def get_parameters(folder):
parameters = {}
for xml_file in glob.glob(os.path.join(folder, "*.xml")):
if 'report' in xml_file:
continue
try:
config = read_config(xml_file)
initial_data_parameters = get_xml_node(
config, "config.fvm.initialData.parameters")
for initial_data_parameter in initial_data_parameters.getElementsByTagName(
"parameter"):
name = get_in_xml(initial_data_parameter, "name")
length = int(get_in_xml(initial_data_parameter, "length"))
if length == 1:
value = float(get_in_xml(initial_data_parameter, "value"))
parameters[name] = value
print(parameters)
except Exception as e:
print(e)
return parameters
parser.add_argument('--number_of_samples_per_run',
type=int,
required=True,
help='Number of samples per run/individual file')
parser.add_argument('--config',
type=str,
required=True,
help="Path to configuration file")
args = parser.parse_args()
config = read_config(args.config)
samples = get_in_xml(config, "config.uq.samples")
if int(samples) % args.number_of_samples_per_run:
raise Exception("number_of_samples_per_run must be a multiple of the total number of samples. Given:" +\
f"\tnumber_of_samples_per_run: {args.number_of_samples_per_run}\n" +\
f"\ttotal number of samples : {samples}")
number_of_config_files = int(samples) // args.number_of_samples_per_run
for n in range(number_of_config_files):
sample_start = n * args.number_of_samples_per_run
sample_end = (n + 1) * args.number_of_samples_per_run
outfolder = f"sample_{sample_start}_{sample_end}"
os.mkdir(outfolder)
type=str,
help='Moves the results to another folder after simulation is done')
parser.add_argument('--base_path',
type=str,
default=repo.working_dir,
help='Base path of this repository')
args = parser.parse_args()
configuration_file = args.config
configuration_path = os.path.abspath(os.path.dirname(configuration_file))
config = read_config(configuration_file)
resolution = int(
get_in_xml(config, 'config.fvm.grid.dimension').split(" ")[0])
number_of_nodes_per_direction = max(1, resolution // 256)
total_number_of_nodes = number_of_nodes_per_direction**3 * args.multi_sample
r_command_append = "rusage[ngpus_excl_p=8,mem=8000] span[ptile=8]"
job_chain = os.path.abspath(configuration_file)
job_chain = ''.join(ch for ch in job_chain if ch.isalnum() or ch == '_')
command_to_run = [
'bsub',
'-R',
r_command_append,
'-W',
for n, perturbation in enumerate(args.perturbations):
perturbation_folder = "p{}".format(perturbation.replace(".", "_"))
os.mkdir(perturbation_folder)
for m, resolution in enumerate(args.resolutions):
resolution_folder = f"{perturbation_folder}/N{resolution}"
os.mkdir(resolution_folder)
samples = args.samples[m]
set_in_xml(config, "config.uq.samples", samples)
set_in_xml(config, "config.fvm.grid.dimension",
f"{resolution} {resolution} {resolution}")
python_file = get_in_xml(config, "config.initialData.python")
initial_data_parameters = get_xml_node(
config, "config.initialData.parameters")
for initial_data_parameter in initial_data_parameters.getElementsByTagName(
"parameter"):
name = get_in_xml(initial_data_parameter, "name")
if name == "epsilon":
set_in_xml(initial_data_parameter, "value", perturbation)
shutil.copyfile(
os.path.join(os.path.dirname(args.config), python_file),
os.path.join(resolution_folder, python_file))
parser.add_argument(
'--multi_sample',
type=int,
default=1,
help='Number of processes to use in the sample direction')
parser.add_argument('--dry_run',
action='store_true',
help='Only do a dry run, no actual submission done')
args = parser.parse_args()
configuration_file = args.config
configuration_path = os.path.abspath(os.path.dirname(configuration_file))
config = read_config(configuration_file)
name = get_in_xml(config, 'config.fvm.name').strip()
resolution = int(
get_in_xml(config, 'config.fvm.grid.dimension').split(" ")[0])
number_of_nodes_per_direction = max(1, resolution // 256)
total_number_of_nodes = number_of_nodes_per_direction**3 * args.multi_sample
submit_file = f"""#!/bin/bash -l
#SBATCH --job-name="{name}_{resolution}"
#SBATCH --time=24:00:00
#SBATCH --nodes={total_number_of_nodes}
#SBATCH --ntasks-per-core=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --partition=normal