def test_job_depends():
if platform.platform().lower().startswith("linux"):
job_spec = JobSpec(
command=f"bash {data_path}/sleepy.sh",
working_dir=pwd,
log_file="test.log",
priority=5,
depends=[],
)
else:
job_spec = JobSpec(
command=f"{data_path}/sleepy.bat",
working_dir=pwd,
log_file="test.log",
priority=5,
depends=[],
)
q = JobQueue()
# response = client.post("qsub", json=[job_spec.dict()])
# dependency = response.json()
# dependency = ujson.loads(dependency)
job_ids = q.submit([job_spec])
job_spec = JobSpec(
depends=job_ids,
command=f'{data_path}/echo_it.bat "goodbye"',
working_dir=pwd,
)
q.submit([job_spec])
def test_prune():
# DEFAULT_CONFIG.prune_job_limt = 10
q = JobQueue()
q.completed_limit = 10
for i in range(15):
js1 = JobSpec(command=hello, working_dir=".", priority=10)
job1 = q.submit([js1])
assert len(q.queued_jobs) == 15
assert len(q.running_jobs) == 0
assert len(q.completed_jobs) == 0
for i in range(15):
q.on_job_started(q.next_job().job_id)
assert len(q.queued_jobs) == 0
assert len(q.running_jobs) == 15
assert len(q.completed_jobs) == 0
for job_id, job in list(q.running_jobs.items()):
q.on_job_finished(job_id)
assert len(q.queued_jobs) == 0
assert len(q.running_jobs) == 0
assert len(q.completed_jobs) == 15
q.prune()
assert len(q.queued_jobs) == 0
assert len(q.running_jobs) == 0
assert len(q.completed_jobs) == 5
def test_priority():
q = JobQueue()
js1 = JobSpec(command=hello, working_dir=".", priority=10)
js2 = JobSpec(command=goodbye, working_dir=".", priority=15)
job1 = q.submit([js1, js2])
exec_job_1 = q.next_job()
q.on_job_started(exec_job_1.job_id)
exec_job_2 = q.next_job()
q.on_job_started(exec_job_2.job_id)
assert exec_job_1.job_id == JobID(group=2, index=0)
assert exec_job_2.job_id == JobID(group=1, index=0)
def test_work_item():
q = JobQueue()
js = JobSpec(command="cmd.exe /C sleep 2.5",
working_dir="d:/temp",
cores=2)
job_id = q.submit([js])[0]
job, q2 = q.find_job(job_id)
wi = WorkItem(job=job, cores=[0, 1])
print(wi)
wi.start()
for i in range(10):
print(i)
time.sleep(0.5)
print(wi.get_status())
if not wi.is_running():
break
print("done")
def test_is_queued():
q = JobQueue()
job_spec = JobSpec(
command=f'{data_path}/echo_it.bat "hello"',
working_dir=pwd,
log_file="test.log",
priority=5,
depends=[],
)
job_id = q.submit([job_spec])[0]
# job_id = q.submitted([job_spec])
# response = client.post("qsub", json=[job_spec.dict()])
assert job_id == JobID.parse_obj("1.0")
job = q.find_job(job_id)[0]
assert job.job_spec.command == job_spec.command
assert job.job_spec.priority == 5
assert job.job_spec.working_dir == pwd
assert job.job_spec.log_file == "test.log"
assert job.job_spec.depends == []
assert len(q.queued_jobs) == 1
def test_job_spec():
js = JobSpec(command="test", working_dir="/tmp", priority=10)
assert js.command == "test"
assert js.working_dir == "/tmp"
assert js.priority == 10
assert js.log_file is None
def test_save_and_read_queue():
# DEFAULT_CONFIG.prune_job_limt = 10
q = JobQueue(start_manager_thread=False)
q.completed_limit = 10
for i in range(15):
js1 = JobSpec(command=hello, working_dir=".", priority=10)
job1 = q.submit([js1])
assert len(q.queued_jobs) == 15
assert len(q.running_jobs) == 0
assert len(q.completed_jobs) == 0
for i in range(10):
q.on_job_started(q.next_job().job_id)
assert len(q.queued_jobs) == 5
assert len(q.running_jobs) == 10
assert len(q.completed_jobs) == 0
i = 0
for job_id, job in list(q.running_jobs.items()):
q.on_job_finished(job_id)
i += 1
if i == 5:
break
assert len(q.queued_jobs) == 5
assert len(q.running_jobs) == 5
assert len(q.completed_jobs) == 5
q.save()
q2 = JobQueue()
q2.load()
a, b = len(q.queued_jobs) + len(q.running_jobs), len(q2.queued_jobs)
assert a == b
# assert len(q.running_jobs) == len(q2.running_jobs)
assert len(q.completed_jobs) == len(q2.completed_jobs)
def test_pool():
q = JobQueue()
js = JobSpec(command="cmd.exe /C sleep 2.5",
working_dir="d:/temp",
cores=1)
q.submit([js] * 20)
# job, q2 = q.find_job(job_id)
pool = DynamicProcessPool(q, 20)
pool._start_manager_thread()
time.sleep(4)
print(q.running_jobs.values())
assert len(q.running_jobs) > 0
time.sleep(10)
pool.join(wait=True)
print(q.running_jobs.values())
assert len(q.running_jobs) == 0
def test_job_sorting():
jobs = [
Job(
job_spec=JobSpec(command="", working_dir="", priority=5),
job_id=JobID(group=1, index=0),
),
Job(
job_spec=JobSpec(command="", working_dir="", priority=5),
job_id=JobID(group=2, index=0),
),
Job(
job_spec=JobSpec(command="", working_dir="", priority=4),
job_id=JobID(group=3, index=0),
),
Job(
job_spec=JobSpec(command="", working_dir="", priority=6),
job_id=JobID(group=4, index=0),
),
Job(
job_spec=JobSpec(command="", working_dir="", priority=5),
job_id=JobID(group=5, index=1),
),
Job(
job_spec=JobSpec(command="", working_dir="", priority=5),
job_id=JobID(group=5, index=0),
),
]
jobs2 = list(sorted(jobs))
for j in jobs2:
print(j)
assert jobs2[0].job_id.group == 4
assert jobs2[-1].job_id.group == 3
def qsub(
command,
args,
priority=1,
logfile=None,
log=False,
depends=None,
debug=False,
walltime=None,
cores=1,
port=config.port,
ip_address=config.ip_address,
alternate_runner=False,
):
"""Submits one job to the queue"""
command_str = command + " " + " ".join(f'"{arg}"' for arg in args)
working_dir = encode_path(os.getcwd())
if len(depends) == 1 and " " in depends[0]:
depends = depends[0].split()
# print(depends)
if depends:
depends = [JobID.parse_obj(d) for d in depends]
else:
depends = []
if walltime:
if ":" in walltime:
hrs, minutes, sec = [int(x) for x in walltime.split(":")]
seconds = sec + 60 * minutes + hrs * 3600
else:
walltime = float(walltime)
if log and not logfile:
logfile = str(Path(command).with_suffix(".lqts.log"))
job_spec = JobSpec(
command=command_str,
working_dir=working_dir,
log_file=logfile,
priority=priority,
depends=depends,
walltime=walltime,
cores=cores,
alternate_runner=alternate_runner,
)
config.port = port
config.ip_address = ip_address
response = requests.post(f"{config.url}/qsub", json=[job_spec.dict()])
if response.status_code == 200:
if debug:
print(response)
json_data = response.json()
if len(json_data) <= 20:
print(" ".join(str(JobID(**item)) for item in response.json()))
else:
print(JobID(**json_data[0]).group)
else:
print(response)
def _qsub_argfile(
command,
argfile,
priority=1,
log=False,
depends=None,
debug=False,
submit_delay=0.0,
cores=1,
port=config.port,
ip_address=config.ip_address,
alternate_runner=False,
walltime=None,
):
from glob import glob
# files = glob(files)
job_specs = []
working_dir = encode_path(os.getcwd())
depends = [JobID.parse(d) for d in depends]
with open(argfile) as f:
for iline, argline in enumerate(f):
command_str = f"{command} {argline}"
# print(command)
if log:
log_file = str(
Path(argfile).with_suffix(f".lqts.{iline:0>3}.log"))
else:
log_file = None
js = JobSpec(
command=command_str,
working_dir=working_dir,
log_file=log_file,
priority=priority,
depends=depends,
cores=cores,
alternate_runner=alternate_runner,
)
job_specs.append(js.dict())
if debug:
for js in job_specs:
print(js)
config.port = port
config.ip_address = ip_address
response = requests.post(f"{config.url}/qsub", json=job_specs)
if response.status_code == 200:
if debug:
print(response)
json_data = response.json()
if len(json_data) <= 20:
print(" ".join(str(JobID(**item)) for item in response.json()))
else:
print(JobID(**json_data[0]).group)
else:
print(response)
def qsub_multi(
commands,
args,
priority=1,
logfile=None,
depends=None,
debug=False,
log=False,
cores=1,
port=config.port,
ip_address=config.ip_address,
alternate_runner=False,
):
"""
Submits mutilple jobs to the queue.
Use this if have have multiple commands that you wish to run and
you can specify them with a glob pattern
$ qsub mycommand*.bat -- --option1 --option2 value2
"""
from glob import iglob
commands = iglob(commands)
job_specs = []
working_dir = encode_path(os.getcwd())
depends = [JobID.parse(d) for d in depends]
for command in commands:
# print(f, print(args))
command_str = f"{command} " + " ".join(f'"{arg}"' for arg in args)
# print(command)
if log:
logfile = str(Path(command).with_suffix(".lqts.log"))
else:
logfile = None
js = JobSpec(
command=command_str,
working_dir=working_dir,
log_file=logfile,
priority=priority,
depends=depends,
cores=cores,
alternate_runner=alternate_runner,
)
job_specs.append(js.dict())
if debug:
for js in job_specs:
print(js)
config.port = port
config.ip_address = ip_address
response = requests.post(f"{config.url}/qsub", json=job_specs)
if response.status_code == 200:
if debug:
print(response)
json_data = response.json()
if len(json_data) <= 20:
print(" ".join(str(JobID(**item)) for item in response.json()))
else:
print(JobID(**json_data[0]).group)
else:
print(response)
def qsub_cmulti(command,
file_pattern,
args,
priority=1,
logfile=None,
depends=None,
debug=False,
log=False,
cores=1,
port=config.port,
ip_address=config.ip_address,
alternate_runner=False,
changewd=False):
"""
Submits mutlitiple jobs to the queue.
Runs **command** for each file in **files**. Pass in args.
$ qsub mycommand.exe MyInputFile*.inp -- --do --it
[-----------] [--------------] [--------]
command filepattern args
"""
from glob import iglob
files = iglob(file_pattern)
job_specs = []
working_dir = encode_path(os.getcwd())
depends = [JobID.parse(d) for d in depends]
for f in files:
if changewd:
working_dir = str(Path(f).resolve().parent)
f = Path(f).name
# print(f, print(args))
command_str = f"{command} {f} " + " ".join(f'"{arg}"' for arg in args)
# print(command)
if log:
logfile = str(Path(f).with_suffix(".lqts.log"))
else:
logfile = None
js = JobSpec(
command=command_str,
working_dir=working_dir,
log_file=logfile,
priority=priority,
depends=depends,
cores=cores,
alternate_runner=alternate_runner,
)
job_specs.append(js.dict())
if debug:
for js in job_specs:
print(js)
config.port = port
config.ip_address = ip_address
response = requests.post(f"{config.url}/qsub", json=job_specs)
if response.status_code == 200:
if debug:
print(response)
json_data = response.json()
if len(json_data) <= 20:
print(" ".join(str(JobID(**item)) for item in response.json()))
else:
print(JobID(**json_data[0]).group)
else:
print(response)
def get_job_spec():
js = JobSpec(command=hello, working_dir=".", priority=10)
return js
workercount=app.pool.max_workers)
script_block = env.get_template("js_script_template.jinja").render()
c = Counter([job.status.value for job in jobs])
for letter in "QDRC":
if letter not in c:
c[letter] = 0
summary_text = " ".join(f"{s}:{c}" for s, c in c.items())
page_text = page_template.render(
page_title="Queue Status",
navbar="",
buttonbar=buttonbar,
summary=summary_text,
table=render_qstat_table(jobs, include_complete),
script_block=script_block,
)
return page_text
if __name__ == "__main__":
job = Job(
job_id=JobID(group=1, index=2),
job_spec=JobSpec(command="cmd /c echo hello", working_dir="/tmp"),
)
print(render_qstat_page(jobs=[job]))