def so_dirs_path(self, flags):
"""
Assemble path for shared libraries in nonstandard directories.
"""
retval = separate_args(self.pkg.config.rpath)
i = len(retval) - 1
if i < 0:
return
count = 0
pkg_lib = os.path.join(self.pkg.get_dir('libdir'), self.pkg.name)
if os.path.isdir(pkg_lib):
retval[i] += ":" + pkg_lib
count += 1
if type(flags) == str:
args = separate_args(flags)
else:
args = flags
for arg in args:
if (arg[0:2] == '-L' and arg[0:10] != '-L/usr/lib'
and arg[0:6] != '-L/lib'):
retval[i] += ":" + arg[2:]
count += 1
if count == 0:
retval = ""
return retval
def get_flags(self, flag):
"""
Determine compilation flags for a given flag type.
"""
cmd_line = self.get_pkg_path_flags(flag)
# Build the command line, and split possible multiple arguments in lists.
for lib in self.pkg.config.deplibs:
if (self.pkg.config.libs[lib].have == "yes"
and (not self.pkg.config.libs[lib].dynamic_load)):
cmd_line += separate_args(
self.pkg.config.libs[lib].flags[flag])
# Specific handling of low-level libraries, which should come last,
# such as -lm and -lpthread:
# If -lm appears multiple times, only add it at the end of the
# libraries, so that fast versions of the library may appear first
if flag == 'libs':
for lib in ['-lpthread', '-lm']:
n = cmd_line.count(lib)
if n > 0:
for i in range(n):
cmd_line.remove(lib)
cmd_line.append(lib)
# Adapt for relocation on build stage on some systems
self.flags_relocation(flag, cmd_line)
return cmd_line
def run_studymanager_command(_c, _log, pythondir=None):
"""
Run command with arguments.
Redirection of the stdout or stderr of the command.
"""
assert type(_c) == str or type(_c) == unicode
log.debug("run_studymanager_command: %s" % _c)
try:
_log.seek(0, os.SEEK_END)
except:
_log.seek(0, 2)
def __text(_t):
return "\n\nExecution failed --> %s: %s" \
"\n - command: %s" \
"\n - directory: %s\n\n" % \
(_t, str(retcode), _c, os.getcwd())
_l = ""
cmd = separate_args(_c)
env = os.environ.copy()
if pythondir:
pythondir = enquote_arg(pythondir)
pythonpath = pythondir + ':' + env.get("PYTHONPATH", '')
env.update([("PYTHONPATH", pythonpath)])
try:
t1 = time.time()
retcode = run_command(cmd, stdout=_log, stderr=_log, env=env)
t2 = time.time()
if retcode < 0:
_l = __text("command was terminated by signal")
elif retcode > 0:
_l = __text("command return")
except OSError:
import traceback
import sys
exc_info = sys.exc_info()
bt = traceback.format_exception(*exc_info)
for l in bt:
_log.write(l)
retcode = 0
del exc_info
_l = __text("unknown command")
t1 = 0.
t2 = 0.
_log.flush()
if _l:
_log.write(_l)
return retcode, "%.2f" % (t2 - t1)
def get_coupling(self):
"""
Get the coupling option in the run command
"""
args = separate_args(self.lines[self.run_cmd_line_id])
return get_command_single_value(args, ('--coupling', '--coupling='))
def get_nprocs(self):
"""
Get the nprocs option in the run command
"""
args = separate_args(self.lines[self.run_cmd_line_id])
return get_command_single_value(args, ('--nprocs', '--nprocs=', '-n'))
def get_parameters(self):
"""
Get the parameters option in the run command
"""
args = separate_args(self.lines[self.run_cmd_line_id])
return get_command_single_value(args, ('--param', '--param=', '-p'))
def get_compute_build(self):
"""
Get the compute-build option in the run command
"""
args = separate_args(self.lines[self.run_cmd_line_id])
return get_command_single_value(
args, ('--compute-build', '--compute-build='))
def get_nthreads(self):
"""
Get the nthreads option in the run command
"""
args = separate_args(self.lines[self.run_cmd_line_id])
return get_command_single_value(
args, ('--threads-per-task', '--threads-per-task=', '-nt'))
def set_run_stage(self, stage, present=False):
"""
Specify the given stage in the run command
"""
line = self.lines[self.run_cmd_line_id]
args = update_command_no_value(separate_args(line), ('--' + stage, ),
present)
self.lines[self.run_cmd_line_id] = assemble_args(args)
def set_nprocs(self, parameters):
"""
Set the nprocs option in the run command
"""
line = self.lines[self.run_cmd_line_id]
args = update_command_single_value(separate_args(line),
('--nprocs', '--nprocs=', '-n'),
enquote_arg(parameters))
self.lines[self.run_cmd_line_id] = assemble_args(args)
def set_coupling(self, coupling):
"""
Set the coupling option in the run command
"""
line = self.lines[self.run_cmd_line_id]
args = update_command_single_value(separate_args(line),
('--coupling',),
enquote_arg(coupling))
self.lines[self.run_cmd_line_id] = assemble_args(args)
def set_compute_build(self, parameters):
"""
Set the compute-build option in the run command
"""
line = self.lines[self.run_cmd_line_id]
args = update_command_single_value(
separate_args(line), ('--compute-build', '--compute-build='),
enquote_arg(parameters))
self.lines[self.run_cmd_line_id] = assemble_args(args)
def get_run_stage(self, stage):
"""
Return True if a given stage is specified in the run command,
False otherwise
"""
args = separate_args(self.lines[self.run_cmd_line_id])
s_arg = '--' + stage
if s_arg in args:
return True
return False
def set_nthreads(self, parameters):
"""
Set the nthreads option in the run command
"""
line = self.lines[self.run_cmd_line_id]
args = update_command_single_value(
separate_args(line),
('--threads-per-task', '--threads-per-task=', '-nt'),
enquote_arg(parameters))
self.lines[self.run_cmd_line_id] = assemble_args(args)
def get_run_command(self):
"""
Determine the name of the main command of the runcase, and the associated
line in the file; this allows mixing Code_Saturne and NEPTUNE_CFD
cases in the same study.
"""
# Read the runcase script from the Repository.
self.cmd_name = None
self.run_cmd_line_id = -1
for i in range(len(self.lines) - 1, -1, -1):
line = self.lines[i]
# Skip comment and empty lines
if len(line) == 0:
continue
if line[0] == '#' or line[0:4] == 'rem ':
continue
j = line.find('#')
if j > -1:
line = line[0:j]
args = separate_args(line.strip())
if args.count('run') == 1:
if args.index('run') == 1: # "<package_name> run"
for name in ('code_saturne', 'neptune_cfd'):
if sys.platform.startswith('win'):
test_name = name
if args[0].find(test_name) == 0:
self.cmd_name = name
self.run_cmd_line_id = i
return
test_name = '\\' + name
if args[0].find(test_name) == 0:
self.cmd_name = name
self.run_cmd_line_id = i
return
elif args[0] == name:
self.cmd_name = name
self.run_cmd_line_id = i
return
# We should have exited before reaching this.
err_str = "Error: unable to determine the name of the script for " + self.path + os.linesep
sys.stderr.write(err_str)
def get_run_id(self):
"""
Get the run id, id_prefix, and id_suffix options in the run command
"""
args = separate_args(self.lines[self.run_cmd_line_id])
run_id = get_command_single_value(args, ('--id', '--id='))
run_id_prefix = get_command_single_value(
args, ('--id-prefix', '--id-prefix='))
run_id_suffix = get_command_single_value(
args, ('--id-suffix', '--id-suffix='))
return run_id, run_id_prefix, run_id_suffix
def get_flags(self, flag, base_name=None):
"""
Determine compilation flags for a given flag type.
"""
cmd_line = self.get_pkg_path_flags(flag)
# Build the command line, and split possible multiple arguments in lists.
for lib in self.pkg.config.deplibs:
if (self.pkg.config.libs[lib].have == "yes"
and (not self.pkg.config.libs[lib].dynamic_load)):
cmd_line += separate_args(
self.pkg.config.libs[lib].flags[flag])
if flag == 'cppflags' and base_name:
add_dirs = []
if base_name in self.pkg.config.exec_include:
add_dirs.append(self.pkg.config.exec_include[base_name])
for a_d in add_dirs:
d = os.path.join(self.pkg.get_dir("includedir"), a_d)
if os.path.isdir(d):
add_flag = "-I" + d
if add_flag not in cmd_line:
cmd_line.insert(0, add_flag)
# Specific handling of low-level libraries, which should come last,
# such as -lm and -lpthread:
# If -lm appears multiple times, only add it at the end of the
# libraries, so that fast versions of the library may appear first
if flag == 'libs':
for lib in ['-lpthread', '-lm']:
n = cmd_line.count(lib)
if n > 0:
for i in range(n):
cmd_line.remove(lib)
cmd_line.append(lib)
# Adapt for relocation on build stage on some systems
self.flags_relocation(flag, cmd_line)
return cmd_line
def set_run_id(self, run_id=None, run_id_prefix=None, run_id_suffix=None):
"""
Set the run id, id_prefix, and id_suffix options in the run command
"""
line = self.lines[self.run_cmd_line_id]
args = separate_args(line)
if run_id != None:
args = update_command_single_value(args, ('--id', '--id='),
enquote_arg(run_id))
if run_id_prefix != None:
args = update_command_single_value(args,
('--id-prefix', '--id-prefix='),
enquote_arg(run_id_prefix))
if run_id_suffix != None:
args = update_command_single_value(args,
('--id-suffix', '--id-suffix='),
enquote_arg(run_id_suffix))
self.lines[self.run_cmd_line_id] = assemble_args(args)
def link_obj(self,
exec_name,
obj_files=None,
opt_libs=None,
stdout=sys.stdout,
stderr=sys.stderr):
"""
Link function.
"""
retval = 0
# Short names
pkg = self.pkg
# Directories
call_dir = None
temp_dir = None
o_files = obj_files
p_libs = self.get_flags('libs')
# Special handling for some linkers (such as Mac OS X), for which
# no multiple definitions are allowable in static mode;
# in this case, extract archive, then overwrite with user files.
if pkg.config.special_user_link == 'ar_x':
call_dir = os.getcwd()
temp_dir = tempfile.mkdtemp(suffix=".cs_link")
os.chdir(temp_dir)
lib0 = os.path.join(self.get_ar_lib_dir(),
'lib' + p_libs[0][2:] + '.a')
p_libs = p_libs[1:]
cmd = ['ar', 'x', lib0]
if run_command(
cmd, pkg=pkg, echo=True, stdout=stdout,
stderr=stderr) != 0:
retval = 1
if obj_files:
import shutil
for f in obj_files:
if os.path.isabs(f):
f_src = f
else:
f_src = os.path.join(call_dir, f)
shutil.copy2(f_src, temp_dir)
dir_files = os.listdir(os.getcwd())
o_files = fnmatch.filter(dir_files, '*.o')
# Prepare link command
cmd = [self.get_compiler('ld')]
cmd += ["-o", exec_name]
if o_files:
cmd += o_files
# If present, address sanitizer needs to come first
if '-lasan' in p_libs:
p_libs.remove('-lasan')
cmd += ['-lasan']
if os.path.basename(exec_name) in self.pkg.config.exec_libs:
cmd += [self.pkg.config.exec_libs[os.path.basename(exec_name)]]
if opt_libs != None:
if len(opt_libs) > 0:
cmd += separate_args(opt_libs)
cmd += self.get_flags('ldflags')
cmd += p_libs
if pkg.config.rpath != "":
cmd += self.so_dirs_path(cmd)
# Clean paths in link flags
cmd_new = []
for c in cmd:
if c[:2] == '-L':
c = '-L' + os.path.normpath(c[2:])
if cmd_new.count(c) < 1:
cmd_new.append(c)
else:
cmd_new.append(c)
cmd = cmd_new
# Call linker
if retval == 0:
if run_command(
cmd, pkg=pkg, echo=True, stdout=stdout,
stderr=stderr) != 0:
retval = 1
# Cleanup for special cases
if temp_dir:
if not os.path.isabs(exec_name):
import shutil
shutil.copy2(exec_name, os.path.join(call_dir, exec_name))
for f in os.listdir(temp_dir):
os.remove(os.path.join(temp_dir, f))
os.chdir(call_dir)
os.rmdir(temp_dir)
return retval
def compile_src(self,
src_list=None,
opt_cflags=None,
opt_cxxflags=None,
opt_fcflags=None,
keep_going=False,
stdout=sys.stdout,
stderr=sys.stderr):
"""
Compilation function.
"""
retval = 0
# Short names
pkg = self.pkg
# Find files to compile in source path
c_files = fnmatch.filter(src_list, '*.c')
h_files = fnmatch.filter(src_list, '*.h')
cxx_files = fnmatch.filter(src_list, '*.cxx') + fnmatch.filter(
src_list, '*.cpp')
hxx_files = fnmatch.filter(src_list, '*.hxx') + fnmatch.filter(
src_list, '*.hpp')
f_files = fnmatch.filter(src_list, '*.[fF]90')
o_files = fnmatch.filter(src_list, '*.o')
# Determine additional include directories
c_include_dirs = []
for f in h_files:
c_include_dirs.append(os.path.dirname(f))
c_include_dirs = sorted(set(c_include_dirs))
cxx_include_dirs = []
for f in hxx_files:
cxx_include_dirs.append(os.path.dirname(f))
cxx_include_dirs = sorted(set(cxx_include_dirs))
f_include_dirs = []
for f in f_files:
f_include_dirs.append(os.path.dirname(f))
f_include_dirs = sorted(set(cxx_include_dirs))
# Compile files
for f in c_files:
if (retval != 0 and not keep_going):
break
cmd = [self.get_compiler('cc')]
if opt_cflags != None:
cmd += separate_args(opt_cflags)
for d in c_include_dirs:
cmd += ["-I", d]
cmd.append('-DHAVE_CONFIG_H')
if os.path.basename(f) == 'cs_base.c':
cmd += ['-DLOCALEDIR=\\"' + pkg.get_dir('localedir') + '\\"', \
'-DPKGDATADIR=\\"' + pkg.get_dir('pkgdatadir') + '\\"']
cmd += self.get_flags('cppflags')
cmd += separate_args(pkg.config.flags['cflags'])
cmd += ["-c", f]
if run_command(
cmd, pkg=pkg, echo=True, stdout=stdout,
stderr=stderr) != 0:
retval = 1
o_files.append(self.obj_name(f))
for f in cxx_files:
if (retval != 0 and not keep_going):
break
cmd = [self.get_compiler('cxx')]
if opt_cxxflags != None:
cmd += separate_args(opt_cxxflags)
for d in cxx_include_dirs:
cmd += ["-I", d]
for d in c_include_dirs:
cmd += ["-I", d]
cmd.append('-DHAVE_CONFIG_H')
cmd += self.get_flags('cppflags')
cmd += separate_args(pkg.config.flags['cxxflags'])
cmd += ["-c", f]
if run_command(
cmd, pkg=pkg, echo=True, stdout=stdout,
stderr=stderr) != 0:
retval = 1
o_files.append(self.obj_name(f))
for f in f_files:
if (retval != 0 and not keep_going):
break
cmd = [self.get_compiler('fc')]
f_base = os.path.basename(f)
o_name = self.obj_name(f)
if f_base == 'cs_user_boundary_conditions.f90':
o_name = "cs_f_user_boundary_conditions.o"
cmd += ["-o", o_name]
if f_base == 'cs_user_parameters.f90':
o_name = "cs_f_user_parameters.o"
cmd += ["-o", o_name]
if f_base == 'cs_user_extra_operations.f90':
o_name = "cs_f_user_extra_operations.o"
cmd += ["-o", o_name]
if f_base == 'cs_user_initialization.f90':
o_name = "cs_f_user_initialization.o"
cmd += ["-o", o_name]
if f_base == 'cs_user_physical_properties.f90':
o_name = "cs_f_user_physical_properties.o"
cmd += ["-o", o_name]
if f_base == 'cs_user_porosity.f90':
o_name = "cs_f_user_porosity.o"
cmd += ["-o", o_name]
if opt_fcflags != None:
cmd += separate_args(opt_fcflags)
for d in f_include_dirs:
cmd += ["-I", d]
if pkg.config.fcmodinclude != "-I":
cmd += [pkg.config.fcmodinclude, srcdir]
cmd += ["-I", pkg.get_dir('pkgincludedir')]
if pkg.config.fcmodinclude != "-I":
cmd += [pkg.config.fcmodinclude, pkg.get_dir('pkgincludedir')]
cmd += separate_args(pkg.config.flags['fcflags'])
cmd += ["-c", f]
if run_command(
cmd, pkg=pkg, echo=True, stdout=stdout,
stderr=stderr) != 0:
retval = 1
o_files.append(o_name)
return retval, o_files
def get_run_args(self):
"""
Get the run command and arguments, as a list
"""
return separate_args(self.lines[self.run_cmd_line_id])