"""
Library for case.setup.
case_setup is a member of class Case from file case.py
"""
import os
from CIME.XML.standard_module_setup import *
from CIME.config import Config
from CIME.XML.machines import Machines
from CIME.BuildTools.configure import (
generate_env_mach_specific,
copy_depends_files,
)
from CIME.utils import (
run_and_log_case_status,
get_batch_script_for_job,
safe_copy,
file_contains_python_function,
import_from_file,
copy_local_macros_to_dir,
)
from CIME.utils import batch_jobid
from CIME.utils import transform_vars
from CIME.test_status import *
from CIME.locked_files import unlock_file, lock_file
import errno, shutil
logger = logging.getLogger(__name__)
###############################################################################
def _build_usernl_files(case, model, comp):
###############################################################################
"""
Create user_nl_xxx files, expects cwd is caseroot
"""
model = model.upper()
if model == "DRV":
model_file = case.get_value("CONFIG_CPL_FILE")
else:
model_file = case.get_value("CONFIG_{}_FILE".format(model))
expect(
model_file is not None,
"Could not locate CONFIG_{}_FILE in config_files.xml".format(model),
)
model_dir = os.path.dirname(model_file)
expect(
os.path.isdir(model_dir),
"cannot find cime_config directory {} for component {}".format(model_dir, comp),
)
comp_interface = case.get_value("COMP_INTERFACE")
multi_driver = case.get_value("MULTI_DRIVER")
ninst = 1
if multi_driver:
ninst_max = case.get_value("NINST_MAX")
if comp_interface != "nuopc" and model not in ("DRV", "CPL", "ESP"):
ninst_model = case.get_value("NINST_{}".format(model))
expect(
ninst_model == ninst_max,
"MULTI_DRIVER mode, all components must have same NINST value. NINST_{} != {}".format(
model, ninst_max
),
)
if comp == "cpl":
if not os.path.exists("user_nl_cpl"):
safe_copy(os.path.join(model_dir, "user_nl_cpl"), ".")
else:
if comp_interface == "nuopc":
ninst = case.get_value("NINST")
elif ninst == 1:
ninst = case.get_value("NINST_{}".format(model))
default_nlfile = "user_nl_{}".format(comp)
model_nl = os.path.join(model_dir, default_nlfile)
user_nl_list = _get_user_nl_list(case, default_nlfile, model_dir)
# Note that, even if there are multiple elements of user_nl_list (i.e., we are
# creating multiple user_nl files for this component with different names), all of
# them will start out as copies of the single user_nl_comp file in the model's
# source tree - unless the file has _stream in its name
for nlfile in user_nl_list:
if ninst > 1:
for inst_counter in range(1, ninst + 1):
inst_nlfile = "{}_{:04d}".format(nlfile, inst_counter)
if not os.path.exists(inst_nlfile):
# If there is a user_nl_foo in the case directory, copy it
# to user_nl_foo_INST; otherwise, copy the original
# user_nl_foo from model_dir
if os.path.exists(nlfile):
safe_copy(nlfile, inst_nlfile)
elif "_stream" in nlfile:
safe_copy(os.path.join(model_dir, nlfile), inst_nlfile)
elif os.path.exists(model_nl):
safe_copy(model_nl, inst_nlfile)
else:
# ninst = 1
if not os.path.exists(nlfile):
if "_stream" in nlfile:
safe_copy(os.path.join(model_dir, nlfile), nlfile)
elif os.path.exists(model_nl):
safe_copy(model_nl, nlfile)
###############################################################################
def _get_user_nl_list(case, default_nlfile, model_dir):
"""Get a list of user_nl files needed by this component
Typically, each component has a single user_nl file: user_nl_comp. However, some
components use multiple user_nl files. These components can define a function in
cime_config/buildnml named get_user_nl_list, which returns a list of user_nl files
that need to be staged in the case directory. For example, in a run where CISM is
modeling both Antarctica and Greenland, its get_user_nl_list function will return
['user_nl_cism', 'user_nl_cism_ais', 'user_nl_cism_gris'].
If that function is NOT defined in the component's buildnml, then we return the given
default_nlfile.
"""
# Check if buildnml is present in the expected location, and if so, whether it
# contains the function "get_user_nl_list"; if so, we'll import the module and call
# that function; if not, we'll fall back on the default value.
buildnml_path = os.path.join(model_dir, "buildnml")
has_function = False
if os.path.isfile(buildnml_path) and file_contains_python_function(
buildnml_path, "get_user_nl_list"
):
has_function = True
if has_function:
comp_buildnml = import_from_file("comp_buildnml", buildnml_path)
return comp_buildnml.get_user_nl_list(case)
else:
return [default_nlfile]
###############################################################################
def _create_macros_cmake(
caseroot, cmake_macros_dir, mach_obj, compiler, case_cmake_path
):
###############################################################################
if not os.path.isfile(os.path.join(caseroot, "Macros.cmake")):
safe_copy(os.path.join(cmake_macros_dir, "Macros.cmake"), caseroot)
if not os.path.exists(os.path.join(caseroot, "cmake_macros")):
shutil.copytree(cmake_macros_dir, case_cmake_path)
copy_depends_files(
mach_obj.get_machine_name(), mach_obj.machines_dir, caseroot, compiler
)
###############################################################################
def _create_macros(
case, mach_obj, caseroot, compiler, mpilib, debug, comp_interface, sysos
):
###############################################################################
"""
creates the Macros.make, Depends.compiler, Depends.machine, Depends.machine.compiler
and env_mach_specific.xml if they don't already exist.
"""
reread = not os.path.isfile("env_mach_specific.xml")
new_cmake_macros_dir = case.get_value("CMAKE_MACROS_DIR")
if reread:
case.flush()
generate_env_mach_specific(
caseroot,
mach_obj,
compiler,
mpilib,
debug,
comp_interface,
sysos,
False,
threaded=case.get_build_threaded(),
noenv=True,
)
case.read_xml()
case_cmake_path = os.path.join(caseroot, "cmake_macros")
_create_macros_cmake(
caseroot, new_cmake_macros_dir, mach_obj, compiler, case_cmake_path
)
copy_local_macros_to_dir(
case_cmake_path, extra_machdir=case.get_value("EXTRA_MACHDIR")
)
###############################################################################
def _case_setup_impl(
case, caseroot, clean=False, test_mode=False, reset=False, keep=None
):
###############################################################################
os.chdir(caseroot)
non_local = case.get_value("NONLOCAL")
models = case.get_values("COMP_CLASSES")
mach = case.get_value("MACH")
compiler = case.get_value("COMPILER")
debug = case.get_value("DEBUG")
mpilib = case.get_value("MPILIB")
sysos = case.get_value("OS")
comp_interface = case.get_value("COMP_INTERFACE")
extra_machines_dir = case.get_value("EXTRA_MACHDIR")
expect(mach is not None, "xml variable MACH is not set")
mach_obj = Machines(machine=mach, extra_machines_dir=extra_machines_dir)
# Check that $DIN_LOC_ROOT exists or can be created:
if not non_local:
din_loc_root = case.get_value("DIN_LOC_ROOT")
testcase = case.get_value("TESTCASE")
if not os.path.isdir(din_loc_root):
try:
os.makedirs(din_loc_root)
except OSError as e:
if e.errno == errno.EACCES:
logger.info("Invalid permissions to create {}".format(din_loc_root))
expect(
not (not os.path.isdir(din_loc_root) and testcase != "SBN"),
"inputdata root is not a directory or is not readable: {}".format(
din_loc_root
),
)
# Remove batch scripts
if reset or clean:
# clean setup-generated files
batch_script = get_batch_script_for_job(case.get_primary_job())
files_to_clean = [
batch_script,
"env_mach_specific.xml",
"Macros.make",
"Macros.cmake",
"cmake_macros",
]
for file_to_clean in files_to_clean:
if os.path.exists(file_to_clean) and not (keep and file_to_clean in keep):
if os.path.isdir(file_to_clean):
shutil.rmtree(file_to_clean)
else:
os.remove(file_to_clean)
logger.info("Successfully cleaned {}".format(file_to_clean))
if not test_mode:
# rebuild the models (even on restart)
case.set_value("BUILD_COMPLETE", False)
# Cannot leave case in bad state (missing env_mach_specific.xml)
if clean and not os.path.isfile("env_mach_specific.xml"):
case.flush()
generate_env_mach_specific(
caseroot,
mach_obj,
compiler,
mpilib,
debug,
comp_interface,
sysos,
False,
threaded=case.get_build_threaded(),
noenv=True,
)
case.read_xml()
if not clean:
if not non_local:
case.load_env()
_create_macros(
case, mach_obj, caseroot, compiler, mpilib, debug, comp_interface, sysos
)
# Set tasks to 1 if mpi-serial library
if mpilib == "mpi-serial":
case.set_value("NTASKS", 1)
# Check ninst.
# In CIME there can be multiple instances of each component model (an ensemble) NINST is the instance of that component.
comp_interface = case.get_value("COMP_INTERFACE")
if comp_interface == "nuopc":
ninst = case.get_value("NINST")
multi_driver = case.get_value("MULTI_DRIVER")
for comp in models:
ntasks = case.get_value("NTASKS_{}".format(comp))
if comp == "CPL":
continue
if comp_interface != "nuopc":
ninst = case.get_value("NINST_{}".format(comp))
if multi_driver:
if comp_interface != "nuopc":
expect(
case.get_value("NINST_LAYOUT_{}".format(comp)) == "concurrent",
"If multi_driver is TRUE, NINST_LAYOUT_{} must be concurrent".format(
comp
),
)
case.set_value("NTASKS_PER_INST_{}".format(comp), ntasks)
else:
if ninst > ntasks:
if ntasks == 1:
case.set_value("NTASKS_{}".format(comp), ninst)
ntasks = ninst
else:
expect(
False,
"NINST_{comp} value {ninst} greater than NTASKS_{comp} {ntasks}".format(
comp=comp, ninst=ninst, ntasks=ntasks
),
)
case.set_value(
"NTASKS_PER_INST_{}".format(comp), max(1, int(ntasks / ninst))
)
if os.path.exists(get_batch_script_for_job(case.get_primary_job())):
logger.info(
"Machine/Decomp/Pes configuration has already been done ...skipping"
)
case.initialize_derived_attributes()
case.set_value("SMP_PRESENT", case.get_build_threaded())
else:
case.check_pelayouts_require_rebuild(models)
unlock_file("env_build.xml")
unlock_file("env_batch.xml")
case.flush()
case.check_lockedfiles()
case.initialize_derived_attributes()
cost_per_node = case.get_value("COSTPES_PER_NODE")
case.set_value("COST_PES", case.num_nodes * cost_per_node)
threaded = case.get_build_threaded()
case.set_value("SMP_PRESENT", threaded)
if threaded and case.total_tasks * case.thread_count > cost_per_node:
smt_factor = max(
1.0, int(case.get_value("MAX_TASKS_PER_NODE") / cost_per_node)
)
case.set_value(
"TOTALPES",
case.iotasks
+ int(
(case.total_tasks - case.iotasks)
* max(1.0, float(case.thread_count) / smt_factor)
),
)
else:
case.set_value(
"TOTALPES",
(case.total_tasks - case.iotasks) * case.thread_count
+ case.iotasks,
)
# May need to select new batch settings if pelayout changed (e.g. problem is now too big for prev-selected queue)
env_batch = case.get_env("batch")
env_batch.set_job_defaults([(case.get_primary_job(), {})], case)
# create batch files
env_batch.make_all_batch_files(case)
if Config.instance().make_case_run_batch_script and not case.get_value(
"TEST"
):
input_batch_script = os.path.join(
case.get_value("MACHDIR"), "template.case.run.sh"
)
env_batch.make_batch_script(
input_batch_script,
"case.run",
case,
outfile=get_batch_script_for_job("case.run.sh"),
)
# Make a copy of env_mach_pes.xml in order to be able
# to check that it does not change once case.setup is invoked
case.flush()
logger.debug("at copy TOTALPES = {}".format(case.get_value("TOTALPES")))
lock_file("env_mach_pes.xml")
lock_file("env_batch.xml")
# Create user_nl files for the required number of instances
if not os.path.exists("user_nl_cpl"):
logger.info("Creating user_nl_xxx files for components and cpl")
# loop over models
for model in models:
comp = case.get_value("COMP_{}".format(model))
logger.debug("Building {} usernl files".format(model))
_build_usernl_files(case, model, comp)
if comp == "cism":
glcroot = case.get_value("COMP_ROOT_DIR_GLC")
run_cmd_no_fail(
"{}/cime_config/cism.template {}".format(glcroot, caseroot)
)
_build_usernl_files(case, "drv", "cpl")
# Create needed directories for case
case.create_dirs()
logger.info(
"If an old case build already exists, might want to run 'case.build --clean' before building"
)
# Some tests need namelists created here (ERP) - so do this if we are in test mode
if (
test_mode or Config.instance().case_setup_generate_namelist
) and not non_local:
logger.info("Generating component namelists as part of setup")
case.create_namelists()
# Record env information
env_module = case.get_env("mach_specific")
if mach == "zeus":
overrides = env_module.get_overrides_nodes(case)
logger.debug("Updating Zeus nodes {}".format(overrides))
env_module.make_env_mach_specific_file("sh", case)
env_module.make_env_mach_specific_file("csh", case)
if not non_local:
env_module.save_all_env_info("software_environment.txt")
logger.info(
"You can now run './preview_run' to get more info on how your case will be run"
)
###############################################################################
[docs]def case_setup(self, clean=False, test_mode=False, reset=False, keep=None):
###############################################################################
caseroot, casebaseid = self.get_value("CASEROOT"), self.get_value("CASEBASEID")
phase = "setup.clean" if clean else "case.setup"
functor = lambda: _case_setup_impl(
self, caseroot, clean=clean, test_mode=test_mode, reset=reset, keep=keep
)
is_batch = self.get_value("BATCH_SYSTEM") is not None
msg_func = None
if is_batch:
jobid = batch_jobid()
msg_func = lambda *args: jobid if jobid is not None else ""
if self.get_value("TEST") and not test_mode:
test_name = casebaseid if casebaseid is not None else self.get_value("CASE")
with TestStatus(test_dir=caseroot, test_name=test_name) as ts:
try:
run_and_log_case_status(
functor,
phase,
custom_starting_msg_functor=msg_func,
custom_success_msg_functor=msg_func,
caseroot=caseroot,
is_batch=is_batch,
)
except BaseException: # Want to catch KeyboardInterrupt too
ts.set_status(SETUP_PHASE, TEST_FAIL_STATUS)
raise
else:
if clean:
ts.set_status(SETUP_PHASE, TEST_PEND_STATUS)
else:
ts.set_status(SETUP_PHASE, TEST_PASS_STATUS)
else:
run_and_log_case_status(
functor,
phase,
custom_starting_msg_functor=msg_func,
custom_success_msg_functor=msg_func,
caseroot=caseroot,
is_batch=is_batch,
)
# put the following section here to make sure the rundir is generated first
machdir = self.get_value("MACHDIR")
mach = self.get_value("MACH")
ngpus_per_node = self.get_value("NGPUS_PER_NODE")
overrides = {}
overrides["ngpus_per_node"] = ngpus_per_node
input_template = os.path.join(machdir, "mpi_run_gpu.{}".format(mach))
if os.path.isfile(input_template):
# update the wrapper script that sets the device id for each MPI rank
output_text = transform_vars(
open(input_template, "r").read(), case=self, overrides=overrides
)
# write it out to the run dir
rundir = self.get_value("RUNDIR")
output_name = os.path.join(rundir, "set_device_rank.sh")
logger.info("Creating file {}".format(output_name))
with open(output_name, "w") as f:
f.write(output_text)
# make the wrapper script executable
if os.path.isfile(output_name):
os.system("chmod +x " + output_name)
else:
expect(
False, "The file {} is not written out correctly.".format(output_name)
)