def write_size(self, template):
"""Write SIZE file from SIZE.j2 template."""
if mpi.rank == 0:
size_file = self.sim.path_run / "SIZE"
logger.info(f"Writing SIZE file... {size_file}")
with open(size_file, "w") as fp:
self.oper.write_size(
template, fp, comments=self.sim.params.short_name_type_run)
def write_box(self, template):
"""Write <case name>.box file from box.j2 template."""
if mpi.rank == 0:
box_file = self.sim.path_run / f"{self.name_pkg}.box"
logger.info(f"Writing box file... {box_file}")
with open(box_file, "w") as fp:
self.sim.oper.write_box(
template, fp, comments=self.sim.params.short_name_type_run)
def _save_info_solver_params_xml(self, replace=False):
"""Saves the par file, along with FluidSim's params_simul.xml and info.xml"""
params = self.sim.params
if mpi.rank == 0 and self._has_to_save and params.NEW_DIR_RESULTS:
par_file = Path(self.path_run) / f"{self.name_solver}.par"
logger.info(
f"Writing params files... {par_file}, params_simul.xml, "
"info_solver.xml")
with open(par_file, "w") as fp:
params.nek._write_par(fp)
super()._save_info_solver_params_xml(replace,
comment=f"snek5000 {__version__}")
def get_configfile(cls, host=None):
"""Get path of the Snakemake configuration file for the current machine.
All configuration files are stored under ``etc`` sub-package.
"""
if not host:
host = os.getenv("SNIC_RESOURCE",
os.getenv("GITHUB_WORKFLOW", gethostname()))
root = cls.get_root()
configfile = root / "etc" / f"{host}.yml"
if not configfile.exists():
logger.warning(
"Expected a configuration file describing compilers and flags: "
f"{configfile}")
configfile = Path(get_asset("default_configfile.yml"))
logger.info(f"Using default configuration instead: {configfile}")
return configfile
def post_init(self):
if mpi.rank == 0:
_banner_length = 42
logger.info("*" * _banner_length)
logger.info(f"solver: {self.__class__}")
logger.info(f"path_run: {self.path_run}")
logger.info("*" * _banner_length)
# This also calls _save_info_solver_params_xml
super().post_init()
# Write source files to compile the simulation
if mpi.rank == 0 and self._has_to_save and self.sim.params.NEW_DIR_RESULTS:
self.copy(self.path_run)
def copy(self, new_dir, force=False):
"""Copy case files to a new directory. The directory does not have to be present.
:param new_dir: A str or Path-like instance pointing to the new directory.
:param force: Force copy would overwrite if files already exist.
"""
# Avoid race conditions! Should be only executed by rank 0.
if mpi.rank != 0:
return
abs_paths = self.get_paths()
subpackages = self._get_subpackages()
root = self.root
def conditional_ignore(src, names):
"""Ignore if not found in ``abs_paths``."""
src = Path(src)
include = abs_paths + [root / subpkg for subpkg in subpackages]
exclude = tuple(name for name in names if not any(
(src / name) == path for path in include))
logger.debug("".join((
f"- src: {src}",
"\n- include:\n",
"\n ".join(str(name) for name in include),
"\n- exclude:\n",
"\n ".join(exclude),
"\n----",
)))
return exclude
new_root = Path(new_dir)
try:
logger.info("Copying with shutil.copytree ...")
copytree_kwargs = dict(src=root,
dst=new_root,
symlinks=False,
ignore=conditional_ignore)
# Python 3.8+
shutil.copytree(**copytree_kwargs, dirs_exist_ok=True)
except (TypeError, shutil.Error):
try:
logger.warning(
"Python < 3.8: shutil.copytree may not proceed if directories exist."
)
# Hoping that new_root has not been created
shutil.copytree(**copytree_kwargs)
except FileExistsError as e:
logger.warning(e)
logger.info("Copying with shutil.copy2 ...")
# Copy one by one from the scratch
if not new_root.exists():
logger.debug(f"Creating {new_root} ...")
os.makedirs(new_root, exist_ok=True)
for abs_path in abs_paths:
rel_path = abs_path.relative_to(root)
new_path = new_root / rel_path
if not new_path.parent.exists():
os.makedirs(new_path.parent)
logger.debug(f"Copying {new_path}")
if new_path.exists():
if force:
logger.warning(
f"{new_path} would be overwritten ...")
else:
logger.warning(
f"{new_path} exists, skipping. Use force=True to overwrite."
)
continue
shutil.copy2(abs_path, new_path)
finally:
logger.info(f"Copied: {root} -> {new_root}")