def main(args, logger: Logger = get_basic_logger()):
params = utils.load_sim_params(os.path.join(args.rel_dir, "sim_params.yaml"))
sim_dir = params.sim_dir
mgmt_db_loc = params.mgmt_db_location
submit_yes = True if args.auto else confirm("Also submit the job for you?")
# get the srf(rup) name without extensions
srf_name = os.path.splitext(os.path.basename(params.srf_file))[0]
# if srf(variation) is provided as args, only create the slurm
# with same name provided
if args.srf is not None and srf_name != args.srf:
return
write_directory = args.write_directory if args.write_directory else sim_dir
# get lf_sim_dir
lf_sim_dir = os.path.join(sim_dir, "LF")
header_dict = {
"platform_specific_args": get_platform_node_requirements(
platform_config[const.PLATFORM_CONFIG.MERGE_TS_DEFAULT_NCORES.name]
),
"wallclock_limit": default_run_time_merge_ts,
"job_name": "merge_ts.{}".format(srf_name),
"job_description": "post emod3d: merge_ts",
"additional_lines": "###SBATCH -C avx",
}
command_template_parameters = {
"run_command": platform_config[const.PLATFORM_CONFIG.RUN_COMMAND.name],
"merge_ts_path": binary_version.get_unversioned_bin(
"merge_tsP3_par", get_machine_config(args.machine)["tools_dir"]
),
}
body_template_params = (
"{}.sl.template".format(merge_ts_name_prefix),
{"lf_sim_dir": lf_sim_dir},
)
script_prefix = "{}_{}".format(merge_ts_name_prefix, srf_name)
script_file_path = write_sl_script(
write_directory,
sim_dir,
const.ProcessType.merge_ts,
script_prefix,
header_dict,
body_template_params,
command_template_parameters,
)
if submit_yes:
submit_script_to_scheduler(
script_file_path,
const.ProcessType.merge_ts.value,
sim_struct.get_mgmt_db_queue(mgmt_db_loc),
sim_dir,
srf_name,
target_machine=args.machine,
logger=logger,
)
def generate_empirical_script(np, extended, cybershake_folder, realisations,
out_dir):
# extended is '-e' or ''
faults = map(simulation_structure.get_fault_from_realisation, realisations)
run_data = zip(realisations, faults)
run_data = [(rel, fault) for (rel, fault) in run_data
if rrup_file_exists(cybershake_folder, rel)]
# determine NP
# TODO: empirical are currently not parallel, update this when they are
np = 1
# load sim_params for vs30_file
# this is assuming all simulation use the same vs30 in root_params.yaml
sim_dir = simulation_structure.get_sim_dir(cybershake_folder,
run_data[0][0])
sim_params = utils.load_sim_params(
simulation_structure.get_sim_params_yaml_path(sim_dir))
timestamp_format = "%Y%m%d_%H%M%S"
timestamp = datetime.now().strftime(timestamp_format)
template_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"..", "templates/")
header = resolve_header(
platform_config[const.PLATFORM_CONFIG.TEMPLATES_DIR.name],
wallclock_limit="00:30:00",
job_name="empirical",
version="slurm",
memory="2G",
exe_time="%j",
job_description="Empirical Engine",
additional_lines="",
template_path=platform_config[const.PLATFORM_CONFIG.HEADER_FILE.name],
write_directory=out_dir,
platform_specific_args={"n_tasks": np},
)
context = generate_context(
template_dir,
"empirical.sl.template",
{
"run_data": run_data,
"np": np,
"extended": extended,
"vs30_file": sim_params.stat_vs_est,
"mgmt_db_location": cybershake_folder,
},
)
sl_name = os.path.join(out_dir, "run_empirical_{}.sl".format(timestamp))
content = "{}\n{}".format(header, context)
write_sl(sl_name, content)
return sl_name
def get_runs_dir_params(runs_dir: str, fault_names: List[str],
realisations: np.ndarray):
"""Gets the parameters from the runs directory. Assumes that all realisations of a
fault have the same parameters
"""
data = []
for ix, fault_name in enumerate(fault_names):
r = realisations[ix][0]
params = utils.load_sim_params(
os.path.join(runs_dir, fault_name, r, "sim_params.yaml"))
data.append(
(params.dt, params.hf.dt, params.FD_STATLIST, params.hf.slip))
return np.rec.array(
data,
dtype=[
("dt", np.float32),
("hf_dt", np.float32),
("fd_statlist", np.object),
("slip", np.object),
],
)
def install_fault(
fault_name,
n_rel,
root_folder,
version,
stat_file_path,
seed=HF_DEFAULT_SEED,
extended_period=False,
vm_perturbations=False,
ignore_vm_perturbations=False,
vm_qpqs_files=False,
ignore_vm_qpqs_files=False,
keep_dup_station=True,
components=None,
logger: Logger = get_basic_logger(),
):
config_dict = utils.load_yaml(
os.path.join(
platform_config[PLATFORM_CONFIG.TEMPLATES_DIR.name],
"gmsim",
version,
ROOT_DEFAULTS_FILE_NAME,
)
)
# Load variables from cybershake config
v1d_full_path = os.path.join(
platform_config[PLATFORM_CONFIG.VELOCITY_MODEL_DIR.name],
"Mod-1D",
config_dict.get("v_1d_mod"),
)
site_v1d_dir = config_dict.get("site_v1d_dir")
hf_stat_vs_ref = config_dict.get("hf_stat_vs_ref")
vs30_file_path = stat_file_path.replace(".ll", ".vs30")
vs30ref_file_path = stat_file_path.replace(".ll", ".vs30ref")
# this variable has to be empty
# TODO: fix this legacy issue, very low priority
event_name = ""
# get all srf from source
srf_dir = simulation_structure.get_srf_dir(root_folder, fault_name)
list_srf = glob.glob(os.path.join(srf_dir, "*_REL*.srf"))
if len(list_srf) == 0:
list_srf = glob.glob(os.path.join(srf_dir, "*.srf"))
list_srf.sort()
if n_rel is not None and len(list_srf) != n_rel:
message = (
"Error: fault {} failed. Number of realisations do "
"not match number of SRF files".format(fault_name)
)
logger.log(NOPRINTCRITICAL, message)
raise RuntimeError(message)
# Get & validate velocity model directory
vel_mod_dir = simulation_structure.get_fault_VM_dir(root_folder, fault_name)
valid_vm, message = validate_vm.validate_vm(vel_mod_dir, srf=list_srf[0])
if not valid_vm:
message = "Error: VM {} failed {}".format(fault_name, message)
logger.log(NOPRINTCRITICAL, message)
raise RuntimeError(message)
# Load the variables from vm_params.yaml
vm_params_path = os.path.join(vel_mod_dir, VM_PARAMS_FILE_NAME)
vm_params_dict = utils.load_yaml(vm_params_path)
yes_model_params = (
False # statgrid should normally be already generated with Velocity Model
)
sim_root_dir = simulation_structure.get_runs_dir(root_folder)
fault_yaml_path = simulation_structure.get_fault_yaml_path(sim_root_dir, fault_name)
root_yaml_path = simulation_structure.get_root_yaml_path(sim_root_dir)
for srf in list_srf:
logger.info("Installing {}".format(srf))
# try to match find the stoch with same basename
realisation_name = os.path.splitext(os.path.basename(srf))[0]
stoch_file_path = simulation_structure.get_stoch_path(
root_folder, realisation_name
)
sim_params_file = simulation_structure.get_source_params_path(
root_folder, realisation_name
)
if not os.path.isfile(stoch_file_path):
message = "Error: Corresponding Stoch file is not found: {}".format(
stoch_file_path
)
logger.log(NOPRINTCRITICAL, message)
raise RuntimeError(message)
# install pairs one by one to fit the new structure
sim_dir = simulation_structure.get_sim_dir(root_folder, realisation_name)
(root_params_dict, fault_params_dict, sim_params_dict) = install_simulation(
version=version,
sim_dir=sim_dir,
rel_name=realisation_name,
run_dir=sim_root_dir,
vel_mod_dir=vel_mod_dir,
srf_file=srf,
stoch_file=stoch_file_path,
stat_file_path=stat_file_path,
vs30_file_path=vs30_file_path,
vs30ref_file_path=vs30ref_file_path,
yes_statcords=False,
fault_yaml_path=fault_yaml_path,
root_yaml_path=root_yaml_path,
cybershake_root=root_folder,
site_v1d_dir=site_v1d_dir,
hf_stat_vs_ref=hf_stat_vs_ref,
v1d_full_path=v1d_full_path,
sim_params_file=sim_params_file,
seed=seed,
logger=logger,
extended_period=extended_period,
vm_perturbations=vm_perturbations,
ignore_vm_perturbations=ignore_vm_perturbations,
vm_qpqs_files=vm_qpqs_files,
ignore_vm_qpqs_files=ignore_vm_qpqs_files,
components=components,
)
if (
root_params_dict is None
or fault_params_dict is None
or sim_params_dict is None
):
# Something has gone wrong, returning without saving anything
logger.critical(f"Critical Error some params dictionary are None")
return
if root_params_dict is not None and not isclose(
vm_params_dict["flo"], root_params_dict["flo"]
):
logger.critical(
"The parameter 'flo' does not match in the VM params and root params files. "
"Please ensure you are installing the correct gmsim version"
)
return
create_mgmt_db.create_mgmt_db(
[], simulation_structure.get_mgmt_db(root_folder), srf_files=srf
)
utils.setup_dir(os.path.join(root_folder, "mgmt_db_queue"))
root_params_dict["mgmt_db_location"] = root_folder
# Generate the fd files, create these at the fault level
fd_statcords, fd_statlist = generate_fd_files(
simulation_structure.get_fault_dir(root_folder, fault_name),
vm_params_dict,
stat_file=stat_file_path,
logger=logger,
keep_dup_station=keep_dup_station,
)
fault_params_dict[FaultParams.stat_coords.value] = fd_statcords
fault_params_dict[FaultParams.FD_STATLIST.value] = fd_statlist
# root_params_dict['hf_stat_vs_ref'] = cybershake_cfg['hf_stat_vs_ref']
dump_all_yamls(sim_dir, root_params_dict, fault_params_dict, sim_params_dict)
# test if the params are accepted by steps HF and BB
sim_params = utils.load_sim_params(os.path.join(sim_dir, "sim_params.yaml"))
# check hf
# temporary change the script name to hf_sim, due to how error message are shown
main_script_name = sys.argv[0]
sys.argv[0] = "hf_sim.py"
command_template, add_args = hf_gen_command_template(
sim_params, list(HPC)[0].name, seed
)
run_command = gen_args_cmd(
ProcessType.HF.command_template, command_template, add_args
)
hf_args_parser(cmd=run_command)
# check bb
sys.argv[0] = "bb_sim.py"
command_template, add_args = bb_gen_command_template(sim_params)
run_command = gen_args_cmd(
ProcessType.BB.command_template, command_template, add_args
)
bb_args_parser(cmd=run_command)
# change back, to prevent unexpected error
sys.argv[0] = main_script_name
def main(
args: argparse.Namespace,
est_model: est.EstModel = None,
logger: Logger = get_basic_logger(),
):
params = utils.load_sim_params(
os.path.join(args.rel_dir, "sim_params.yaml"))
submit_yes = True if args.auto else confirm("Also submit the job for you?")
logger.debug("params.srf_file {}".format(params.srf_file))
# Get the srf(rup) name without extensions
srf_name = os.path.splitext(os.path.basename(params.srf_file))[0]
if args.srf is None or srf_name == args.srf:
logger.debug("not set_params_only")
# get lf_sim_dir
sim_dir = os.path.abspath(params.sim_dir)
lf_sim_dir = sim_struct.get_lf_dir(sim_dir)
# default_core will be changed is user passes ncore
nt = int(float(params.sim_duration) / float(params.dt))
target_qconfig = get_machine_config(args.machine)
retries = args.retries if hasattr(args, "retries") else None
est_cores, est_run_time, wct = get_lf_cores_and_wct(
est_model,
logger,
nt,
params,
sim_dir,
srf_name,
target_qconfig,
args.ncore,
retries,
)
binary_path = binary_version.get_lf_bin(params.emod3d.emod3d_version,
target_qconfig["tools_dir"])
# use the original estimated run time for determining the checkpoint, or uses a minimum of 3 checkpoints
steps_per_checkpoint = int(
min(nt / (60.0 * est_run_time) * const.CHECKPOINT_DURATION,
nt // 3))
write_directory = (args.write_directory
if args.write_directory else params.sim_dir)
set_runparams.create_run_params(
sim_dir, steps_per_checkpoint=steps_per_checkpoint, logger=logger)
header_dict = {
"wallclock_limit": wct,
"job_name": "emod3d.{}".format(srf_name),
"job_description": "emod3d slurm script",
"additional_lines": "#SBATCH --hint=nomultithread",
"platform_specific_args":
get_platform_node_requirements(est_cores),
}
command_template_parameters = {
"run_command":
platform_config[const.PLATFORM_CONFIG.RUN_COMMAND.name],
"emod3d_bin": binary_path,
"lf_sim_dir": lf_sim_dir,
}
body_template_params = ("run_emod3d.sl.template", {})
script_prefix = "run_emod3d_{}".format(srf_name)
script_file_path = write_sl_script(
write_directory,
params.sim_dir,
const.ProcessType.EMOD3D,
script_prefix,
header_dict,
body_template_params,
command_template_parameters,
)
if submit_yes:
submit_script_to_scheduler(
script_file_path,
const.ProcessType.EMOD3D.value,
sim_struct.get_mgmt_db_queue(params.mgmt_db_location),
params.sim_dir,
srf_name,
target_machine=args.machine,
logger=logger,
)
def create_run_params(
sim_dir,
srf_name=None,
steps_per_checkpoint=None,
logger: Logger = get_basic_logger(),
):
params = utils.load_sim_params(os.path.join(sim_dir, "sim_params.yaml"))
emod3d_version = params["emod3d"]["emod3d_version"]
emod3d_filepath = binary_version.get_lf_bin(emod3d_version)
e3d_yaml = os.path.join(
platform_config[constants.PLATFORM_CONFIG.TEMPLATES_DIR.name],
"gmsim",
params.version,
"emod3d_defaults.yaml",
)
e3d_dict = utils.load_yaml(e3d_yaml)
# skip all logic if a specific srf_name is provided
if srf_name is None or srf_name == os.path.splitext(
basename(params.srf_file))[0]:
# EMOD3D adds a timeshift to the event rupture time
# this must be accounted for as EMOD3D does not extend the sim duration by the amount of time shift
# As flo is in Hz, the sim_duration_extension is in s
# Version 3.0.4 was the last version of EMOD3D to have a shift of 1/flo,
# while versions after it have a shift of 3/flo
sim_duration_extension = 1 / float(params.flo)
if compare_versions(emod3d_version,
MAXIMUM_EMOD3D_TIMESHIFT_1_VERSION) > 0:
sim_duration_extension *= 3
extended_sim_duration = float(
params.sim_duration) + sim_duration_extension
srf_file_basename = os.path.splitext(os.path.basename(
params.srf_file))[0]
e3d_dict["version"] = emod3d_version + "-mpi"
e3d_dict["name"] = params.run_name
e3d_dict["n_proc"] = 512
e3d_dict["nx"] = params.nx
e3d_dict["ny"] = params.ny
e3d_dict["nz"] = params.nz
e3d_dict["h"] = params.hh
e3d_dict["dt"] = params.dt
e3d_dict["nt"] = str(
int(round(extended_sim_duration / float(params.dt))))
e3d_dict["flo"] = float(params.flo)
e3d_dict["faultfile"] = params.srf_file
e3d_dict["vmoddir"] = params.vel_mod_dir
e3d_dict["modellon"] = params.MODEL_LON
e3d_dict["modellat"] = params.MODEL_LAT
e3d_dict["modelrot"] = params.MODEL_ROT
e3d_dict["main_dump_dir"] = os.path.join(params.sim_dir, "LF",
"OutBin")
e3d_dict["seiscords"] = params.stat_coords
e3d_dict["user_scratch"] = os.path.join(params.user_root, "scratch")
e3d_dict["seisdir"] = os.path.join(e3d_dict["user_scratch"],
params.run_name, srf_file_basename,
"SeismoBin")
e3d_dict["ts_total"] = str(
int(extended_sim_duration /
(float(e3d_dict["dt"]) * float(e3d_dict["dtts"]))))
e3d_dict["ts_file"] = os.path.join(e3d_dict["main_dump_dir"],
params.run_name + "_xyts.e3d")
e3d_dict["ts_out_dir"] = os.path.join(params.sim_dir, "LF", "TSlice",
"TSFiles")
e3d_dict["restartdir"] = os.path.join(params.sim_dir, "LF", "Restart")
if steps_per_checkpoint:
e3d_dict["dump_itinc"] = e3d_dict["restart_itinc"] = int(
steps_per_checkpoint)
e3d_dict["restartname"] = params.run_name
e3d_dict["logdir"] = os.path.join(params.sim_dir, "LF", "Rlog")
e3d_dict["slipout"] = os.path.join(params.sim_dir, "LF", "SlipOut",
"slipout-k2")
# other locations
e3d_dict["wcc_prog_dir"] = emod3d_filepath
e3d_dict["vel_mod_params_dir"] = params.vel_mod_dir
e3d_dict["sim_dir"] = params.sim_dir
e3d_dict["stat_file"] = params.stat_file
e3d_dict["grid_file"] = params.GRIDFILE
e3d_dict["model_params"] = params.MODEL_PARAMS
if params.emod3d:
for key, value in params.emod3d.items():
if key in e3d_dict:
e3d_dict[key] = value
else:
logger.debug(
"{} not found as a key in e3d file. Ignoring variable. Value is {}."
.format(key, value))
shared.write_to_py(os.path.join(params.sim_dir, "LF", "e3d.par"),
e3d_dict)
def main(
args: argparse.Namespace,
est_model: est.EstModel = None,
logger: Logger = get_basic_logger(),
):
params = utils.load_sim_params(
os.path.join(args.rel_dir, "sim_params.yaml"))
# check if the args is none, if not, change the version
if args.version is not None and args.version in ["mpi", "run_hf_mpi"]:
version = args.version
ll_name_prefix = "run_hf_mpi"
else:
if args.version is not None:
logger.error(
"{} cannot be recognize as a valid version option. version is set to default: {}"
.format(
args.version,
platform_config[
const.PLATFORM_CONFIG.HF_DEFAULT_VERSION.name],
))
version = platform_config[
const.PLATFORM_CONFIG.HF_DEFAULT_VERSION.name]
ll_name_prefix = platform_config[
const.PLATFORM_CONFIG.HF_DEFAULT_VERSION.name]
logger.debug("version: {}".format(version))
# modify the logic to use the same as in install_bb:
# sniff through params_base to get the names of srf,
# instead of running through file directories.
# loop through all srf file to generate related slurm scripts
srf_name = os.path.splitext(os.path.basename(params.srf_file))[0]
# if srf(variation) is provided as args, only create
# the slurm with same name provided
if args.srf is None or srf_name == args.srf:
nt = get_hf_nt(params)
fd_count = len(shared.get_stations(params.FD_STATLIST))
# TODO:make it read through the whole list
# instead of assuming every stoch has same size
nsub_stoch, sub_fault_area = srf.get_nsub_stoch(params.hf.slip,
get_area=True)
if est_model is None:
est_model = os.path.join(
platform_config[
const.PLATFORM_CONFIG.ESTIMATION_MODELS_DIR.name], "HF")
est_core_hours, est_run_time, est_cores = est.est_HF_chours_single(
fd_count,
nsub_stoch,
nt,
args.ncore,
est_model,
scale_ncores=SCALE_NCORES,
logger=logger,
)
# scale up the est_run_time if it is a re-run (with check-pointing)
# creates and extra variable so we keep the orignial estimated run time for other purpose
est_run_time_scaled = est_run_time
if hasattr(args, "retries") and int(args.retries) > 0:
# check if HF.bin is read-able = restart-able
try:
from qcore.timeseries import HFSeis
bin = HFSeis(sim_struct.get_hf_bin_path(params.sim_dir))
except:
logger.debug("Retried count > 0 but HF.bin is not readable")
else:
est_run_time_scaled = est_run_time * (int(args.retries) + 1)
wct = set_wct(est_run_time_scaled, est_cores, args.auto)
hf_sim_dir = sim_struct.get_hf_dir(params.sim_dir)
write_directory = (args.write_directory
if args.write_directory else params.sim_dir)
underscored_srf = srf_name.replace("/", "__")
header_dict = {
"platform_specific_args":
get_platform_node_requirements(est_cores),
"wallclock_limit": wct,
"job_name": "hf.{}".format(underscored_srf),
"job_description": "HF calculation",
"additional_lines": "###SBATCH -C avx",
}
command_template_parameters, add_args = gen_command_template(
params, args.machine, seed=args.seed)
body_template_params = (
"{}.sl.template".format(ll_name_prefix),
{
"hf_sim_dir": hf_sim_dir,
"test_hf_script": "test_hf.sh"
},
)
script_prefix = "{}_{}".format(ll_name_prefix, underscored_srf)
script_file_path = write_sl_script(
write_directory,
params.sim_dir,
const.ProcessType.HF,
script_prefix,
header_dict,
body_template_params,
command_template_parameters,
add_args,
)
# Submit the script
submit_yes = True if args.auto else confirm(
"Also submit the job for you?")
if submit_yes:
submit_script_to_scheduler(
script_file_path,
const.ProcessType.HF.value,
sim_struct.get_mgmt_db_queue(params.mgmt_db_location),
params.sim_dir,
srf_name,
target_machine=args.machine,
logger=logger,
)
def main(
args: argparse.Namespace,
est_model: est.EstModel = None,
logger: Logger = get_basic_logger(),
):
params = utils.load_sim_params(os.path.join(args.rel_dir, "sim_params.yaml"))
ncores = platform_config[const.PLATFORM_CONFIG.BB_DEFAULT_NCORES.name]
version = args.version
if version in ["mpi", "run_bb_mpi"]:
sl_name_prefix = "run_bb_mpi"
else:
if version is not None:
logger.error(
"{} cannot be recognized as a valid option. version is set to default:".format(
version,
platform_config[const.PLATFORM_CONFIG.BB_DEFAULT_VERSION.name],
)
)
version = platform_config[const.PLATFORM_CONFIG.BB_DEFAULT_VERSION.name]
sl_name_prefix = platform_config[const.PLATFORM_CONFIG.BB_DEFAULT_VERSION.name]
logger.debug(version)
srf_name = os.path.splitext(os.path.basename(params.srf_file))[0]
if args.srf is None or srf_name == args.srf:
# TODO: save status as HF. refer to submit_hf
# Use HF nt for wct estimation
nt = get_hf_nt(params)
fd_count = len(shared.get_stations(params.FD_STATLIST))
if est_model is None:
est_model = os.path.join(
platform_config[const.PLATFORM_CONFIG.ESTIMATION_MODELS_DIR.name], "BB"
)
est_core_hours, est_run_time = est.est_BB_chours_single(
fd_count, nt, ncores, est_model
)
# creates and extra variable so we keep the original estimated run time for other purpos
est_run_time_scaled = est_run_time
if hasattr(args, "retries") and int(args.retries) > 0:
# check if BB.bin is read-able = restart-able
try:
from qcore.timeseries import BBSeis
bin = BBSeis(simulation_structure.get_bb_bin_path(params.sim_dir))
except:
logger.debug("Retried count > 0 but BB.bin is not readable")
else:
est_run_time_scaled = est_run_time * (int(args.retries) + 1)
wct = set_wct(est_run_time_scaled, ncores, args.auto)
write_directory = (
args.write_directory if args.write_directory else params.sim_dir
)
underscored_srf = srf_name.replace("/", "__")
header_dict = {
"wallclock_limit": wct,
"job_name": "bb.{}".format(underscored_srf),
"job_description": "BB calculation",
"additional_lines": "###SBATCH -C avx",
"platform_specific_args": get_platform_node_requirements(ncores),
}
body_template_params = (
"{}.sl.template".format(sl_name_prefix),
{"test_bb_script": "test_bb.sh"},
)
command_template_parameters, add_args = gen_command_template(params)
script_prefix = "{}_{}".format(sl_name_prefix, underscored_srf)
script_file_path = write_sl_script(
write_directory,
params.sim_dir,
const.ProcessType.BB,
script_prefix,
header_dict,
body_template_params,
command_template_parameters,
add_args,
)
# Submit the script
submit_yes = True if args.auto else confirm("Also submit the job for you?")
if submit_yes:
submit_script_to_scheduler(
script_file_path,
const.ProcessType.BB.value,
simulation_structure.get_mgmt_db_queue(params.mgmt_db_location),
params.sim_dir,
srf_name,
target_machine=args.machine,
logger=logger,
)
def submit_im_calc_slurm(
sim_dir: str,
write_dir: str = None,
simple_out: bool = True,
adv_ims: bool = False,
target_machine: str = get_target_machine(
const.ProcessType.IM_calculation).name,
est_model: EstModel = path.join(
platform_config[const.PLATFORM_CONFIG.ESTIMATION_MODELS_DIR.name],
"IM"),
logger: Logger = get_basic_logger(),
):
"""Creates the IM calc slurm scrip, also submits if specified
The options_dict is populated by the DEFAULT_OPTIONS, values can be changed by
passing in a dict containing the entries that require changing. Merges the
two dictionaries, the passed in one has higher priority.
"""
# Load the yaml params
params = utils.load_sim_params(
sim_struct.get_sim_params_yaml_path(sim_dir), load_vm=True)
realisation_name = params[const.SimParams.run_name.value]
fault_name = sim_struct.get_fault_from_realisation(realisation_name)
station_count = len(load_station_file(params["FD_STATLIST"]).index)
header_options = {
const.SlHdrOptConsts.description.value:
"Calculates intensity measures.",
const.SlHdrOptConsts.memory.value:
"2G",
const.SlHdrOptConsts.version.value:
"slurm",
"exe_time":
const.timestamp,
const.SlHdrOptConsts.additional.value:
"#SBATCH --hint=nomultithread"
if platform_config[const.PLATFORM_CONFIG.SCHEDULER.name] == "slurm"
else [""],
}
body_options = {
const.SlBodyOptConsts.component.value: "",
"realisation_name": realisation_name,
const.SlBodyOptConsts.fault_name.value: fault_name,
"np":
platform_config[const.PLATFORM_CONFIG.IM_CALC_DEFAULT_N_CORES.name],
"sim_IM_calc_dir": sim_struct.get_im_calc_dir(sim_dir),
"output_csv": sim_struct.get_IM_csv(sim_dir),
"output_info": sim_struct.get_IM_info(sim_dir),
"models": "",
const.SlBodyOptConsts.mgmt_db.value: "",
"n_components": "",
"match_obs_stations": False,
}
command_options = {
const.SlBodyOptConsts.sim_dir.value:
sim_dir,
const.SlBodyOptConsts.component.value:
"",
const.SlBodyOptConsts.sim_name.value:
realisation_name,
const.SlBodyOptConsts.fault_name.value:
fault_name,
const.SlBodyOptConsts.n_procs.value:
platform_config[const.PLATFORM_CONFIG.IM_CALC_DEFAULT_N_CORES.name],
const.SlBodyOptConsts.extended.value:
"",
const.SlBodyOptConsts.simple_out.value:
"",
const.SlBodyOptConsts.advanced_IM.value:
"",
"pSA_periods":
"",
}
# Convert option settings to values
if write_dir is None:
write_dir = sim_dir
# Simple vs adv im settings
if adv_ims:
# Common values
proc_type = const.ProcessType.advanced_IM
sl_template = "adv_im_calc.sl.template"
script_prefix = "adv_im_calc"
body_options["models"] = " ".join(
params[const.SlBodyOptConsts.advanced_IM.value]["models"])
command_options[
const.SlBodyOptConsts.advanced_IM.
value] = f"-a {body_options['models']} --OpenSees {qconfig['OpenSees']} "
# create temporary station list if "match_obs_stations" is directory
if path.isdir(
str(params[const.SlBodyOptConsts.advanced_IM.value]
["match_obs_stations"])):
logger.debug(
"match_obs_station specificed: {params[const.SlBodyOptConsts.advanced_IM.value]['match_obs_stations']}"
)
# retreived station list from observed/fault(eventname)/Vol*/data/accBB/station.
obs_accBB_dir_glob = path.join(
params[const.SlBodyOptConsts.advanced_IM.value]
["match_obs_stations"],
f"{fault_name}/*/*/accBB",
)
obs_accBB_dir = glob.glob(obs_accBB_dir_glob)
if len(obs_accBB_dir) > 1:
logger.error(
"got more than one folder globbed. please double check the path to the match_obs_stations is correct."
)
sys.exit()
station_names_tmp = get_observed_stations(obs_accBB_dir[0])
# write to a tmp file
tmp_station_file = path.join(sim_dir, "tmp_station_file")
with open(tmp_station_file, "w") as f:
for station in station_names_tmp:
f.write(f"{station} ")
command_options[const.SlBodyOptConsts.advanced_IM.value] = (
command_options[const.SlBodyOptConsts.advanced_IM.value] +
f"--station_names `cat {tmp_station_file}`")
# header_options[const.SlHdrOptConsts.n_tasks.value] = body_options["np"] = qconfig["cores_per_node"]
# Time for one station to run in hours
# This should be a machine property. Or take the largest across all machines used
time_for_one_station = 0.5
est_run_time = (np.ceil(station_count / qconfig["cores_per_node"]) *
2 * time_for_one_station)
else:
proc_type = const.ProcessType.IM_calculation
sl_template = "sim_im_calc.sl.template"
script_prefix = "sim_im_calc"
if simple_out:
command_options[const.SlBodyOptConsts.simple_out.value] = "-s"
if params["ims"][const.RootParams.extended_period.name]:
command_options[const.SlBodyOptConsts.extended.value] = "-e"
period_count = len(
np.unique(
np.append(params["ims"]["pSA_periods"], const.EXT_PERIOD)))
else:
period_count = len(params["ims"]["pSA_periods"])
if "pSA_periods" in params["ims"]:
command_options[
"pSA_periods"] = f"-p {' '.join(str(p) for p in params['ims']['pSA_periods'])}"
comps_to_store = params["ims"][const.SlBodyOptConsts.component.value]
command_options[const.SlBodyOptConsts.component.
value] = "-c " + " ".join(comps_to_store)
body_options["n_components"] = len(comps_to_store)
# Get wall clock estimation
logger.info(
"Running wall clock estimation for IM sim for realisation {}".
format(realisation_name))
_, est_run_time = est_IM_chours_single(
station_count,
int(float(params["sim_duration"]) / float(params["dt"])),
comps_to_store,
period_count,
body_options["np"],
est_model,
)
# Header options requiring upstream settings
# special treatment for im_calc, as the scaling feature in estimation is not suitable
# cap the wct, otherwise cannot submit
est_run_time = min(est_run_time * CH_SAFETY_FACTOR, qconfig["MAX_JOB_WCT"])
# set ch_safety_factor=1 as we scale it already.
header_options["wallclock_limit"] = get_wct(est_run_time,
ch_safety_factor=1)
logger.debug("Using WCT for IM_calc: {header_options['wallclock_limit']}")
header_options["job_name"] = "{}_{}".format(proc_type.str_value,
fault_name)
header_options["platform_specific_args"] = get_platform_node_requirements(
body_options["np"])
script_file_path = write_sl_script(
write_dir,
sim_dir,
proc_type,
script_prefix,
header_options,
(sl_template, body_options),
command_options,
)
submit_script_to_scheduler(
script_file_path,
proc_type.value,
sim_struct.get_mgmt_db_queue(params["mgmt_db_location"]),
sim_dir,
realisation_name,
target_machine=target_machine,
logger=logger,
)
def main(args):
# This should come from constants
log_dir = os.path.join(args.sim_dir, "ch_log", const.METADATA_LOG_FILENAME)
metadata_dict = getattr(args, METADATA_VALUES)
# Determine run_time from start and end time
if (const.MetadataField.start_time.value in metadata_dict.keys()
and const.MetadataField.end_time.value in metadata_dict.keys()):
tdelta = datetime.strptime(
metadata_dict[const.MetadataField.end_time.value],
const.METADATA_TIMESTAMP_FMT,
) - datetime.strptime(
metadata_dict[const.MetadataField.start_time.value],
const.METADATA_TIMESTAMP_FMT,
)
metadata_dict[
const.MetadataField.run_time.value] = tdelta.total_seconds()
# Load the params
params = utils.load_sim_params(os.path.join(args.sim_dir,
"sim_params.yaml"),
load_vm=True)
if "dt" in params.bb:
bb_dt = params.bb.dt
else:
bb_dt = min(params.dt, params.hf.dt)
# params metadata for LF
if args.proc_type == const.ProcessType.EMOD3D.str_value:
metadata_dict[const.MetadataField.nt.value] = int(
float(params.sim_duration) / float(params.dt))
metadata_dict[const.MetadataField.nx.value] = params.nx
metadata_dict[const.MetadataField.ny.value] = params.ny
metadata_dict[const.MetadataField.nz.value] = params.nz
# HF
elif args.proc_type == const.ProcessType.HF.str_value:
metadata_dict[const.MetadataField.nt.value] = int(
float(params.sim_duration) / float(params.hf.dt))
metadata_dict[const.MetadataField.nsub_stoch.value] = get_nsub_stoch(
params["hf"]["slip"], get_area=False)
# BB
elif args.proc_type == const.ProcessType.BB.str_value:
metadata_dict[const.MetadataField.dt.value] = bb_dt
# IM_calc
elif args.proc_type == const.ProcessType.IM_calculation.str_value:
metadata_dict[const.MetadataField.nt.value] = int(
float(params.sim_duration) / float(bb_dt))
# This should come from a constants file
im_calc_csv_file = os.path.join(
args.sim_dir, "IM_calc",
"{}.csv".format(os.path.basename(args.sim_dir)))
im_comp = list(
pd.read_csv(im_calc_csv_file).component.unique().astype("U"))
metadata_dict[const.MetadataField.im_comp.value] = im_comp
metadata_dict[const.MetadataField.im_comp_count.value] = len(im_comp)
# Advanced_IM
elif args.proc_type == const.ProcessType.advanced_IM.str_value:
metadata_dict[const.MetadataField.nt.value] = int(
float(params.sim_duration) / float(bb_dt))
store_metadata(log_dir,
args.proc_type,
metadata_dict,
sim_name=os.path.basename(args.sim_dir))
def submit_task(
sim_dir,
proc_type,
run_name,
root_folder,
parent_logger,
retries=None,
hf_seed=const.HF_DEFAULT_SEED,
models=None,
):
task_logger = qclogging.get_task_logger(parent_logger, run_name, proc_type)
verification_dir = sim_struct.get_verification_dir(sim_dir)
# Metadata logging setup
ch_log_dir = os.path.abspath(os.path.join(sim_dir, "ch_log"))
if not os.path.isdir(ch_log_dir):
os.mkdir(ch_log_dir)
params = utils.load_sim_params(
sim_struct.get_sim_params_yaml_path(sim_dir))
submitted_time = datetime.now().strftime(const.METADATA_TIMESTAMP_FMT)
log_file = os.path.join(sim_dir, "ch_log", const.METADATA_LOG_FILENAME)
def submit_script_to_scheduler(script_name, target_machine=None, **kwargs):
shared_automated_workflow.submit_script_to_scheduler(
script_name,
proc_type,
sim_struct.get_mgmt_db_queue(root_folder),
sim_dir,
run_name,
target_machine=target_machine,
logger=task_logger,
)
if proc_type == const.ProcessType.EMOD3D.value:
# These have to include the default values (same for all other process types)!
args = argparse.Namespace(
auto=True,
srf=run_name,
ncore=platform_config[
const.PLATFORM_CONFIG.LF_DEFAULT_NCORES.name],
account=platform_config[
const.PLATFORM_CONFIG.DEFAULT_ACCOUNT.name],
machine=get_target_machine(const.ProcessType.EMOD3D).name,
rel_dir=sim_dir,
write_directory=sim_dir,
retries=retries,
)
task_logger.debug("Submit EMOD3D arguments: {}".format(args))
submit_lf_main(args, est_model=models[0], logger=task_logger)
store_metadata(
log_file,
const.ProcessType.EMOD3D.str_value,
{"submit_time": submitted_time},
logger=task_logger,
)
elif proc_type == const.ProcessType.merge_ts.value:
args = argparse.Namespace(
auto=True,
srf=run_name,
account=platform_config[
const.PLATFORM_CONFIG.DEFAULT_ACCOUNT.name],
machine=get_target_machine(const.ProcessType.merge_ts).name,
rel_dir=sim_dir,
write_directory=sim_dir,
)
task_logger.debug(
"Submit post EMOD3D (merge_ts) arguments: {}".format(args))
submit_post_lf_main(args, task_logger)
store_metadata(
log_file,
const.ProcessType.merge_ts.str_value,
{"submit_time": submitted_time},
logger=task_logger,
)
elif proc_type == const.ProcessType.plot_ts.value:
# plot_ts.py does not mkdir dir if output dir does not exist,
# whereas im_plot does.
if not os.path.isdir(verification_dir):
os.mkdir(verification_dir)
arguments = OrderedDict({
"XYTS_PATH":
os.path.join(
sim_struct.get_lf_outbin_dir(sim_dir),
"{}_xyts.e3d".format(run_name.split("_")[0]),
),
"SRF_PATH":
sim_struct.get_srf_path(root_folder, run_name),
"OUTPUT_TS_PATH":
os.path.join(verification_dir, run_name),
"MGMT_DB_LOC":
root_folder,
"SRF_NAME":
run_name,
})
script = get_platform_specific_script(const.ProcessType.plot_ts,
arguments)
submit_script_to_scheduler(script,
target_machine=get_target_machine(
const.ProcessType.plot_ts).name)
elif proc_type == const.ProcessType.HF.value:
args = argparse.Namespace(
auto=True,
srf=run_name,
seed=hf_seed,
ncore=platform_config[
const.PLATFORM_CONFIG.HF_DEFAULT_NCORES.name],
version=platform_config[
const.PLATFORM_CONFIG.HF_DEFAULT_VERSION.name],
site_specific=None,
account=platform_config[
const.PLATFORM_CONFIG.DEFAULT_ACCOUNT.name],
machine=get_target_machine(const.ProcessType.HF).name,
rel_dir=sim_dir,
write_directory=sim_dir,
debug=False,
retries=retries,
)
task_logger.debug("Submit HF arguments: {}".format(args))
submit_hf_main(args, models[1], task_logger)
store_metadata(
log_file,
const.ProcessType.HF.str_value,
{"submit_time": submitted_time},
logger=task_logger,
)
elif proc_type == const.ProcessType.BB.value:
args = argparse.Namespace(
auto=True,
srf=run_name,
version=platform_config[
const.PLATFORM_CONFIG.BB_DEFAULT_VERSION.name],
account=platform_config[
const.PLATFORM_CONFIG.DEFAULT_ACCOUNT.name],
machine=get_target_machine(const.ProcessType.BB).name,
rel_dir=sim_dir,
write_directory=sim_dir,
retries=retries,
)
task_logger.debug("Submit BB arguments: {}".format(args))
submit_bb_main(args, models[2], task_logger)
store_metadata(
log_file,
const.ProcessType.BB.str_value,
{"submit_time": submitted_time},
logger=task_logger,
)
elif proc_type == const.ProcessType.IM_calculation.value:
submit_im_calc_slurm(
sim_dir=sim_dir,
simple_out=True,
target_machine=get_target_machine(
const.ProcessType.IM_calculation).name,
est_model=models[3],
logger=task_logger,
)
task_logger.debug(
f"Submit IM calc arguments: sim_dir: {sim_dir}, simple_out: True, target_machine: {get_target_machine(const.ProcessType.IM_calculation).name}"
)
store_metadata(
log_file,
const.ProcessType.IM_calculation.str_value,
{"submit_time": submitted_time},
logger=task_logger,
)
elif proc_type == const.ProcessType.IM_plot.value:
im_plot_template = "{script_location} {csv_path} {station_file_path} {output_xyz_dir} {srf_path} {model_params_path} {mgmt_db_loc} {run_name}"
script = im_plot_template.format(
csv_path=os.path.join(sim_struct.get_IM_csv(sim_dir)),
station_file_path=params.stat_file,
output_xyz_dir=os.path.join(verification_dir, "IM_plot"),
srf_path=sim_struct.get_srf_path(root_folder, run_name),
model_params_path=params.MODEL_PARAMS,
mgmt_db_loc=root_folder,
run_name=run_name,
script_location=os.path.expandvars(
"$gmsim/workflow/scripts/im_plot.sl"),
)
submit_script_to_scheduler(script,
target_machine=get_target_machine(
const.ProcessType.IM_plot).name)
elif proc_type == const.ProcessType.rrup.value:
submit_script_to_scheduler(
get_platform_specific_script(
const.ProcessType.rrup,
OrderedDict({
"REL": sim_dir,
"MGMT_DB_LOC": root_folder
}),
),
target_machine=get_target_machine(const.ProcessType.rrup).name,
)
elif proc_type == const.ProcessType.Empirical.value:
extended_period_switch = "-e" if params["ims"][
"extended_period"] else ""
sl_script = generate_empirical_script(1, extended_period_switch,
root_folder, [run_name], sim_dir)
submit_script_to_scheduler(
sl_script,
target_machine=get_target_machine(
const.ProcessType.Empirical).name,
)
elif proc_type == const.ProcessType.Verification.value:
raise NotImplementedError("Verification is not currently working")
elif proc_type == const.ProcessType.clean_up.value:
submit_script_to_scheduler(
get_platform_specific_script(
const.ProcessType.clean_up,
OrderedDict({
"SIM_DIR": sim_dir,
"SRF_NAME": run_name,
"MGMT_DB_LOC": root_folder,
}),
),
target_machine=get_target_machine(const.ProcessType.clean_up).name,
)
elif proc_type == const.ProcessType.LF2BB.value:
submit_script_to_scheduler(
get_platform_specific_script(
const.ProcessType.LF2BB,
OrderedDict({
"REL_LOC":
sim_dir,
"MGMT_DB_LOC":
root_folder,
"VSITE_FILE":
params.stat_vs_est,
"REM_ARGS":
"'" + " ".join([
"--{} {}".format(key, item)
for key, item in params.bb.items()
]) + "'",
}),
),
target_machine=get_target_machine(const.ProcessType.LF2BB).name,
)
elif proc_type == const.ProcessType.HF2BB.value:
submit_script_to_scheduler(
get_platform_specific_script(
const.ProcessType.HF2BB,
OrderedDict({
"REL_LOC":
sim_dir,
"MGMT_DB_LOC":
root_folder,
"REM_ARGS":
"'" + " ".join([
"--{} {}".format(key, item)
for key, item in params.bb.items()
]) + "'",
}),
),
target_machine=get_target_machine(const.ProcessType.HF2BB).name,
)
elif proc_type == const.ProcessType.plot_srf.value:
submit_script_to_scheduler(
get_platform_specific_script(
const.ProcessType.plot_srf,
OrderedDict({
"SRF_DIR":
sim_struct.get_srf_dir(root_folder, run_name),
"OUTPUT_DIR":
sim_struct.get_sources_plot_dir(root_folder, run_name),
"MGMT_DB_LOC":
root_folder,
"SRF_NAME":
run_name,
}),
),
target_machine=get_target_machine(const.ProcessType.plot_srf).name,
)
elif proc_type == const.ProcessType.advanced_IM.value:
submit_im_calc_slurm(
sim_dir=sim_dir,
adv_ims=True,
target_machine=get_target_machine(
const.ProcessType.IM_calculation).name,
est_model=models[3],
logger=task_logger,
)
task_logger.debug(
f"Submit Advanced_IM calc arguments:sim_dir: {sim_dir}, adv_im: True, target_machine: {get_target_machine(const.ProcessType.IM_calculation).name}"
)
store_metadata(
log_file,
const.ProcessType.advanced_IM.str_value,
{"submit_time": submitted_time},
logger=task_logger,
)
qclogging.clean_up_logger(task_logger)