qmonitor

#!/g/data/hh5/public/apps/nci_scripts/python-analysis3
# Copyright 2020 Scott Wales
# author: Scott Wales <scott.wales@unimelb.edu.au>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""
Monitor a PBS queue job
"""

import argparse
import tqdm
import subprocess
import json
import time
import pandas
import importlib
from qtools import qstat, decode_bytes


def metrics(stat):
    cpu = 0
    mem = 0
    wall = 0

    if stat['job_state'] == 'R':
        mem_request = decode_bytes(stat['Resource_List']['mem'])
        mem_used = decode_bytes(stat['resources_used']['mem'])
        mem = mem_used / mem_request * 100

        cpu_time = pandas.to_timedelta(stat['resources_used']['cput'])
        wall_used = pandas.to_timedelta(stat['resources_used']['walltime'])
        ncpus = stat['Resource_List']['ncpus']

        try:
            cpu = cpu_time / wall_used / ncpus * 100
        except ZeroDivisionError:
            cpu = 0

        wall = wall_used.seconds

    return cpu, mem, wall


def monitor(jobid):
    stat = None
    while stat is None:
        try:
            stat = list(qstat([jobid], show_finished=True).values())[0]
        except:
            time.sleep(30)

    c, m, w = metrics(stat)

    wall_request = pandas.to_timedelta(stat['Resource_List']['walltime']).seconds

    bar_format = '{l_bar}{bar}'
    cpu = tqdm.tqdm(unit="%", desc="CPU", total=100.0, position=0, bar_format=bar_format, leave=True)
    mem = tqdm.tqdm(unit="%", desc="MEM", total=100.0, position=1, bar_format=bar_format, leave=True)
    wall = tqdm.tqdm(unit='s', desc="TIME", total=wall_request, position=2, bar_format=bar_format, leave=True)

    while stat["job_state"] in ["Q", "R"]:
        c, m, w = metrics(stat)

        cpu.reset()
        cpu.update(c)
        cpu.refresh()

        mem.reset()
        mem.update(m)
        mem.refresh()

        wall.reset()
        wall.update(w)
        wall.refresh()

        time.sleep(60)
        try:
            # Handle PBS server outages
            newstat = list(qstat([jobid], show_finished=True).values())[0]
            stat = newstat
        except:
            pass

    cpu.close()
    mem.close()
    wall.close()


def main():
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument("jobid")
    args = parser.parse_args()

    monitor(args.jobid)


if __name__ == "__main__":
    main()