autosubmit.job¶

Main module for Autosubmit. Only contains an interface class to all functionality implemented on Autosubmit

class autosubmit.job.job.Job(name, job_id, status, priority)¶

Class to handle all the tasks with Jobs at HPC. A job is created by default with a name, a jobid, a status and a type. It can have children and parents. The inheritance reflects the dependency between jobs. If Job2 must wait until Job1 is completed then Job2 is a child of Job1. Inversely Job1 is a parent of Job2

Parameters:	name (str) – job’s name job_id (int) – job’s id status (Status) – job initial status priority (int) – job’s priority

add_edge_info(parent_name, special_variables)¶

Adds edge information to the job

Parameters:	parent_name (str) – parent name special_variables (dict) – special variables

add_parent(*parents)¶

Add parents for the job. It also adds current job as a child for all the new parents

Parameters:	parents (*Job) – job’s parents to add

check_completion(default_status=-1, over_wallclock=False)¶: Check the presence of COMPLETED file. Change status to COMPLETED if COMPLETED file exists and to FAILED otherwise. :param default_status: status to set if job is not completed. By default, is FAILED :type default_status: Status

check_end_time()¶

Returns end time from stat file

Returns:	date and time
Return type:	str

check_retrials_end_time()¶

Returns list of end datetime for retrials from total stats file

Returns:	date and time
Return type:	list[int]

check_retrials_start_time()¶

Returns list of start datetime for retrials from total stats file

Returns:	date and time
Return type:	list[int]

check_retrials_submit_time()¶

Returns list of submit datetime for retrials from total stats file

Returns:	date and time
Return type:	list[int]

check_running_after(date_limit)¶: Checks if the job was running after the given date :param date_limit: reference date :type date_limit: datetime.datetime :return: True if job was running after the given date, false otherwise :rtype: bool

check_script(as_conf, parameters, show_logs=False)¶

Checks if script is well-formed

Parameters:	parameters (dict) – script parameters as_conf (AutosubmitConfig) – configuration file show_logs (Bool) – Display output
Returns:	true if not problem has been detected, false otherwise
Return type:	bool

check_start_time()¶

Returns job’s start time

Returns:	start time
Return type:	str

check_started_after(date_limit)¶: Checks if the job started after the given date :param date_limit: reference date :type date_limit: datetime.datetime :return: True if job started after the given date, false otherwise :rtype: bool

children¶

Returns a list containing all children of the job

Returns:	child jobs
Return type:	set

children_names_str¶: Comma separated list of children’s names

compare_by_id(other)¶

Compare jobs by ID

Parameters:	other (Job) – job to compare
Returns:	comparison result
Return type:	bool

compare_by_name(other)¶

Compare jobs by name

Parameters:	other (Job) – job to compare
Returns:	comparison result
Return type:	bool

compare_by_status(other)¶

Compare jobs by status value

Parameters:	other (Job) – job to compare
Returns:	comparison result
Return type:	bool

create_script(as_conf)¶

Creates script file to be run for the job

Parameters:	as_conf (AutosubmitConfig) – configuration object
Returns:	script’s filename
Return type:	str

delete_child(child)¶

Removes a child from the job

Parameters:	child (Job) – child to remove

delete_parent(parent)¶

Remove a parent from the job

Parameters:	parent (Job) – parent to remove

get_last_retrials()¶

Returns the retrials of a job, including the last COMPLETED run. The selection stops, and does not include, when the previous COMPLETED job is located or the list of registers is exhausted.

Returns:	list of dates of retrial [submit, start, finish] in datetime format
Return type:	list of list

has_children()¶

Returns true if job has any children, else return false

Returns:	true if job has any children, otherwise return false
Return type:	bool

has_parents()¶

Returns true if job has any parents, else return false

Returns:	true if job has any parent, otherwise return false
Return type:	bool

inc_fail_count()¶: Increments fail count

static is_a_completed_retrial(fields)¶: Returns true only if there are 4 fields: submit start finish status, and status equals COMPLETED.

is_ancestor(job)¶: Check if the given job is an ancestor :param job: job to be checked if is an ancestor :return: True if job is an ancestor, false otherwise :rtype bool

is_over_wallclock(start_time, wallclock)¶: Check if the job is over the wallclock time, it is an alternative method to avoid platform issues :param start_time: :param wallclock: :return:

is_parent(job)¶: Check if the given job is a parent :param job: job to be checked if is a parent :return: True if job is a parent, false otherwise :rtype bool

log_job()¶: Prints job information in log

long_name¶

Job’s long name. If not setted, returns name

Returns:	long name
Return type:	str

parents¶

Returns parent jobs list

Returns:	parent jobs
Return type:	set

platform¶

Returns the platform to be used by the job. Chooses between serial and parallel platforms

:return HPCPlatform object for the job to use :rtype: HPCPlatform

print_job()¶: Prints debug information about the job

print_parameters()¶: Print sjob parameters in log

queue¶

Returns the queue to be used by the job. Chooses between serial and parallel platforms

:return HPCPlatform object for the job to use :rtype: HPCPlatform

remove_redundant_parents()¶: Checks if a parent is also an ancestor, if true, removes the link in both directions. Useful to remove redundant dependencies.

status_str¶: String representation of the current status

total_processors¶: Number of processors requested by job. Reduces ‘:’ separated format if necessary.

update_content(as_conf)¶

Create the script content to be run for the job

Parameters:	as_conf (config) – config
Returns:	script code
Return type:	str

update_parameters(as_conf, parameters, default_parameters={'M': '%M%', 'M_': '%M_%', 'Y': '%Y%', 'Y_': '%Y_%', 'd': '%d%', 'd_': '%d_%', 'm': '%m%', 'm_': '%m_%'})¶

Refresh parameters value

Parameters:	default_parameters (dict) – as_conf (AutosubmitConfig) – parameters (dict) –

update_status(as_conf, failed_file=False)¶

Updates job status, checking COMPLETED file if needed

Parameters:	copy_remote_logs – boolean, if True, copies remote logs to local failed_file – boolean, if True, checks if the job failed
Returns:

write_end_time(completed, enabled=False)¶: Writes ends date and time to TOTAL_STATS file :param completed: True if job was completed successfully, False otherwise :type completed: bool

write_start_time(enabled=False)¶: Writes start date and time to TOTAL_STATS file :return: True if succesful, False otherwise :rtype: bool

write_submit_time(enabled=False, hold=False)¶: Writes submit date and time to TOTAL_STATS file. It doesn’t write if hold == True.

write_total_stat_by_retries(total_stats, first_retrial=False)¶: Writes all data to TOTAL_STATS file :param total_stats: data gathered by the wrapper :type total_stats: dict :param first_retrial: True if this is the first retry, False otherwise :type first_retrial: bool

class autosubmit.job.job.WrapperJob(name, job_id, status, priority, job_list, total_wallclock, num_processors, platform, as_config, hold)¶

Defines a wrapper from a package.

Calls Job constructor.

Parameters:

name (String) – Name of the Package
job_id (Integer) – ID of the first Job of the package
status (String) – ‘READY’ when coming from submit_ready_jobs()
priority (Integer) – 0 when coming from submit_ready_jobs()
job_list (List() of Job() objects) – List of jobs in the package
total_wallclock (String Formatted) – Wallclock of the package
num_processors (Integer) – Number of processors for the package
platform (Platform Object. e.g. EcPlatform()) – Platform object defined for the package
as_config (AutosubmitConfig object) – Autosubmit basic configuration object

class autosubmit.job.job_common.StatisticsSnippetBash¶: Class to handle the statistics snippet of a job. It contains header and tailer for local and remote jobs

class autosubmit.job.job_common.StatisticsSnippetEmpty¶: Class to handle the statistics snippet of a job. It contains header and footer for local and remote jobs

class autosubmit.job.job_common.StatisticsSnippetPython(version='3')¶: Class to handle the statistics snippet of a job. It contains header and tailer for local and remote jobs

class autosubmit.job.job_common.StatisticsSnippetR¶: Class to handle the statistics snippet of a job. It contains header and tailer for local and remote jobs

class autosubmit.job.job_common.Status¶: Class to handle the status of a job

class autosubmit.job.job_common.Type¶: Class to handle the status of a job

autosubmit.job.job_common.increase_wallclock_by_chunk(current, increase, chunk)¶

Receives the wallclock times an increases it according to a quantity times the number of the current chunk. The result cannot be larger than 48:00. If Chunk = 0 then no increment.

Parameters:	current (str) – WALLCLOCK HH:MM increase (str) – WCHUNKINC HH:MM chunk (int) – chunk number
Returns:	HH:MM wallclock
Return type:	str

autosubmit.job.job_common.parse_output_number(string_number)¶

Parses number in format 1.0K 1.0M 1.0G

Parameters:	string_number (str) – String representation of number
Returns:	number in float format
Return type:	float

class autosubmit.job.job_list.JobList(expid, config, parser_factory, job_list_persistence, as_conf)¶

Class to manage the list of jobs to be run by autosubmit

add_logs(logs)¶: add logs to the current job_list :return: logs :rtype: dict(tuple)

backup_load()¶

Recreates a stored job list from the persistence

Returns:	loaded job list object
Return type:	JobList

backup_save()¶: Persists the job list

check_scripts(as_conf)¶

When we have created the scripts, all parameters should have been substituted. %PARAMETER% handlers not allowed

Parameters:	as_conf (AutosubmitConfig) – experiment configuration

expid¶

Returns the experiment identifier

Returns:	experiment’s identifier
Return type:	str

generate(date_list, member_list, num_chunks, chunk_ini, parameters, date_format, default_retrials, default_job_type, wrapper_type=None, wrapper_jobs={}, new=True, notransitive=False, update_structure=False, run_only_members=[], show_log=True, jobs_data={}, as_conf='')¶

Creates all jobs needed for the current workflow

Parameters:

default_job_type (str) – default type for jobs
date_list (list) – start dates
member_list (list) – members
num_chunks (int) – number of chunks to run
chunk_ini (int) – the experiment will start by the given chunk
parameters (dict) – experiment parameters
date_format (str) – option to format dates
default_retrials (int) – default retrials for ech job
new (bool) – is it a new generation?
wrapper_type – Type of wrapper defined by the user in autosubmit_.yml [wrapper] section.
wrapper_jobs (String) – Job types defined in autosubmit_.yml [wrapper sections] to be wrapped.

get_active(platform=None, wrapper=False)¶

Returns a list of active jobs (In platforms queue + Ready)

Parameters:	platform (HPCPlatform) – job platform
Returns:	active jobs
Return type:	list

get_all(platform=None, wrapper=False)¶

Returns a list of all jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	all jobs
Return type:	list

get_chunk_list()¶

Get inner chunk list

Returns:	chunk list
Return type:	list

get_completed(platform=None, wrapper=False)¶

Returns a list of completed jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	completed jobs
Return type:	list

get_date_list()¶

Get inner date list

Returns:	date list
Return type:	list

get_delayed(platform=None)¶

Returns a list of delayed jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	delayed jobs
Return type:	list

get_failed(platform=None, wrapper=False)¶

Returns a list of failed jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	failed jobs
Return type:	list

get_finished(platform=None, wrapper=False)¶

Returns a list of jobs finished (Completed, Failed)

Parameters:	platform (HPCPlatform) – job platform
Returns:	finished jobs
Return type:	list

get_held_jobs(platform=None)¶

Returns a list of jobs in the platforms (Held)

Parameters:	platform (HPCPlatform) – job platform
Returns:	jobs in platforms
Return type:	list

get_in_queue(platform=None, wrapper=False)¶

Returns a list of jobs in the platforms (Submitted, Running, Queuing, Unknown,Held)

Parameters:	platform (HPCPlatform) – job platform
Returns:	jobs in platforms
Return type:	list

get_job_by_name(name)¶

Returns the job that its name matches parameter name

Parameters:	name (str) – name to look for
Returns:	found job
Return type:	job

get_job_list()¶

Get inner job list

Returns:	job list
Return type:	list

get_job_names(lower_case=False)¶

Returns a list of all job names :param: lower_case: if true, returns lower case job names :type: lower_case: bool

Returns:	all job names
Return type:	list

get_job_related(select_jobs_by_name='', select_all_jobs_by_section='', filter_jobs_by_section='', two_step_start=True)¶

Parameters:	select_jobs_by_name – job name select_all_jobs_by_section – section name filter_jobs_by_section – section, date , member? , chunk?
Returns:	jobs_list names
Return type:	list

get_jobs_by_section(section_list)¶: Returns the job that its name matches parameter section :parameter section_list: list of sections to look for :type section_list: list :return: found job :rtype: job

get_logs()¶

Returns a dict of logs by jobs_name jobs

Returns:	logs
Return type:	dict(tuple)

get_member_list()¶

Get inner member list

Returns:	member list
Return type:	list

get_not_in_queue(platform=None, wrapper=False)¶

Returns a list of jobs NOT in the platforms (Ready, Waiting)

Parameters:	platform (HPCPlatform) – job platform
Returns:	jobs not in platforms
Return type:	list

get_ordered_jobs_by_date_member(section)¶

Get the dictionary of jobs ordered according to wrapper’s expression divided by date and member

Returns:	jobs ordered divided by date and member
Return type:	dict

get_prepared(platform=None)¶

Returns a list of prepared jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	prepared jobs
Return type:	list

get_queuing(platform=None, wrapper=False)¶

Returns a list of jobs queuing

Parameters:	platform (HPCPlatform) – job platform
Returns:	queuedjobs
Return type:	list

get_ready(platform=None, hold=False, wrapper=False)¶

Returns a list of ready jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	ready jobs
Return type:	list

get_running(platform=None, wrapper=False)¶

Returns a list of jobs running

Parameters:	platform (HPCPlatform) – job platform
Returns:	running jobs
Return type:	list

get_skipped(platform=None)¶

Returns a list of skipped jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	skipped jobs
Return type:	list

get_submitted(platform=None, hold=False, wrapper=False)¶

Returns a list of submitted jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	submitted jobs
Return type:	list

get_suspended(platform=None, wrapper=False)¶

Returns a list of jobs on unknown state

Parameters:	platform (HPCPlatform) – job platform
Returns:	unknown state jobs
Return type:	list

get_uncompleted(platform=None, wrapper=False)¶

Returns a list of completed jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	completed jobs
Return type:	list

get_uncompleted_and_not_waiting(platform=None, wrapper=False)¶

Returns a list of completed jobs and waiting

Parameters:	platform (HPCPlatform) – job platform
Returns:	completed jobs
Return type:	list

get_unknown(platform=None, wrapper=False)¶

Returns a list of jobs on unknown state

Parameters:	platform (HPCPlatform) – job platform
Returns:	unknown state jobs
Return type:	list

get_unsubmitted(platform=None, wrapper=False)¶

Returns a list of unsummited jobs

Parameters:	platform (HPCPlatform) – job platform
Returns:	all jobs
Return type:	list

get_waiting(platform=None, wrapper=False)¶

Returns a list of jobs waiting

Parameters:	platform (HPCPlatform) – job platform
Returns:	waiting jobs
Return type:	list

get_waiting_remote_dependencies(platform_type='slurm')¶: Returns a list of jobs waiting on slurm scheduler :param platform_type: platform type :type platform_type: str :return: waiting jobs :rtype: list

graph¶

Returns the graph

Returns:	graph
Return type:	networkx graph

load()¶

Recreates a stored job list from the persistence

Returns:	loaded job list object
Return type:	JobList

static load_file(filename)¶

Recreates a stored joblist from the pickle file

Parameters:	filename (str) – pickle file to load
Returns:	loaded joblist object
Return type:	JobList

parameters¶: List of parameters common to all jobs :return: parameters :rtype: dict

print_with_status(statusChange=None, nocolor=False, existingList=None)¶

Returns the string representation of the dependency tree of the Job List

Parameters:	statusChange (List of strings) – List of changes in the list, supplied in set status nocolor (Boolean) – True if the result should not include color codes existingList (List of Job Objects) – External List of Jobs that will be printed, this excludes the inner list of jobs.
Returns:	String representation
Return type:	String

remove_rerun_only_jobs(notransitive=False)¶: Removes all jobs to be run only in reruns

rerun(job_list_unparsed, monitor=False)¶: Updates job list to rerun the jobs specified by a job list :param job_list_unparsed: list of jobs to rerun :type job_list_unparsed: list :param monitor: if True, the job list will be monitored :type monitor: bool

static retrieve_packages(BasicConfig, expid, current_jobs=None)¶

Retrieves dictionaries that map the collection of packages in the experiment

Parameters:	BasicConfig (Configuration Object) – Basic configuration expid (String) – Experiment ID current_jobs (list) – list of names of current jobs
Returns:	job to package, package to job, package to package_id, package to symbol
Return type:	Dictionary(Job Object, Package), Dictionary(Package, List of Job Objects), Dictionary(String, String), Dictionary(String, String)

static retrieve_times(status_code, name, tmp_path, make_exception=False, job_times=None, seconds=False, job_data_collection=None)¶: Retrieve job timestamps from database. :param status_code: Code of the Status of the job :type status_code: Integer :param name: Name of the job :type name: String :param tmp_path: Path to the tmp folder of the experiment :type tmp_path: String :param make_exception: flag for testing purposes :type make_exception: Boolean :param job_times: Detail from as_times.job_times for the experiment :type job_times: Dictionary Key: job name, Value: 5-tuple (submit time, start time, finish time, status, detail id) :return: minutes the job has been queuing, minutes the job has been running, and the text that represents it :rtype: int, int, str

save()¶: Persists the job list

sort_by_id()¶

Returns a list of jobs sorted by id

Returns:	jobs sorted by ID
Return type:	list

sort_by_name()¶

Returns a list of jobs sorted by name

Returns:	jobs sorted by name
Return type:	list

sort_by_status()¶

Returns a list of jobs sorted by status

Returns:	job sorted by status
Return type:	list

sort_by_type()¶

Returns a list of jobs sorted by type

Returns:	job sorted by type
Return type:	list

update_from_file(store_change=True)¶: Updates jobs list on the fly from and update file :param store_change: if True, renames the update file to avoid reloading it at the next iteration

update_genealogy(new=True, notransitive=False, update_structure=False)¶: When we have created the job list, every type of job is created. Update genealogy remove jobs that have no templates :param new: if it is a new job list or not :type new: bool

update_list(as_conf, store_change=True, fromSetStatus=False, submitter=None, first_time=False)¶

Updates job list, resetting failed jobs and changing to READY all WAITING jobs with all parents COMPLETED

Parameters:	as_conf (AutosubmitConfig) – autosubmit config object
Returns:	True if job status were modified, False otherwise
Return type:	bool