def __coupled_run_cfg__(self,
distrep,
coupled_domains=[]):
"""
"""
if len(coupled_domains) == 0:
return
run_conf_path = os.path.join(distrep, 'run.cfg')
run_conf = cs_run_conf.run_conf(run_conf_path,
package=self.package,
create_if_missing=True)
domains = ""
for i, dom in enumerate(coupled_domains):
dom_name = dom["domain"]
if i != 0:
domains+=":"
domains+=dom_name
for key in dom.keys():
run_conf.set(dom_name, key, dom[key])
if domains != "":
run_conf.set('setup', 'coupled_domains', domains)
run_conf.save()
def generate_run_config_file(path, resource_name, r_c, s_c, pkg):
"""
Generate a minimalist run configuration file in the execution directory
for successive run steps.
Returns job submission info dictionnary
"""
sections = {}
if path and r_c['casedir']:
in_case = cs_case.is_exec_dir_in_case(r_c['casedir'],
os.path.dirname(path))
if not in_case:
sections['paths'] = {'case': r_c['casedir']}
if r_c['dest_dir']:
sections['paths']['top_results_directory'] = r_c['dest_dir']
if 'coupled_domains' in r_c:
if r_c['coupled_domains'] != []:
dom_str=''
for i, d in enumerate(r_c['coupled_domains']):
dom_name = d['domain']
if i != 0:
dom_str += ':'
dom_str += dom_name
# Add the domain section
sections[dom_name] = {key:str(d[key]) for key in d.keys()}
sections['setup'] = {'coupled_domains': dom_str}
sections['run'] = {'compute_build': r_c['compute_build'],
'id': r_c['run_id'],
'stage': False,
'initialize': s_c['initialize'],
'compute': s_c['run_solver'],
'finalize': s_c['save_results']}
r_d = {}
for kw in ('n_procs', 'n_threads', 'time_limit'):
if r_c[kw]:
r_d[kw] = r_c[kw]
for kw in ('job_parameters', 'job_header',
'compute_prologue', 'compute_epilogue'):
if r_c[kw]:
r_d[kw] = r_c[kw]
sections[resource_name] = r_d
run_conf = cs_run_conf.run_conf(None)
run_conf.sections = sections
run_conf.save(path, new=True)
def __init__(self, path=None, pkg=None, import_legacy=False):
"""
Constructor.
"""
self.pkg = pkg
if self.pkg == None:
from code_saturne.cs_package import package
pkg = package()
self.run_conf = None
self.path = path
# Configuration-based information
i_c = cs_run_conf.get_install_config_info(self.pkg)
self.resource_name = cs_run_conf.get_resource_name(i_c)
self.compute_builds = i_c['compute_builds']
self.batch = cs_batch.batch(self.pkg)
# Convert from legacy runcase if not updated yet
# (delaying application of file changes to save).
# in this case, the run_conf object is pre-loaded so that
# the "save" operation can apply the (conversion) changes
# even when the configuration file has not been loaded.
self.runcase_path = None
if self.path:
if import_legacy and not os.path.isfile(self.path):
dirname = os.path.dirname(self.path)
if os.path.basename(dirname) == 'DATA':
dirname = os.path.join(os.path.basename(dirname), 'SCRIPTS')
runcase_path = os.path.join(dirname, 'runcase')
if os.path.isfile(runcase_path):
self.runcase_path = runcase_path
if self.runcase_path:
from code_saturne import cs_runcase
runcase = cs_runcase.runcase(runcase_path,
package=self.pkg)
sections = runcase.run_conf_sections(resource_name=self.resource_name,
batch_template=i_c['batch'])
self.run_conf = cs_run_conf.run_conf(self.path,
package=self.pkg,
create_if_missing=True)
for sn in sections:
if not sn in self.run_conf.sections:
run_conf.sections[sn] = {}
for kw in sections[sn]:
self.run_conf.sections[sn][kw] = sections[sn][kw]
def load_cfg_file(self, cfgfile=None):
"""
Load a configuration file
"""
self.cfgfile = cfgfile
if self.cfgfile:
from code_saturne import cs_run_conf
self.run_conf = cs_run_conf.run_conf(self.cfgfile)
if self.run_conf:
for dom in self.run_conf.get_coupling_parameters():
self.add_tab_data(dom)
if self.data != []:
self.file_loaded = True
self.data_modified = False
def __build_run_cfg__(self,
distrep,
casename,
coupling=None,
cathare_path=None):
"""
Retrieve batch file for the current system
Update batch file for the study
"""
run_conf_path = os.path.join(distrep, 'run.cfg')
if self.copy is not None:
ref_run_conf_path = os.path.join(self.copy, 'DATA', 'run.cfg')
try:
shutil.copy(ref_run_conf_path, run_conf_path)
except Exception:
pass
# Add info from parent in case of copy
run_conf = cs_run_conf.run_conf(run_conf_path,
package=self.package,
create_if_missing=True)
if coupling:
run_conf.set('setup', 'coupling', coupling)
# If a cathare LIBPATH is given, it is added to LD_LIBRARY_PATH.
# This modification is needed for the dlopen of the cathare .so file
if cathare_path:
i_c = cs_run_conf.get_install_config_info(self.package)
resource_name = cs_run_conf.get_resource_name(i_c)
v25_3_line = "export v25_3=%s\n" % cathare_path
new_line = "export LD_PATH_LIBRARY=$v25_3/%s/" + ":$LD_LIBRARY_PATH\n"
add_lines = v25_3_line
add_lines += new_line % ("lib")
add_lines += new_line % ("ICoCo/lib")
run_conf.set(resource_name, 'compute_prologue', add_lines)
run_conf.save()
def __build_run_cfg__(self, distrep, casename):
"""
Retrieve batch file for the current system
Update batch file for the study
"""
run_conf_path = os.path.join(distrep, 'run.cfg')
if self.copy is not None:
ref_run_conf_path = os.path.join(self.copy, 'DATA', 'run.cfg')
try:
shutil.copy(ref_run_conf_path, run_conf_path)
except Exception:
pass
# Add info from parent in case of copy
run_conf = cs_run_conf.run_conf(run_conf_path,
package=self.package,
create_if_missing=True)
run_conf.save()
def generate_run_config_file(path, resource_name, r_c, s_c, pkg):
"""
Generate a minimalist run configuration file in the execution directory
for successive run steps.
Returns job submission info dictionnary
"""
sections = {}
if 'coupling' in r_c:
if r_c['coupling']:
sections['setup'] = {'coupling': r_c['coupling']}
sections['run'] = {
'id': r_c['run_id'],
'stage': False,
'initialize': s_c['initialize'],
'compute': s_c['run_solver'],
'finalize': s_c['save_results']
}
r_d = {}
for kw in ('n_procs', 'n_threads', 'time_limit'):
if r_c[kw]:
r_d[kw] = r_c[kw]
for kw in ('job_parameters', 'job_header', 'compute_prologue',
'compute_epilogue'):
if r_c[kw]:
r_d[kw] = r_c[kw]
sections[resource_name] = r_d
run_conf = cs_run_conf.run_conf(None)
run_conf.sections = sections
run_conf.save(path, new=True)
def load(self):
"""
Load or the associated run_conf object if not already done.
"""
if self.run_conf:
return
# Load or build run configuration
self.run_conf = cs_run_conf.run_conf(self.path,
package=self.pkg,
create_if_missing=True)
self.run_dict = {}
self.job_dict = {}
# Generic job running information (subset of possible "run" info)
self.run_dict['id'] = self.run_conf.get('run', 'id')
self.run_dict['compute_build'] = self.run_conf.get('run', 'compute_build')
self.run_dict['initialize'] = self.run_conf.get_bool('run', 'initialize')
self.run_dict['compute'] = None
self.run_dict['finalize'] = None
# Resource-specific info (subset of resource-based info, and batch)
self.job_dict['n_procs'] = self.run_conf.get_int(self.resource_name,
'n_procs')
self.job_dict['n_threads'] = self.run_conf.get_int(self.resource_name,
'n_threads')
self.job_header_lines = None
if self.batch.rm_type:
job_header = self.run_conf.get(self.resource_name, 'job_header')
if not job_header:
self.run_conf.rebuild_resource()
job_header = self.run_conf.get(self.resource_name, 'job_header')
if job_header != None:
self.job_header_lines = job_header.split(os.linesep)
if self.job_header_lines != None:
self.batch.parse_lines(self.job_header_lines)
# Save initial values (to determine which are changed)
self.setup_ini = self.run_dict.get('setup', 'param')
self.run_dict_ini = {}
for k in self.run_dict:
self.run_dict_ini[k] = self.run_dict[k]
self.job_dict_ini = {}
for k in self.job_dict:
self.job_dict_ini[k] = self.job_dict[k]
self.job_header_lines_ini = None
if self.job_header_lines:
self.job_header_lines_ini = list(self.job_header_lines)
# Fix incompatible options if needed
# (add entries to dictionnaries so __is_changed__ will detect update)
if self.run_conf.get_bool('run', 'stage') == False:
if not self.run_dict_ini['id']:
self.run_dict_ini['stage'] = False
self.run_dict['stage'] = None
# Query info related to compute build
self.updateComputeBuildInfo(self.run_dict['compute_build'])
def update_case(options, pkg):
topdir = os.getcwd()
study_name = os.path.basename(os.getcwd())
i_c = cs_run_conf.get_install_config_info(pkg)
resource_name = cs_run_conf.get_resource_name(i_c)
for case in options.case_names:
os.chdir(topdir)
if case == ".":
case, staging_dir = get_case_dir()
if not case:
sys.stderr.write(" o Skipping '%s', which does not seem "
"to be a case directory\n" % topdir)
continue
casename = os.path.basename(case)
else:
casename = case
if options.verbose > 0:
sys.stdout.write(" o Updating case '%s' paths...\n" % casename)
datadir = os.path.join(pkg.get_dir("pkgdatadir"))
os.chdir(case)
# Write a local wrapper to main command
data = 'DATA'
if not os.path.isdir(data):
os.mkdir(data)
dataref_distpath = os.path.join(datadir, 'user')
user = os.path.join(data, 'REFERENCE')
# Only update user_scripts reference, not data
# (we should try to deprecate the copying of reference data
# or use the GUI to align it with the active options)
if os.path.exists(user):
abs_f = os.path.join(datadir, 'data', 'user', 'cs_user_scripts.py')
shutil.copy(abs_f, user)
unset_executable(user)
for s in ("SaturneGUI", "NeptuneGUI"):
old_gui_script = os.path.join(data, s)
if os.path.isfile(old_gui_script):
os.remove(old_gui_script)
# Rebuild launch script
create_local_launcher(pkg, data)
# User source files directory
src = 'SRC'
if not os.path.isdir(src):
os.mkdir(src)
user_ref_distpath = os.path.join(datadir, 'user_sources')
for srcdir in ('REFERENCE', 'EXAMPLES', 'EXAMPLES_neptune_cfd'):
if os.path.isdir(os.path.join(user_ref_distpath, srcdir)):
copy_directory(os.path.join(user_ref_distpath, srcdir),
os.path.join(src, srcdir),
True)
unset_executable(os.path.join(src, srcdir))
# Results directory (only one for all instances)
resu = 'RESU'
if not os.path.isdir(resu):
os.mkdir(resu)
# Script directory (only one for all instances)
run_conf_file = os.path.join(topdir, case, 'DATA', 'run.cfg')
batch_file = os.path.join(topdir, case, 'SCRIPTS', 'runcase')
if sys.platform.startswith('win'):
batch_file = batch_file + '.bat'
run_conf = cs_run_conf.run_conf(run_conf_file,
package=pkg,
rebuild=True)
if os.path.isfile(batch_file):
runcase = cs_runcase.runcase(batch_file,
package=pkg)
sections = runcase.run_conf_sections(resource_name=resource_name,
batch_template=i_c['batch'])
for sn in sections:
if not sn in run_conf.sections:
run_conf.sections[sn] = {}
for kw in sections[sn]:
run_conf.sections[sn][kw] = sections[sn][kw]
os.remove(batch_file)
scripts_dir = os.path.join(topdir, case, 'SCRIPTS')
try:
os.rmdir(scripts_dir)
except Exception:
pass
run_conf.save()
def create_case(self, casename):
"""
Create a case for a Code_Saturne study.
"""
casedirname = casename
datadir = self.package.get_dir("pkgdatadir")
data_distpath = os.path.join(datadir, 'data')
if os.path.exists(casedirname):
sys.stdout.write(" o Case '%s' already exists\n" % casename)
return
if self.verbose > 0:
sys.stdout.write(" o Creating case '%s'...\n" % casename)
os.mkdir(casedirname)
os.chdir(casedirname)
if self.copy is not None:
if not (os.path.exists(os.path.join(self.copy, 'DATA', 'REFERENCE')) \
or os.path.exists(os.path.join(self.copy, 'SRC', 'REFERENCE'))):
self.use_ref = False
# Data directory
data = 'DATA'
os.mkdir(data)
abs_setup_distpath = os.path.join(data_distpath, 'setup.xml')
if os.path.isfile(abs_setup_distpath) and not self.copy:
shutil.copy(abs_setup_distpath, data)
unset_executable(data)
if self.use_ref:
thch_distpath = os.path.join(data_distpath, 'user')
ref = os.path.join(data, 'REFERENCE')
shutil.copytree(thch_distpath, ref)
unset_executable(ref)
# Write a wrapper for code and launching
create_local_launcher(self.package, data)
# Generate run.cfg file or copy one
run_conf = None
run_conf_path = os.path.join(data, 'run.cfg')
if not self.copy:
run_conf = cs_run_conf.run_conf(run_conf_path,
package=self.package,
rebuild=True)
# User source files directory
src = 'SRC'
if self.use_ref:
user_distpath = os.path.join(datadir, 'user_sources')
shutil.copytree(user_distpath, src)
unset_executable(src)
else:
os.mkdir(src)
# Copy data and source files from another case
if self.copy is not None:
# Data files
ref_data = os.path.join(self.copy, data)
data_files = os.listdir(ref_data)
for f in data_files:
abs_f = os.path.join(ref_data, f)
if os.path.isfile(abs_f) and \
f not in ["SaturneGUI",
"NeptuneGUI",
self.package.name]:
shutil.copy(abs_f, data)
unset_executable(os.path.join(data, f))
# Source files
ref_src = os.path.join(self.copy, src)
if os.path.exists(ref_src):
src_files = os.listdir(ref_src)
else:
src_files = []
for f in src_files:
abs_f = os.path.join(ref_src, f)
if os.path.isfile(abs_f):
shutil.copy(abs_f, src)
unset_executable(os.path.join(src, f))
# If run.cfg was not present in initial case, generate it
if not os.path.isfile(run_conf_path):
run_conf = cs_run_conf.run_conf(run_conf_path,
package=self.package,
rebuild=True)
# Runcase (for legacy structures)
runcase_path = os.path.join(self.copy, 'SCRIPTS', 'runcase')
if os.path.isfile(runcase_path):
i_c = cs_run_conf.get_install_config_info(self.package)
resource_name = cs_run_conf.get_resource_name(i_c)
runcase = cs_runcase.runcase(runcase_path,
package=self.package)
sections = runcase.run_conf_sections(resource_name=resource_name,
batch_template=i_c['batch'])
for sn in sections:
if not sn in run_conf.sections:
run_conf.sections[sn] = {}
for kw in sections[sn]:
run_conf.sections[sn][kw] = sections[sn][kw]
# Now write run.cfg if not copied
if run_conf != None:
run_conf.save()
# Results directory
resu = 'RESU'
if not os.path.isdir(resu):
os.mkdir(resu)
def create_case(self, casename):
"""
Create a case for a Code_Saturne study.
"""
casedirname = casename
if self.verbose > 0:
sys.stdout.write(" o Creating case '%s'...\n" % casename)
datadir = self.package.get_dir("pkgdatadir")
data_distpath = os.path.join(datadir, 'data')
try:
os.mkdir(casedirname)
except:
sys.exit(1)
os.chdir(casedirname)
if self.copy is not None:
if not (os.path.exists(os.path.join(self.copy, 'DATA', 'REFERENCE')) \
or os.path.exists(os.path.join(self.copy, 'SRC', 'REFERENCE'))):
self.use_ref = False
# Data directory
data = 'DATA'
os.mkdir(data)
abs_setup_distpath = os.path.join(data_distpath, 'setup.xml')
if os.path.isfile(abs_setup_distpath) and not self.copy:
shutil.copy(abs_setup_distpath, data)
unset_executable(data)
if self.use_ref:
thch_distpath = os.path.join(data_distpath, 'thch')
ref = os.path.join(data, 'REFERENCE')
os.mkdir(ref)
for f in [
'dp_C3P', 'dp_C3PSJ', 'dp_C4P', 'dp_ELE', 'dp_FUE',
'dp_transformers', 'meteo'
]:
abs_f = os.path.join(thch_distpath, f)
if os.path.isfile(abs_f):
shutil.copy(abs_f, ref)
unset_executable(ref)
abs_f = os.path.join(datadir, 'cs_user_scripts.py')
shutil.copy(abs_f, ref)
unset_executable(ref)
# Write a wrapper for code and launching
create_local_launcher(self.package, data)
# Generate run.cfg file or copy one
run_conf = None
run_conf_path = os.path.join(data, 'run.cfg')
if not self.copy:
run_conf = cs_run_conf.run_conf(run_conf_path,
package=self.package,
rebuild=True)
# User source files directory
src = 'SRC'
os.mkdir(src)
if self.use_ref:
user_distpath = os.path.join(datadir, 'user')
user_examples_distpath = os.path.join(datadir, 'user_examples')
user = os.path.join(src, 'REFERENCE')
user_examples = os.path.join(src, 'EXAMPLES')
shutil.copytree(user_distpath, user)
shutil.copytree(user_examples_distpath, user_examples)
add_datadirs = []
if self.package.name == 'neptune_cfd':
add_datadirs.append(
os.path.join(self.package.get_dir("datadir"),
self.package.name))
for d in add_datadirs:
user_distpath = os.path.join(d, 'user')
user_examples_distpath = os.path.join(d, 'user_examples')
if os.path.isdir(user_distpath):
s_files = os.listdir(user_distpath)
for f in s_files:
shutil.copy(os.path.join(user_distpath, f), user)
if os.path.isdir(user_examples_distpath):
s_files = os.listdir(user_examples_distpath)
for f in s_files:
shutil.copy(os.path.join(user_examples_distpath, f),
user_examples)
unset_executable(user)
unset_executable(user_examples)
# Copy data and source files from another case
if self.copy is not None:
# Data files
ref_data = os.path.join(self.copy, data)
data_files = os.listdir(ref_data)
for f in data_files:
abs_f = os.path.join(ref_data, f)
if os.path.isfile(abs_f) and \
f not in [self.package.guiname,
self.package.name]:
shutil.copy(abs_f, data)
unset_executable(os.path.join(data, f))
# Source files
ref_src = os.path.join(self.copy, src)
if os.path.exists(ref_src):
src_files = os.listdir(ref_src)
else:
src_files = []
for f in src_files:
abs_f = os.path.join(ref_src, f)
if os.path.isfile(abs_f):
shutil.copy(abs_f, src)
unset_executable(os.path.join(src, f))
# If run.cfg was not present in initial case, generate it
if not os.path.isfile(run_conf_path):
run_conf = cs_run_conf.run_conf(run_conf_path,
package=self.package,
rebuild=True)
# Runcase (for legacy structures)
runcase_path = os.path.join(self.copy, 'SCRIPTS', 'runcase')
if os.path.isfile(runcase_path):
i_c = cs_run_conf.get_install_config_info(self.package)
resource_name = cs_run_conf.get_resource_name(i_c)
runcase = cs_runcase.runcase(runcase_path,
package=self.package)
sections = runcase.run_conf_sections(
resource_name=resource_name,
batch_template=i_c['batch'])
for sn in sections:
if not sn in run_conf.sections:
run_conf.sections[sn] = {}
for kw in sections[sn]:
run_conf.sections[sn][kw] = sections[sn][kw]
# Now write run.cfg if not copied
if run_conf != None:
run_conf.save()
# Results directory
resu = 'RESU'
if not os.path.isdir(resu):
os.mkdir(resu)
def read_run_config_file(i_c, r_c, s_c, pkg, run_conf=None):
"""
Process the passed command line arguments.
"""
run_config_path = ""
if r_c['staging_dir']:
run_config_path = os.path.join(r_c['staging_dir'], 'run.cfg')
elif r_c['casedir']:
casedir = r_c['casedir']
if r_c['coupled_domains'] != []:
run_config_path = os.path.join(casedir, 'run.cfg')
else:
run_config_path = os.path.join(casedir, 'DATA', 'run.cfg')
# Ensure some keys are set in all cases to simplify future tests
run_conf_kw= ('job_parameters', 'job_header',
'run_prologue', 'run_epilogue',
'compute_prologue', 'compute_epilogue')
for kw in run_conf_kw:
if not kw in r_c:
r_c[kw] = None
if run_conf == None:
if not os.path.isfile(run_config_path):
print('Warning:', file = sys.stderr)
print(' \'run.cfg\' not found in case directory; case update recommended.',
file = sys.stderr)
print('', file = sys.stderr)
return
# Only load run.cfg if not already done
if run_conf and s_c['stage'] != False:
if not run_conf.path == run_config_path:
run_conf = None
if not run_conf:
run_conf = cs_run_conf.run_conf(run_config_path, package=pkg)
# Case path if not determined yet
# (when destination or staging directory is outside case directory)
if 'paths' in run_conf.sections:
if not r_c['casedir']:
if 'case' in run_conf.sections['paths']:
r_c['casedir'] = run_conf.sections['paths']['case']
if not r_c['dest_dir']:
if 'top_results_directory' in run_conf.sections['paths']:
r_c['dest_dir'] = run_conf.sections['paths']['top_results_directory']
# Parameters file
for kw in ('param',):
if run_conf.get('setup', kw):
r_c[kw] = run_conf.get('setup', kw)
# Run id
if not r_c['run_id']:
r_c['run_id'] = run_conf.get('run', 'id')
if not r_c['force_id']:
r_c['force_id'] = run_conf.get_bool('run', 'force_id')
# Compute stages
update_run_steps(s_c, run_conf)
# Resources: try to find a matching section, using
# resource_name, batch, and job_defaults in decreasing priority.
if not r_c['compute_build']:
r_c['compute_build'] = run_conf.get_bool('run', 'compute_build')
resource_name = i_c['resource_name']
if not resource_name or not resource_name in run_conf.sections:
resource_name = i_c['batch']
if resource_name:
resource_name = os.path.basename(resource_name).lower()
if not resource_name or not resource_name in run_conf.sections:
resource_name = 'job_defaults'
run_conf_r = None
if resource_name in run_conf.sections:
run_conf_r = run_conf.sections[resource_name]
if run_conf_r:
for kw in ('n_procs', 'n_threads', 'time_limit'):
if kw in r_c:
if r_c[kw] != None:
continue
r_c[kw] = None
v = run_conf.get_int(resource_name, kw)
if v:
r_c[kw] = v
if run_conf_r:
for kw in run_conf_kw:
if r_c[kw] != None:
continue
if kw in run_conf_r:
r_c[kw] = run_conf_r[kw]
# Handle case where files are used
if not (r_c['job_parameters'] or r_c['job_header']):
kw = 'job_header_file'
f_path = None
if kw in run_conf_kw:
f_path = run_conf_kw[kw]
if f_path:
if not os.path.isabs(f_path):
f_prefix = os.path.basename(run_config_path)
f_path= os.path.join(f_prefix, f_path)
if os.path.isfile(f_path):
f = file.open(f_path)
r_c['job_header'] = f.read()
f.close
else:
err_str = """warning in run.cfg: [{0}] {1} = {2}
"{3}" not present (use defaults)"""
print(err_str.format(resource_name, kw, r_c[kw], f_path),
file = sys.stderr)
r_c['job_header'] = None
elif 'jobmanager' in r_c:
err_str = 'warning in run.cfg: [{0}] {1} = {2}; not currently handled (ignored)'
print(err_str.format(resource_name, kw, r_c[kw]),
file = sys.stderr)
r_c[kw] = None
def process_options(options, pkg):
"""
Process the passed command line arguments.
"""
# Stages to run (if no filter given, all are done).
s_c = {'stage': options.stage,
'initialize': options.initialize,
'compute': options.compute,
'finalize': options.finalize}
filter_stages = False
for k in s_c:
if s_c[k]:
filter_stages = True
# Try to determine case directory
casedir = None
staging_dir = None
param = None
compute_build = None
# Also check for possible settings file
run_id = options.id
run_conf = None
run_config_path = os.path.join(os.getcwd(), 'run.cfg')
if os.path.isfile(run_config_path):
run_conf = cs_run_conf.run_conf(run_config_path, package=pkg)
if not run_id and not filter_stages:
if 'run' in run_conf.sections and not filter_stages:
update_run_steps(s_c, run_conf)
if s_c['stage'] == False:
if 'id' in run_conf.sections['run']:
run_id = run_conf.sections['run']['id']
if s_c['stage'] == False and not run_id:
err_str = os.linesep + os.linesep + 'Error:' + os.linesep
err_str += 'Incompatible options in the run.cfg file or command arguments'
err_str += os.linesep
err_str += 'When the "stage" step is set to False, a run id is required.'
raise cs_case_domain.RunCaseError(err_str)
# Check for multiple domain case
# Kept the 'coupling' file def for the definition of the case_dir function
coupling = None
coupled_domains =[]
if run_conf:
coupled_domains = run_conf.get_coupling_parameters()
if coupled_domains != []:
coupling = run_config_path
if coupling and options.param:
cmd_line = sys.argv[0]
for arg in sys.argv[1:]:
cmd_line += ' ' + arg
err_str = os.linesep + os.linesep + 'Error:' + os.linesep
err_str += cmd_line + os.linesep
err_str += '-p/--param option is incompatible with '
err_str += '"coupled_domains" option defined within the run.cfg file.'
raise cs_case_domain.RunCaseError(err_str)
casedir, staging_dir = cs_case.get_case_dir(case=options.case,
param=options.param,
coupling=coupling,
id=run_id)
if casedir == None and staging_dir == None:
cmd_line = sys.argv[0]
for arg in sys.argv[1:]:
cmd_line += ' ' + arg
print('Error:', file = sys.stderr)
print(cmd_line, file = sys.stderr)
print('run from directory \"' + str(os.getcwd()) + '\",', file = sys.stderr)
print('which does not seem to be inside a case directory.', file = sys.stderr)
param = options.param
compute_build = options.compute_build
if not options.force:
force_id = False
else:
force_id = True
# Return associated dictionary (also force number of ranks and threads)
r_c = {'casedir': casedir,
'dest_dir': options.dest,
'staging_dir': staging_dir,
'run_id': run_id,
'param': param,
'coupled_domains': coupled_domains,
'id_prefix': options.id_prefix,
'id_suffix': options.id_suffix,
'suggest_id': options.suggest_id,
'force_id': force_id,
'n_procs': options.nprocs,
'n_threads': options.nthreads,
'time_limit': None,
'compute_build': compute_build}
return r_c, s_c, run_conf
def process_cmd_line(argv, pkg):
"""
Process the passed command line arguments.
"""
if sys.argv[0][-3:] == '.py':
usage = "usage: %prog [options]"
else:
usage = "usage: %prog run [options]"
parser = OptionParser(usage=usage)
parser.add_option("--compute-build",
dest="compute_build",
type="string",
metavar="<build>",
help="base name or full path to the compute build")
parser.add_option("-n",
"--nprocs",
dest="nprocs",
type="int",
metavar="<nprocs>",
help="number of MPI processes for the computation")
parser.add_option("--nt",
"--threads-per-task",
dest="nthreads",
type="int",
help="number of OpenMP threads per task")
parser.add_option("-p",
"--param",
dest="param",
type="string",
metavar="<param>",
help="path or name of the parameters file")
parser.add_option("--case",
dest="case",
type="string",
metavar="<case>",
help="path to the case's directory")
parser.add_option("--coupling",
dest="coupling",
type="string",
metavar="<coupling>",
help="path or name of the coupling descriptor file")
parser.add_option("--id",
dest="id",
type="string",
metavar="<id>",
help="use the given run id")
parser.add_option("--id-prefix",
dest="id_prefix",
type="string",
metavar="<prefix>",
help="prefix the run id with the given string")
parser.add_option("--id-suffix",
dest="id_suffix",
type="string",
metavar="<suffix>",
help="suffix the run id with the given string")
parser.add_option("--suggest-id",
dest="suggest_id",
action="store_true",
help="suggest a run id for the next run")
parser.add_option("--force", dest="force",
action="store_true",
help="run the data preparation stage even if " \
+ "the matching execution directory exists")
parser.add_option("--stage",
dest="stage",
action="store_true",
help="stage data prior to preparation and execution")
parser.add_option("--initialize",
"--preprocess",
dest="initialize",
action="store_true",
help="run the data preparation stage")
parser.add_option("--compute",
"--execute",
dest="compute",
action="store_true",
help="run the compute stage")
parser.add_option("--finalize",
dest="finalize",
action="store_true",
help="run the results copy/cleanup stage")
parser.set_defaults(compute_build=False)
parser.set_defaults(suggest_id=False)
parser.set_defaults(stage=None)
parser.set_defaults(initialize=None)
parser.set_defaults(compute=None)
parser.set_defaults(finalize=None)
parser.set_defaults(param=None)
parser.set_defaults(coupling=None)
parser.set_defaults(domain=None)
parser.set_defaults(id=None)
parser.set_defaults(nprocs=None)
parser.set_defaults(nthreads=None)
# Note: we could use args to pass a calculation status file as an argument,
# which would allow pursuing the later calculation stages.
(options, args) = parser.parse_args(argv)
# Stages to run (if no filter given, all are done).
s_c = {
'stage': options.stage,
'initialize': options.initialize,
'compute': options.compute,
'finalize': options.finalize
}
filter_stages = False
for k in s_c:
if s_c[k]:
filter_stages = True
# Try to determine case directory
casedir = None
staging_dir = None
param = None
compute_build = None
if options.coupling and options.param:
# Multiple domain case
cmd_line = sys.argv[0]
for arg in sys.argv[1:]:
cmd_line += ' ' + arg
err_str = 'Error:' + os.linesep
err_str += cmd_line + os.linesep
err_str += '--coupling and -p/--param options are incompatible.'
raise RunCaseError(err_str)
# Also check for possible settings file
coupling = options.coupling
run_id = options.id
run_conf = None
run_config_path = os.path.join(os.getcwd(), 'run.cfg')
if os.path.isfile(run_config_path):
run_conf = cs_run_conf.run_conf(run_config_path, package=pkg)
if not coupling:
if 'setup' in run_conf.sections:
if 'coupling' in run_conf.sections['setup']:
coupling = run_conf.sections['setup']['coupling']
if not run_id and not filter_stages:
if 'run' in run_conf.sections and not filter_stages:
update_run_steps(s_c, run_conf)
if s_c['stage'] == False:
if 'id' in run_conf.sections['run']:
run_id = run_conf.sections['run']['id']
casedir, staging_dir = cs_case.get_case_dir(case=options.case,
param=options.param,
coupling=coupling,
id=run_id)
if casedir == None:
cmd_line = sys.argv[0]
for arg in sys.argv[1:]:
cmd_line += ' ' + arg
print('Error:', file=sys.stderr)
print(cmd_line, file=sys.stderr)
print('run from directory \"' + str(os.getcwd()) + '\",',
file=sys.stderr)
print('which does not seem to be inside a case directory.',
file=sys.stderr)
param = options.param
# If no parameter file passed, and a setup.xml is present in DATA, run it
if param is None:
has_setup = os.path.isfile(os.path.join(casedir, 'DATA', 'setup.xml'))
if has_setup:
param = "setup.xml"
compute_build = options.compute_build
if not options.force:
force_id = False
else:
force_id = True
# Return associated dictionary (also force number of ranks and threads)
r_c = {
'casedir': casedir,
'staging_dir': staging_dir,
'run_id': run_id,
'param': param,
'coupling': coupling,
'id_prefix': options.id_prefix,
'id_suffix': options.id_suffix,
'suggest_id': options.suggest_id,
'force_id': force_id,
'n_procs': options.nprocs,
'n_threads': options.nthreads,
'time_limit': None,
'compute_build': compute_build
}
return r_c, s_c, run_conf
def coupling(package,
domains,
casedir,
dest_dir=None,
staging_dir=None,
verbose=True,
package_compute=None):
use_saturne = False
use_syrthes = False
use_neptune = False
use_cathare = False
use_py_code = False
# Use alternate compute (back-end) package if defined
config = configparser.ConfigParser()
config.read(package.get_global_configfile())
if package_compute == None:
package_compute = package
# Initialize code domains
sat_domains = []
syr_domains = []
nep_domains = []
cat_domains = []
py_domains = []
if domains == None:
raise RunCaseError('No domains defined.')
for d in domains:
domain_s = d.get('domain')
solver_s = d.get('solver').lower()
script_s = None
param_s = None
if (domain_s == None):
msg = 'Check your coupling definition.\n'
msg += 'domain key is missing.'
raise RunCaseError(msg)
# First, determine parameter file to use for code_saturne
# or associated modules (ensuring backwards compatibiliy)
if solver_s in package.config.solver_modules.keys() \
or solver_s == 'cathare':
param = None
script = d.get('script') # v6.1 and older structure
if script != None:
if script[-4:] == '.xml':
param = script
else:
param = d.get('param')
if not param:
param = d.get('paramfile') # older_name
s_dir = staging_dir
if not s_dir:
s_dir = casedir
if not s_dir:
s_dir = os.getcwd()
if param == None:
run_conf_path = os.path.join(s_dir, domain_s, 'DATA',
'run.cfg')
if os.path.isfile(run_conf_path):
run_conf = cs_run_conf.run_conf(run_conf_path)
if 'setup' in run_conf.sections:
if 'param' in run_conf.sections['setup']:
param = run_conf.sections['setup']['param']
if script and not param: # v6.1 and older case structure
runcase_path = os.path.join(s_dir, domain_s, 'SCRIPTS', script)
if os.path.isfile(runcase_path):
try:
runcase = cs_runcase.runcase(runcase_path)
param = runcase.get_parameters()
except Exception:
err_str = 'Cannot read ' + d.get('solver') \
+ ' script: ' + runcase_path
raise RunCaseError(err_str)
# Remark: if param is undefined, the code_saturne domain will
# default to 'setup.xml' if present.
d['param'] = param
# Now build case domain for the different solvers:
if solver_s in package.config.solver_modules.keys():
dom = domain(package,
package_compute=package_compute,
name=domain_s,
param=d.get('param'),
n_procs_weight=d.get('n_procs_weight'),
n_procs_min=d.get('n_procs_min'),
n_procs_max=d.get('n_procs_max'))
if solver_s == 'code_saturne':
use_saturne = True
sat_domains.append(dom)
elif solver_s == 'neptune_cfd':
use_neptune = True
nep_domains.append(dom)
elif solver_s == 'syrthes':
param_s = d.get('param')
if param_s == None:
param_s = d.get('script') # older name
if (param_s == None):
msg = 'Check your coupling definition.\n'
msg += 'parameters file selection is missing for domain: '
msg += domain_s + '.\n'
raise RunCaseError(msg)
try:
dom = syrthes_domain(package,
cmd_line=d.get('opt'),
name=domain_s,
param=d.get('param'),
n_procs_weight=d.get('n_procs_weight'),
n_procs_min=d.get('n_procs_min'),
n_procs_max=d.get('n_procs_max'),
verbose=verbose)
except Exception:
err_str = 'Cannot create SYRTHES domain. Opt = ' + d.get(
'opt') + '\n'
err_str += ' domain = ' + domain_s + '\n'
err_str += ' n_procs_weight = ' + str(
d.get('n_procs_weight')) + '\n'
raise RunCaseError(err_str)
use_syrthes = True
syr_domains.append(dom)
elif solver_s == 'cathare':
# Current version using Cathare2: the cathare case is converted to a
# .so library which is opened and launched by a neptune_cfd executable
dom = cathare_domain(package,
package_compute=package_compute,
name=domain_s,
param=d.get('param'),
n_procs_weight=None,
n_procs_min=1,
n_procs_max=1,
cathare_case_file=d.get('cathare_case_file'),
neptune_cfd_dom=d.get('neptune_cfd_domain'))
use_cathare = True
cat_domains.append(dom)
elif solver_s == 'python_code':
script_s = d.get('script')
if (script_s == None):
msg = 'Check your coupling definition.\n'
msg += 'Python script file selection is missing for domain: '
msg += domain_s + '.\n'
raise RunCaseError(msg)
# Generic Code_Saturne/Python Script coupling
# The python script can contain any MPI compatible code or supervisor
try:
dom = python_domain(package,
name=domain_s,
cmd_line=d.get('command_line'),
script_name=script_s)
except Exception:
err_str = 'Cannot create Python code domain.\n'
err_str += ' domain = ' + domain_s + '\n'
err_str += ' script = ' + str(d.get('script')) + '\n'
raise RunCaseError(err_str)
use_py_code = True
py_domains.append(dom)
else:
err_str = 'Unknown code type : ' + d.get('solver') + '.\n'
raise RunCaseError(err_str)
# Now handle case for the corresponding calculation domain(s).
c = case(package,
package_compute=package_compute,
case_dir=casedir,
dest_dir=dest_dir,
staging_dir=staging_dir,
domains=sat_domains + nep_domains + cat_domains,
syr_domains=syr_domains,
py_domains=py_domains)
if verbose:
msg = ' Coupling execution between: \n'
if use_saturne == True:
msg += ' o code_saturne [' + str(
len(sat_domains)) + ' domain(s)];\n'
if use_syrthes == True:
msg += ' o SYRTHES [' + str(
len(syr_domains)) + ' domain(s)];\n'
if use_neptune == True:
msg += ' o neptune_cfd [' + str(
len(nep_domains)) + ' domain(s)];\n'
if use_cathare == True:
msg += ' o CATHARE2 [' + str(
len(cat_domains)) + ' domain(s)];\n'
if use_py_code == True:
msg += ' o Python Script [' + str(
len(py_domains)) + ' domain(s)];\n'
sys.stdout.write(msg + '\n')
return c
def read_run_config_file(i_c, r_c, s_c, pkg, run_conf=None):
"""
Process the passed command line arguments.
"""
casedir = r_c['casedir']
run_config_path = ""
setup_default_path = ""
if r_c['coupled_domains'] != []:
run_config_path = os.path.join(casedir, 'run.cfg')
else:
run_config_path = os.path.join(casedir, 'DATA', 'run.cfg')
setup_default_path = os.path.join(casedir, 'DATA', 'setup.xml')
# Ensure some keys are set in all cases to simplify future tests
run_conf_kw = ('job_parameters', 'job_header', 'run_prologue',
'run_epilogue', 'compute_prologue', 'compute_epilogue')
for kw in run_conf_kw:
if not kw in r_c:
r_c[kw] = None
if run_conf == None:
if not os.path.isfile(run_config_path):
print('Warning:', file=sys.stderr)
print(
' \'run.cfg\' not found in case directory; case update recommended.',
file=sys.stderr)
print('', file=sys.stderr)
return
# Only load run.cfg if not already done
if run_conf and s_c['stage'] != False:
if not run_conf.path == run_config_path:
run_conf = None
if not run_conf:
run_conf = cs_run_conf.run_conf(run_config_path, package=pkg)
# Parameters file
for kw in ('param', ):
if run_conf.get('setup', kw):
r_c[kw] = run_conf.get('setup', kw)
if not r_c['param'] and setup_default_path:
if os.path.isfile(setup_default_path):
r_c['param'] = setup_default_path
# Print warning if setup.xml exists but another xml was provided
if r_c['param'] and setup_default_path:
if os.path.basename(
r_c['param']) != os.path.basename(setup_default_path):
if os.path.isfile(setup_default_path):
msg = '*****************************************************\n'
msg += 'Warning:\n'
msg += ' Both %s and %s exist in the DATA folder.\n' % \
(os.path.basename(r_c['param']), \
os.path.basename(setup_default_path))
msg += ' %s will be used for the computation.\n' % \
os.path.basename(r_c['param'])
msg += ' Be aware that to follow code_saturne best practices\n'
msg += ' only one of the two should be present in DATA.\n'
msg += '*****************************************************\n'
print(msg, file=sys.stderr)
# Check that an XML file was provided
if not r_c['param'] and setup_default_path:
msg = 'Remark:\n'
msg += ' No setup.xml file was provided in the DATA folder.\n'
msg += ' Default settings will be used.\n'
print(msg, file=sys.stderr)
# Run id
if not r_c['run_id']:
r_c['run_id'] = run_conf.get('run', 'id')
if not r_c['force_id']:
r_c['force_id'] = run_conf.get_bool('run', 'force_id')
# Compute stages
update_run_steps(s_c, run_conf)
# Resources: try to find a matching section, using
# resource_name, batch, and job_defaults in decreasing priority.
if not r_c['compute_build']:
r_c['compute_build'] = run_conf.get_bool('run', 'compute_build')
resource_name = i_c['resource_name']
if not resource_name or not resource_name in run_conf.sections:
resource_name = i_c['batch']
if resource_name:
resource_name = os.path.basename(resource_name).lower()
if not resource_name or not resource_name in run_conf.sections:
resource_name = 'job_defaults'
run_conf_r = None
if resource_name in run_conf.sections:
run_conf_r = run_conf.sections[resource_name]
if run_conf_r:
for kw in ('n_procs', 'n_threads', 'time_limit'):
if kw in r_c:
if r_c[kw] != None:
continue
r_c[kw] = None
v = run_conf.get_int(resource_name, kw)
if v:
r_c[kw] = v
if run_conf_r:
for kw in run_conf_kw:
if r_c[kw] != None:
continue
if kw in run_conf_r:
r_c[kw] = run_conf_r[kw]
# Handle case where files are used
if not (r_c['job_parameters'] or r_c['job_header']):
kw = 'job_header_file'
f_path = None
if kw in run_conf_kw:
f_path = run_conf_kw[kw]
if f_path:
if not os.path.isabs(f_path):
f_prefix = os.path.basename(run_config_path)
f_path = os.path.join(f_prefix, f_path)
if os.path.isfile(f_path):
f = file.open(f_path)
r_c['job_header'] = f.read()
f.close
else:
err_str = """warning in run.cfg: [{0}] {1} = {2}
"{3}" not present (use defaults)"""
print(err_str.format(resource_name, kw, r_c[kw], f_path),
file=sys.stderr)
r_c['job_header'] = None
elif 'jobmanager' in r_c:
err_str = 'warning in run.cfg: [{0}] {1} = {2}; not currently handled (ignored)'
print(err_str.format(resource_name, kw, r_c[kw]), file=sys.stderr)
r_c[kw] = None
