$\(COMPRESSION_LIBS\))(\s*;.*)$", r"\1 %s\2" % jasperlibs),
]
apply_regex_substitutions(os.path.join('ungrib', 'src', 'Makefile'), regex_subs)
# patch arch/Config.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join("arch", "Config.pl"))
# configure
# determine build type option to look for
self.comp_fam = self.toolchain.comp_family()
build_type_option = None
if LooseVersion(self.version) >= LooseVersion("3.4"):
knownbuildtypes = {
'smpar': 'serial',
'dmpar': 'dmpar'
}
if self.comp_fam == toolchain.INTELCOMP: # @UndefinedVariable
build_type_option = " Linux x86_64, Intel compiler"
elif self.comp_fam == toolchain.GCC: # @UndefinedVariable
build_type_option = "Linux x86_64 g95 compiler"
else:
raise EasyBuildError("Don't know how to figure out build type to select.")
else:
knownbuildtypes = {
'smpar': 'serial',
'dmpar': 'DM parallel'
}
if self.comp_fam == toolchain.INTELCOMP: # @UndefinedVariable
build_type_option = "PC Linux x86_64, Intel compiler"
elif self.comp_fam == toolchain.GCC: # @UndefinedVariable
build_type_option = "PC Linux x86_64, gfortran compiler,"
knownbuildtypes['dmpar'] = knownbuildtypes['dmpar'].upper()
else:
raise EasyBuildError("Don't know how to figure out build type to select.")
# check and fetch selected build type
bt = self.cfg['buildtype']
if bt not in knownbuildtypes.keys():
raise EasyBuildError("Unknown build type: '%s'. Supported build types: %s", bt, knownbuildtypes.keys())
# fetch option number based on build type option and selected build type
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(?%s\)?\s*\n" % (build_type_option, knownbuildtypes[bt])
cmd = "./configure"
qa = {}
no_qa = [".*compiler is.*"]
std_qa = {
# named group in match will be used to construct answer
r"%s(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question: "%(nr)s",
}
run_cmd_qa(cmd, qa, no_qa=no_qa, std_qa=std_qa, log_all=True, simple=True)
# make sure correct compilers and compiler flags are being used
comps = {
'SCC': "%s -I$(JASPERINC) %s" % (os.getenv('CC'), libpnginc),
'SFC': os.getenv('F90'),
'DM_FC': os.getenv('MPIF90'),
'DM_CC': os.getenv('MPICC'),
'FC': os.getenv('MPIF90'),
'CC': os.getenv('MPICC'),
}
regex_subs = [(r"^(%s\s*=\s*).*$" % key, r"\1 %s" % val) for (key, val) in comps.items()]
apply_regex_substitutions('configure.wps', regex_subs)
def configure_step(self):
"""Custom configuration procedure for WRF-Fire."""
comp_fam = self.toolchain.comp_family()
# define $NETCDF* for netCDF dependency
netcdf_fortran = get_software_root('netCDF-Fortran')
if netcdf_fortran:
env.setvar('NETCDF', netcdf_fortran)
else:
raise EasyBuildError(
"Required dependendy netCDF-Fortran is missing")
# define $PHDF5 for parallel HDF5 dependency
hdf5 = get_software_root('HDF5')
if hdf5 and os.path.exists(os.path.join(hdf5, 'bin', 'h5pcc')):
env.setvar('PHDF5', hdf5)
# first, configure WRF part
change_dir(os.path.join(self.cfg['start_dir'], 'WRFV3'))
# instruct WRF-Fire to create netCDF v4 output files
env.setvar('WRFIO_NETCDF4_FILE_SUPPORT', '1')
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join('arch', 'Config_new.pl'))
# determine build type option to look for
known_build_type_options = {
toolchain.INTELCOMP:
"Linux x86_64 i486 i586 i686, ifort compiler with icc",
toolchain.GCC: "x86_64 Linux, gfortran compiler with gcc",
toolchain.PGI: "Linux x86_64, PGI compiler with pgcc",
}
build_type_option = known_build_type_options.get(comp_fam)
if build_type_option is None:
raise EasyBuildError(
"Don't know which WPS configure option to select for compiler family %s",
comp_fam)
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (
build_type_option, self.cfg['buildtype'])
qa = {
"Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:":
'1',
}
std_qa = {
# named group in match will be used to construct answer
r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question:
'%(nr)s',
}
run_cmd_qa('./configure', qa, std_qa=std_qa, log_all=True, simple=True)
cpp_flag = None
if comp_fam == toolchain.INTELCOMP:
cpp_flag = '-fpp'
elif comp_fam == toolchain.GCC:
cpp_flag = '-cpp'
else:
raise EasyBuildError(
"Don't know which flag to use to specify that Fortran files were preprocessed"
)
# patch configure.wrf to get things right
comps = {
'CFLAGS_LOCAL': os.getenv('CFLAGS'),
'DM_FC': os.getenv('MPIF90'),
'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
'FCOPTIM': os.getenv('FFLAGS'),
# specify that Fortran files have been preprocessed with cpp,
# see http://forum.wrfforum.com/viewtopic.php?f=5&t=6086
'FORMAT_FIXED': "-FI %s" % cpp_flag,
'FORMAT_FREE': "-FR %s" % cpp_flag,
}
regex_subs = [(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v)
for (k, v) in comps.items()]
apply_regex_substitutions('configure.wrf', regex_subs)
# also configure WPS part
change_dir(os.path.join(self.cfg['start_dir'], 'WPS'))
# patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
patch_perl_script_autoflush(os.path.join('arch', 'Config.pl'))
# determine build type option to look for
known_build_type_options = {
toolchain.INTELCOMP:
"PC Linux x86_64, Intel compiler",
toolchain.GCC:
"PC Linux x86_64, g95 compiler",
toolchain.PGI:
"PC Linux x86_64 (IA64 and Opteron), PGI compiler 5.2 or higher",
}
build_type_option = known_build_type_options.get(comp_fam)
if build_type_option is None:
raise EasyBuildError(
"Don't know which WPS configure option to select for compiler family %s",
comp_fam)
known_wps_build_types = {
'dmpar': 'DM parallel',
'smpar': 'serial',
}
wps_build_type = known_wps_build_types.get(self.cfg['buildtype'])
if wps_build_type is None:
raise EasyBuildError(
"Don't know which WPS build type to pick for '%s'",
self.cfg['builddtype'])
build_type_question = "\s*(?P<nr>[0-9]+).\s*%s.*%s(?!NO GRIB2)" % (
build_type_option, wps_build_type)
std_qa = {
# named group in match will be used to construct answer
r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question:
'%(nr)s',
}
run_cmd_qa('./configure', {}, std_qa=std_qa, log_all=True, simple=True)
# patch configure.wps to get things right
comps = {
'CC': '%s %s' % (os.getenv('MPICC'), os.getenv('CFLAGS')),
'FC': '%s %s' % (os.getenv('MPIF90'), os.getenv('F90FLAGS'))
}
regex_subs = [(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v)
for (k, v) in comps.items()]
# specify that Fortran90 files have been preprocessed with cpp
regex_subs.extend([
(r"^(F77FLAGS\s*=\s*)", r"\1 %s " % cpp_flag),
(r"^(FFLAGS\s*=\s*)", r"\1 %s " % cpp_flag),
])
apply_regex_substitutions('configure.wps', regex_subs)
