def create_batch_job_script_for_multiple_gids(arguments, gids, script_id):
"""Create a batch job file for different neurons with specific gids for the meshing.
:param arguments:
Command line arguments.
:param gids:
A list of GIDs.
:param script_id:
Script ID.
"""
# Create slurm configuration
slurm_config = slurm_configuration.SlurmConfiguration()
# Update slurm configuration data
# Job number should match the gid
slurm_config.job_number = script_id
# Execution directory, same as output directory
slurm_config.execution_directory = '%s' % arguments.output_directory
# Log directory
slurm_config.logs_directory = '%s/%s' % (
arguments.output_directory, paths_consts.Paths.SLURM_LOGS_FOLDER)
# Generate the batch job configuration string
batch_job_config_string = create_batch_job_config_string(slurm_config)
# Add the shell command to run blender
# Setup the shell command
shell_command = ""
for gid in gids:
# Get all the shell commands that are given for a specific GID
shell_commands = arguments_parser.create_executable_for_single_gid(
arguments, gid) + '\n'
shell_command = ''
for command in shell_commands:
shell_command += command + '\n'
# Add the command to the batch job config string
batch_job_config_string += shell_command
# Write the batch job script to file in the slurm jobs directory
slurm_jobs_directory = '%s/%s' % (arguments.output_directory,
paths_consts.Paths.SLURM_JOBS_FOLDER)
file_ops.write_batch_job_string_to_file(slurm_jobs_directory, script_id,
batch_job_config_string)
def create_batch_job_script_for_morphology_file(arguments, morphology_file):
"""Create a batch job file for a morphology file.
:param arguments:
Command line arguments.
:param morphology_file:
Neuron morphology_file.
"""
# Create slurm configuration
slurm_config = slurm_configuration.SlurmConfiguration()
# Update slurm configuration data
# Job number should match the gid
slurm_config.job_number = 0
# Execution directory, same as output directory
slurm_config.execution_directory = '%s' % arguments.output_directory
# Log directory
slurm_config.logs_directory = '%s/%s' % (
arguments.output_directory, paths_consts.Paths.SLURM_LOGS_FOLDER)
# Generate the batch job configuration string
batch_job_config_string = create_batch_job_config_string(slurm_config)
# Setup the shell command
shell_commands = arguments_parser.create_executable_for_single_morphology_file(
arguments, morphology_file)
shell_command = ''
for command in shell_commands:
shell_command += command + '\n'
# Add the command to the batch job config string
batch_job_config_string += shell_command
# Write the batch job script to file in the slurm jobs directory
slurm_jobs_directory = '%s/%s' % (arguments.output_directory,
paths_consts.Paths.SLURM_JOBS_FOLDER)
file_ops.write_batch_job_string_to_file(slurm_jobs_directory,
morphology_file,
batch_job_config_string)
def create_batch_job_script_for_gid(arguments, gid):
"""Create a batch job file for a neuron with specific GID.
:param arguments:
Command line arguments.
:param gid:
Neuron GID.
"""
# Create slurm configuration
slurm_config = slurm_configuration.SlurmConfiguration()
# Update slurm configuration data
# Job number should match the gid
slurm_config.job_number = int(gid)
# Execution directory, same as output directory
slurm_config.execution_directory = '%s' % arguments.output_directory
# Log directory
slurm_config.logs_directory = '%s/%s' % (
arguments.output_directory, paths_consts.Paths.SLURM_LOGS_FOLDER)
# Generate the batch job configuration string
batch_job_config_string = create_batch_job_config_string(slurm_config)
# Setup the shell command
shell_command = arguments_parser.create_executable_for_single_gid(
arguments, gid)
# Add the command to the batch job config string
batch_job_config_string += shell_command
# Write the batch job script to file in the slurm jobs directory
slurm_jobs_directory = '%s/%s' % (arguments.output_directory,
paths_consts.Paths.SLURM_JOBS_FOLDER)
file_ops.write_batch_job_string_to_file(slurm_jobs_directory, gid,
batch_job_config_string)
# create slurm directory
slurm_directory = "%s/%s" % (args.output_directory, "slurm")
fh.clean_and_create_new_directory(slurm_directory)
logs_directory = "%s/%s" % (args.output_directory, "logs")
fh.clean_and_create_new_directory(logs_directory)
# execute the workflow on the cluster
if args.node == 'cluster':
# write all the batch jobs to the directory
for i, psh_file in enumerate(psh_file_list):
# create the slurm configuration.
slurm_configuration = s_config.SlurmConfiguration()
slurm_configuration.job_number = i
slurm_configuration.log_files_path = logs_directory
# create the slurm configuration string.
slurm_batch_string = slurm.create_batch_config(slurm_configuration)
# create the execution command and then append it to the batch string
execution_command = create_executable_command(args, psh_file)
slurm_batch_string += execution_command
# save the script
script_path = "%s/%s.sh" % (slurm_directory, str(i))
fh.save_file_to_disk(script_path, slurm_batch_string)
# run all the batch scripts