PBS Class Reference

Inheritance diagram for PBS:

Classes
class	PBSResult

Public Member Functions
	__init__ (self, *, backend_args=None)
	can_submit (self, njobs=1)
	qstat (cls, username="", job_ids=None)
	submit (self, job, check_can_submit=True, jobs_per_check=100)
	get_batch_submit_script_path (self, job)
	get_submit_script_path (self, job)

Static Public Member Functions
	create_job_record_from_element (job_elem)

Public Attributes
int	global_job_limit = self.default_global_job_limit
	The active job limit.
int	sleep_between_submission_checks = self.default_sleep_between_submission_checks
	Seconds we wait before checking if we can submit a list of jobs.
dict	backend_args = {**self.default_backend_args, **backend_args}
	The backend args that will be applied to jobs unless the job specifies them itself.

Static Public Attributes
str	cmd_wkdir = "#PBS -d"
	Working directory directive.
str	cmd_stdout = "#PBS -o"
	stdout file directive
str	cmd_stderr = "#PBS -e"
	stderr file directive
str	cmd_queue = "#PBS -q"
	Queue directive.
str	cmd_name = "#PBS -N"
	Job name directive.
list	submission_cmds = []
	Shell command to submit a script, should be implemented in the derived class.
int	default_global_job_limit = 1000
	Default global limit on the total number of submitted/running jobs that the user can have.
int	default_sleep_between_submission_checks = 30
	Default time betweeon re-checking if the active jobs is below the global job limit.
str	submit_script = "submit.sh"
	Default submission script name.
str	exit_code_file = "__BACKEND_CMD_EXIT_STATUS__"
	Default exit code file name.
dict	default_backend_args = {}
	Default backend_args.

Protected Member Functions
	_add_batch_directives (self, job, batch_file)
	_create_job_result (cls, job, batch_output)
	_create_cmd (self, script_path)
	_submit_to_batch (cls, cmd)
	_create_parent_job_result (cls, parent)
	_make_submit_file (self, job, submit_file_path)
	_add_wrapper_script_setup (self, job, batch_file)
	_add_wrapper_script_teardown (self, job, batch_file)

Static Protected Member Functions
	_add_setup (job, batch_file)

Detailed Description

Backend for submitting calibration processes to a qsub batch system.

Definition at line 1357 of file backends.py.

Constructor & Destructor Documentation

__init__()

__init__	(		self,
		*	,
			backend_args = None )

Definition at line 1378 of file backends.py.

    def __init__(self, *, backend_args=None):
        """
        """
        super().__init__(backend_args=backend_args)
 

Member Function Documentation

_add_batch_directives()

_add_batch_directives ( self, job, batch_file )

protected

Add PBS directives to submitted script.

Reimplemented from Batch.

Definition at line 1383 of file backends.py.

    def _add_batch_directives(self, job, batch_file):
        """
        Add PBS directives to submitted script.
        """
        job_backend_args = {**self.backend_args, **job.backend_args}
        batch_queue = job_backend_args["queue"]
        print("#!/bin/bash", file=batch_file)
        print("# --- Start PBS ---", file=batch_file)
        print(" ".join([PBS.cmd_queue, batch_queue]), file=batch_file)
        print(" ".join([PBS.cmd_name, job.name]), file=batch_file)
        print(" ".join([PBS.cmd_wkdir, job.working_dir.as_posix()]), file=batch_file)
        print(" ".join([PBS.cmd_stdout, Path(job.working_dir, _STDOUT_FILE).as_posix()]), file=batch_file)
        print(" ".join([PBS.cmd_stderr, Path(job.working_dir, _STDERR_FILE).as_posix()]), file=batch_file)
        print("# --- End PBS ---", file=batch_file)
 

_add_setup()

_add_setup ( job, batch_file )

staticprotectedinherited

Adds setup lines to the shell script file.

Definition at line 807 of file backends.py.

    def _add_setup(job, batch_file):
        """
        Adds setup lines to the shell script file.
        """
        for line in job.setup_cmds:
            print(line, file=batch_file)
 

_add_wrapper_script_setup()

_add_wrapper_script_setup ( self, job, batch_file )

protectedinherited

Adds lines to the submitted script that help with job monitoring/setup. Mostly here so that we can insert
`trap` statements for Ctrl-C situations.

Definition at line 814 of file backends.py.

    def _add_wrapper_script_setup(self, job, batch_file):
        """
        Adds lines to the submitted script that help with job monitoring/setup. Mostly here so that we can insert
        `trap` statements for Ctrl-C situations.
        """
        start_wrapper = f"""# ---
# trap ctrl-c and call ctrl_c()
trap '(ctrl_c 130)' SIGINT
trap '(ctrl_c 143)' SIGTERM
 
function write_exit_code() {{
  echo "Writing $1 to exit status file"
  echo "$1" > {self.exit_code_file}
  exit $1
}}
 
function ctrl_c() {{
  trap '' SIGINT SIGTERM
  echo "** Trapped Ctrl-C **"
  echo "$1" > {self.exit_code_file}
  exit $1
}}
# ---"""
        print(start_wrapper, file=batch_file)
 

_add_wrapper_script_teardown()

_add_wrapper_script_teardown ( self, job, batch_file )

protectedinherited

Adds lines to the submitted script that help with job monitoring/teardown. Mostly here so that we can insert
an exit code of the job cmd being written out to a file. Which means that we can know if the command was
successful or not even if the backend server/monitoring database purges the data about our job i.e. If PBS
removes job information too quickly we may never know if a job succeeded or failed without some kind of exit
file.

Definition at line 839 of file backends.py.

    def _add_wrapper_script_teardown(self, job, batch_file):
        """
        Adds lines to the submitted script that help with job monitoring/teardown. Mostly here so that we can insert
        an exit code of the job cmd being written out to a file. Which means that we can know if the command was
        successful or not even if the backend server/monitoring database purges the data about our job i.e. If PBS
        removes job information too quickly we may never know if a job succeeded or failed without some kind of exit
        file.
        """
        end_wrapper = """# ---
write_exit_code $?"""
        print(end_wrapper, file=batch_file)
 

_create_cmd()

_create_cmd ( self, script_path )

protected

Reimplemented from Batch.

Definition at line 1406 of file backends.py.

    def _create_cmd(self, script_path):
        """
        """
        submission_cmd = self.submission_cmds[:]
        submission_cmd.append(script_path.as_posix())
        return submission_cmd
 

_create_job_result()

_create_job_result ( cls, job, batch_output )

protected

Reimplemented from Batch.

Definition at line 1399 of file backends.py.

    def _create_job_result(cls, job, batch_output):
        """
        """
        job_id = batch_output.replace("\n", "")
        B2INFO(f"Job ID of {job} recorded as: {job_id}")
        job.result = cls.PBSResult(job, job_id)
 

_create_parent_job_result()

_create_parent_job_result ( cls, parent )

protected

We want to be able to call `ready()` on the top level `Job.result`. So this method needs to exist
so that a Job.result object actually exists. It will be mostly empty and simply updates subjob
statuses and allows the use of ready().

Reimplemented from Backend.

Definition at line 1422 of file backends.py.

    def _create_parent_job_result(cls, parent):
        parent.result = cls.PBSResult(parent, None)
 

_make_submit_file()

_make_submit_file ( self, job, submit_file_path )

protectedinherited

Useful for the HTCondor backend where a submit is needed instead of batch
directives pasted directly into the submission script. It should be overwritten
if needed.

Reimplemented in HTCondor.

Definition at line 1180 of file backends.py.

    def _make_submit_file(self, job, submit_file_path):
        """
        Useful for the HTCondor backend where a submit is needed instead of batch
        directives pasted directly into the submission script. It should be overwritten
        if needed.
        """
 

_submit_to_batch()

_submit_to_batch ( cls, cmd )

protected

Do the actual batch submission command and collect the output to find out the job id for later monitoring.

Reimplemented from Batch.

Definition at line 1414 of file backends.py.

    def _submit_to_batch(cls, cmd):
        """
        Do the actual batch submission command and collect the output to find out the job id for later monitoring.
        """
        sub_out = subprocess.check_output(cmd, stderr=subprocess.STDOUT, universal_newlines=True)
        return sub_out
 

can_submit()

can_submit	(		self,
			njobs = 1 )

Checks the global number of jobs in PBS right now (submitted or running) for this user.
Returns True if the number is lower that the limit, False if it is higher.

Parameters:
    njobs (int): The number of jobs that we want to submit before checking again. Lets us check if we
        are sufficiently below the limit in order to (somewhat) safely submit. It is slightly dangerous to
        assume that it is safe to submit too many jobs since there might be other processes also submitting jobs.
        So njobs really shouldn't be abused when you might be getting close to the limit i.e. keep it <=250
        and check again before submitting more.

Reimplemented from Batch.

Definition at line 1514 of file backends.py.

    def can_submit(self, njobs=1):
        """
        Checks the global number of jobs in PBS right now (submitted or running) for this user.
        Returns True if the number is lower that the limit, False if it is higher.
 
        Parameters:
            njobs (int): The number of jobs that we want to submit before checking again. Lets us check if we
                are sufficiently below the limit in order to (somewhat) safely submit. It is slightly dangerous to
                assume that it is safe to submit too many jobs since there might be other processes also submitting jobs.
                So njobs really shouldn't be abused when you might be getting close to the limit i.e. keep it <=250
                and check again before submitting more.
        """
        B2DEBUG(29, "Calling PBS().can_submit()")
        job_info = self.qstat(username=os.environ["USER"])
        total_jobs = job_info["NJOBS"]
        B2INFO(f"Total jobs active in the PBS system is currently {total_jobs}")
        if (total_jobs + njobs) > self.global_job_limit:
            B2INFO(f"Since the global limit is {self.global_job_limit} we cannot submit {njobs} jobs until some complete.")
            return False
        else:
            B2INFO("There is enough space to submit more jobs.")
            return True
 

create_job_record_from_element()

create_job_record_from_element ( job_elem )

static

Creates a Job dictionary with various job information from the XML element returned by qstat.

Parameters:
    job_elem (xml.etree.ElementTree.Element): The XML Element of the Job

Returns:
    dict: JSON serialisable dictionary of the Job information we are interested in.

Definition at line 1606 of file backends.py.

    def create_job_record_from_element(job_elem):
        """
        Creates a Job dictionary with various job information from the XML element returned by qstat.
 
        Parameters:
            job_elem (xml.etree.ElementTree.Element): The XML Element of the Job
 
        Returns:
            dict: JSON serialisable dictionary of the Job information we are interested in.
        """
        job_dict = {}
        job_dict["Job_Id"] = job_elem.find("Job_Id").text
        job_dict["Job_Name"] = job_elem.find("Job_Name").text
        job_dict["Job_Owner"] = job_elem.find("Job_Owner").text
        job_dict["job_state"] = job_elem.find("job_state").text
        job_dict["queue"] = job_elem.find("queue").text
        return job_dict
 
 

get_batch_submit_script_path()

get_batch_submit_script_path ( self, job )

inherited

Construct the Path object of the script file that we will submit using the batch command.
For most batch backends this is the same script as the bash script we submit.
But for some they require a separate submission file that describes the job.
To implement that you can implement this function in the Backend class.

Reimplemented in HTCondor.

Definition at line 1336 of file backends.py.

    def get_batch_submit_script_path(self, job):
        """
        Construct the Path object of the script file that we will submit using the batch command.
        For most batch backends this is the same script as the bash script we submit.
        But for some they require a separate submission file that describes the job.
        To implement that you can implement this function in the Backend class.
        """
        return Path(job.working_dir, self.submit_script)
 

get_submit_script_path()

get_submit_script_path ( self, job )

inherited

Construct the Path object of the bash script file that we will submit. It will contain
the actual job command, wrapper commands, setup commands, and any batch directives

Definition at line 860 of file backends.py.

    def get_submit_script_path(self, job):
        """
        Construct the Path object of the bash script file that we will submit. It will contain
        the actual job command, wrapper commands, setup commands, and any batch directives
        """
        return Path(job.working_dir, self.submit_script)
 
 

qstat()

qstat	(		cls,
			username = "",
			job_ids = None )

Simplistic interface to the ``qstat`` command. Lets you request information about all jobs or ones matching the filter
['job_id'] or for the username. The result is a JSON dictionary containing come of the useful job attributes returned
by qstat.

PBS is kind of annoying as depending on the configuration it can forget about jobs immediately. So the status of a
finished job is VERY hard to get. There are other commands that are sometimes included that may do a better job.
This one should work for Melbourne's cloud computing centre.

Keyword Args:
    username (str): The username of the jobs we are interested in. Only jobs corresponding to the <username>@hostnames
        will be in the output dictionary.
    job_ids (list[str]): List of Job ID strings, each given by qstat during submission. If this argument is given then
        the output of this function will be only information about this jobs. If this argument is not given, then all jobs
        matching the other filters will be returned.

Returns:
    dict: JSON dictionary of the form (to save you parsing the XML that qstat returns).:

    .. code-block:: python

      {
        "NJOBS": int
        "JOBS":[
                {
                  <key: value>, ...
                }, ...
               ]
      }

Definition at line 1538 of file backends.py.

    def qstat(cls, username="", job_ids=None):
        """
        Simplistic interface to the ``qstat`` command. Lets you request information about all jobs or ones matching the filter
        ['job_id'] or for the username. The result is a JSON dictionary containing come of the useful job attributes returned
        by qstat.
 
        PBS is kind of annoying as depending on the configuration it can forget about jobs immediately. So the status of a
        finished job is VERY hard to get. There are other commands that are sometimes included that may do a better job.
        This one should work for Melbourne's cloud computing centre.
 
        Keyword Args:
            username (str): The username of the jobs we are interested in. Only jobs corresponding to the <username>@hostnames
                will be in the output dictionary.
            job_ids (list[str]): List of Job ID strings, each given by qstat during submission. If this argument is given then
                the output of this function will be only information about this jobs. If this argument is not given, then all jobs
                matching the other filters will be returned.
 
        Returns:
            dict: JSON dictionary of the form (to save you parsing the XML that qstat returns).:
 
            .. code-block:: python
 
              {
                "NJOBS": int
                "JOBS":[
                        {
                          <key: value>, ...
                        }, ...
                       ]
              }
        """
        B2DEBUG(29, f"Calling PBS.qstat(username='{username}', job_id={job_ids})")
        if not job_ids:
            job_ids = []
        job_ids = set(job_ids)
        cmd_list = ["qstat", "-x"]
        # We get an XML serialisable summary from qstat. Requires the shell argument.
        cmd = " ".join(cmd_list)
        B2DEBUG(29, f"Calling subprocess with command = '{cmd}'")
        output = subprocess.check_output(cmd, stderr=subprocess.STDOUT, universal_newlines=True, shell=True)
        jobs_dict = {"NJOBS": 0, "JOBS": []}
        jobs_xml = ET.fromstring(output)
 
        # For a specific job_id we can be a bit more efficient in XML parsing
        if len(job_ids) == 1:
            job_elem = jobs_xml.find(f"./Job[Job_Id='{list(job_ids)[0]}']")
            if job_elem:
                jobs_dict["JOBS"].append(cls.create_job_record_from_element(job_elem))
                jobs_dict["NJOBS"] = 1
            return jobs_dict
 
        # Since the username given is not exactly the same as the one that PBS stores (<username>@host)
        # we have to simply loop through rather than using XPATH.
        for job in jobs_xml.iterfind("Job"):
            job_owner = job.find("Job_Owner").text.split("@")[0]
            if username and username != job_owner:
                continue
            job_id = job.find("Job_Id").text
            if job_ids and job_id not in job_ids:
                continue
            jobs_dict["JOBS"].append(cls.create_job_record_from_element(job))
            jobs_dict["NJOBS"] += 1
            # Remove it so that we don't keep checking for it
            if job_id in job_ids:
                job_ids.remove(job_id)
        return jobs_dict
 

submit()

submit ( self, job, check_can_submit = True, jobs_per_check = 100 )

inherited

Reimplemented from Backend.

Definition at line 1205 of file backends.py.

    def submit(self, job, check_can_submit=True, jobs_per_check=100):
        """
        """
        raise NotImplementedError("This is an abstract submit(job) method that shouldn't have been called. "
                                  "Did you submit a (Sub)Job?")
 

Member Data Documentation

backend_args

dict backend_args = {**self.default_backend_args, **backend_args}

inherited

The backend args that will be applied to jobs unless the job specifies them itself.

Definition at line 797 of file backends.py.

cmd_name

str cmd_name = "#PBS -N"

static

Job name directive.

Definition at line 1370 of file backends.py.

cmd_queue

str cmd_queue = "#PBS -q"

static

Queue directive.

Definition at line 1368 of file backends.py.

cmd_stderr

str cmd_stderr = "#PBS -e"

static

stderr file directive

Definition at line 1366 of file backends.py.

cmd_stdout

str cmd_stdout = "#PBS -o"

static

stdout file directive

Definition at line 1364 of file backends.py.

cmd_wkdir

str cmd_wkdir = "#PBS -d"

static

Working directory directive.

Definition at line 1362 of file backends.py.

default_backend_args

dict default_backend_args = {}

staticinherited

Default backend_args.

Definition at line 789 of file backends.py.

default_global_job_limit

int default_global_job_limit = 1000

staticinherited

Default global limit on the total number of submitted/running jobs that the user can have.

This limit will not affect the total number of jobs that are eventually submitted. But the jobs won't actually be submitted until this limit can be respected i.e. until the number of total jobs in the Batch system goes down. Since we actually submit in chunks of N jobs, before checking this limit value again, this value needs to be a little lower than the real batch system limit. Otherwise you could accidentally go over during the N job submission if other processes are checking and submitting concurrently. This is quite common for the first submission of jobs from parallel calibrations.

Note that if there are other jobs already submitted for your account, then these will count towards this limit.

Definition at line 1156 of file backends.py.

default_sleep_between_submission_checks

int default_sleep_between_submission_checks = 30

staticinherited

Default time betweeon re-checking if the active jobs is below the global job limit.

Definition at line 1158 of file backends.py.

exit_code_file

str exit_code_file = "__BACKEND_CMD_EXIT_STATUS__"

staticinherited

Default exit code file name.

Definition at line 787 of file backends.py.

global_job_limit

int global_job_limit = self.default_global_job_limit

inherited

The active job limit.

This is 'global' because we want to prevent us accidentally submitting too many jobs from all current and previous submission scripts.

Definition at line 1167 of file backends.py.

sleep_between_submission_checks

int sleep_between_submission_checks = self.default_sleep_between_submission_checks

inherited

Seconds we wait before checking if we can submit a list of jobs.

Only relevant once we hit the global limit of active jobs, which is a lot usually.

Definition at line 1170 of file backends.py.

submission_cmds

list submission_cmds = []

staticinherited

Shell command to submit a script, should be implemented in the derived class.

Definition at line 1143 of file backends.py.

submit_script

submit_script = "submit.sh"

staticinherited

Default submission script name.

Definition at line 785 of file backends.py.

---

The documentation for this class was generated from the following file:

• calibration/scripts/caf/backends.py