Package schrodinger :: Package application :: Package macromodel :: Module paraUtils

Module paraUtils

This is a common module for parallel job execution. It provides functionalities to configure and run parallel jobs. Currently this script is used by epik_driver, bmin_driver, and ligprep_driver.

Functions

[hide private]

add_para_job_options(parser, options=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
Adds common para job control options to a SingleDashOptionParser instance.

validate_options(options)
Validate the job control options

print_job_info(argv, driver_script, version)
Check command line arguments passed and environment variables based on the driver.

_subjob_input_id(text)
To be used for the subjob input names sorting.

_append_st_file(st_file, st_writer, raw_append=False, is_compressed=False)
Append structure files.

_print_subjob_logfile(log_file='', start_msg=None, end_msg=None)
Prints given log file with start and end messages.

_timestamp()

_merge_subjobs(backend_instance, subjob_input_mae_files, output_file, output_org, data)
Merge subjobs structure and log files.

_get_jobs_to_run(run_jobs_str, njobs)
Return the list of jobs to run.

_generate_subjobs(job_input_file, job_output_file, options, driver_script, split_input_file=True)
Creates the subjob dirs and fill in data

_run_subjobs(jdj, restart_file)

launch_subjobs(options, driver_script, backend_instance, backend_args, job_input_file, job_output_file, cmd_append='', merge=True, prepare_subjob_callback=None, callback_data={}, split_input_file=True, post_execution_processing_callback=None, post_execution_processing_callback_data={})
Launch subjobs.

Variables

[hide private]

__doc__ = ...

FIRSTCT = 2

JOBCTS = 1

LASTCT = 3
hash(x)

MAX_RETRIES = 6

NC = 10

NJOBS = 0
hash(x)

NO_EXECUTION = 8

OUTPUT_ORG = 7

RESTART = 9

RUN_JOBS = 4

STRICT_END = 5

__package__ = 'schrodinger.application.macromodel'

Function Details

[hide private]

add_para_job_options(parser, options=`[`0`,` 1`,` 2`,` 3`,` 4`,` 5`,` 6`,` 7`,` 8`,` 9`,` 10`]`)

Adds common para job control options to a SingleDashOptionParser instance.

Parameters:

parser (SingleDashOptionParser) - Instance of SingleDashOptionParser
options (List) - List of module enums that indicate what options to add to the parser.

validate_options(options)

Validate the job control options

Parameters:

options (Instance) - object containing values of para job options

print_job_info(argv, driver_script, version)

Check command line arguments passed and environment variables based on the driver.

Parameters:

argv (String) - Command line arguments
driver_script (String) - Driver script name
version (String) - Driver script version

_append_st_file(st_file, st_writer, raw_append=False, is_compressed=False)

Append structure files.

Parameters:

st_file (String) - Structure file name
raw_append (Boolean) - Indicates to append file using raw I/O
is_compressed (Boolean) - Indicates compressed output file. This option is in use only with raw_append option.

_print_subjob_logfile(log_file=`''`, start_msg=None, end_msg=None)

Prints given log file with start and end messages.

Parameters:

log_file (String) - Log file name. Print the content of log_file, if specified
start_msg (String) - Message to place at the start of the log file
end_msg (String) - Message to place at the end of the log file

_merge_subjobs(backend_instance, subjob_input_mae_files, output_file, output_org, data)

Merge subjobs structure and log files.

Parameters:

backend_instance (_Backend) - Instance of the _Backend
subjob_input_mae_files (List) - List of subjob files with parent directory
output_file (String) - Job output file name
output_org (String) - Produce more than one output structure file

_get_jobs_to_run(run_jobs_str, njobs)

Return the list of jobs to run.

Parameters:

run_jobs_str (String) - String of ':' or ',' separated numbers
njobs (Number) - Total number of jobs requested

_generate_subjobs(job_input_file, job_output_file, options, driver_script, split_input_file=True)

Creates the subjob dirs and fill in data

Parameters:

job_input_file (String) - Job input file
job_output_file (String) - Job output file
options (Instance) - object containing values of para job options

launch_subjobs(options, driver_script, backend_instance, backend_args, job_input_file, job_output_file, cmd_append=`''`, merge=True, prepare_subjob_callback=None, callback_data=`{}`, split_input_file=True, post_execution_processing_callback=None, post_execution_processing_callback_data=`{}`)

Launch subjobs.

Parameters:

options (Instance) - object containing values of para job options
driver_script (String) - Driver script name
backend_instance (_Backend) - Instance of the _Backend
backend_args (List) - List of arguments
job_input_file (String) - Job input file
job_output_file (String) - Job output file
cmd_append (String) - Command to be appended to subjob command
merge (Boolean) - Whether to join subjob outputs or not
prepare_subjob_callback (Function) - Function to be called to prepare subjob data
callback_data (Dictionary) - A dictionary to be passed to subjob callback

Variables Details

[hide private]

doc

Value:

"""

 Copyright Schrodinger, LLC. All rights reserved.

 This is a common module for parallel job execution.
 It provides functionalities to configure and run parallel jobs.
 Currently this script is used by epik_driver, bmin_driver, and ligpre
p_driver.
...

Module paraUtils

add_para_job_options(parser, options=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])

validate_options(options)

print_job_info(argv, driver_script, version)

_append_st_file(st_file, st_writer, raw_append=False, is_compressed=False)

_print_subjob_logfile(log_file='', start_msg=None, end_msg=None)

_merge_subjobs(backend_instance, subjob_input_mae_files, output_file, output_org, data)

_get_jobs_to_run(run_jobs_str, njobs)

_generate_subjobs(job_input_file, job_output_file, options, driver_script, split_input_file=True)

launch_subjobs(options, driver_script, backend_instance, backend_args, job_input_file, job_output_file, cmd_append='', merge=True, prepare_subjob_callback=None, callback_data={}, split_input_file=True, post_execution_processing_callback=None, post_execution_processing_callback_data={})

__doc__

add_para_job_options(parser, options=`[`0`,` 1`,` 2`,` 3`,` 4`,` 5`,` 6`,` 7`,` 8`,` 9`,` 10`]`)

_print_subjob_logfile(log_file=`''`, start_msg=None, end_msg=None)

launch_subjobs(options, driver_script, backend_instance, backend_args, job_input_file, job_output_file, cmd_append=`''`, merge=True, prepare_subjob_callback=None, callback_data=`{}`, split_input_file=True, post_execution_processing_callback=None, post_execution_processing_callback_data=`{}`)

doc