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import os
import re
import shlex
import subprocess
import time
from pathlib import Path
from haddock import log, modules_defaults_path
from haddock.core.typing import Any, Container, FilePath, Optional
from haddock.gear.yaml2cfg import read_from_yaml_config
from haddock.libs.libsubprocess import CNSJob
STATE_REGEX = r"JobState=(\w*)"
JOB_STATUS_DIC = {
"PENDING": "submitted",
"RUNNING": "running",
"SUSPENDED": "hold",
"COMPLETING": "running",
"COMPLETED": "finished",
"FAILED": "failed",
"TIMEOUT": "timed-out",
}
TERMINATED_STATUS = (
"finished",
"failed",
"timed-out",
)
# if you change these defaults, change also the values in the
# modules/defaults.cfg file
_tmpcfg = read_from_yaml_config(modules_defaults_path)
HPCScheduler_CONCAT_DEFAULT: int = _tmpcfg["concat"] # original value 1
HPCWorker_QUEUE_LIMIT_DEFAULT: int = _tmpcfg[
"queue_limit"
] # original value 100 # noqa: E501
HPCWorker_QUEUE_DEFAULT: str = _tmpcfg["queue"] # original value ""
del _tmpcfg
class HPCWorker:
"""Defines the HPC Job."""
def __init__(
self,
tasks: list[CNSJob],
num: int,
job_id: Optional[int] = None,
workfload_manager: str = "slurm",
queue: Optional[str] = None,
) -> None:
"""
Define the HPC job.
Parameters
----------
tasks : list of libs.libcns.CNSJob objects
num : int
The number of the worker.
"""
self.tasks = tasks
log.debug(f"HPCWorker ready with {len(self.tasks)}")
self.job_num = num
self.job_id = job_id
self.job_status = "unknown"
self.moddir = Path(tasks[0].envvars["MODDIR"])
self.toppar = tasks[0].envvars["TOPPAR"]
self.cns_folder = tasks[0].envvars["MODULE"]
module_name = Path(tasks[0].envvars["MODDIR"]).resolve().stem.split("_")[-1]
self.job_fname = Path(self.moddir, f"{module_name}_{num}.job")
self.workload_manager = workfload_manager
self.queue = queue
def prepare_job_file(self, queue_type: str = "slurm") -> None:
"""Prepare the job file for all the jobs in the task list."""
job_file_contents = create_job_header_funcs[queue_type](
job_name="haddock3",
queue=self.queue,
ncores=1,
work_dir=self.moddir,
stdout_path=self.job_fname.with_suffix(".out"),
stderr_path=self.job_fname.with_suffix(".err"),
)
job_file_contents += create_CNS_export_envvars(
MODDIR=self.moddir,
MODULE=self.cns_folder,
TOPPAR=self.toppar,
)
job_file_contents += f"cd {self.moddir}{os.linesep}"
for job in self.tasks:
cmd = (
f"{job.cns_exec} < {job.input_file} > {job.output_file}" f"{os.linesep}"
)
job_file_contents += cmd
self.job_fname.write_text(job_file_contents)
def run(self) -> None:
"""Execute the tasks."""
self.prepare_job_file(queue_type=self.workload_manager)
cmd = f"sbatch {self.job_fname}"
p = subprocess.run(shlex.split(cmd), capture_output=True)
self.job_id = int(p.stdout.decode("utf-8").split()[-1])
self.job_status = "submitted"
def update_status(self) -> str:
"""Retrieve the status of this worker."""
cmd = f"scontrol show jobid -dd {self.job_id}"
p = subprocess.run(shlex.split(cmd), capture_output=True)
out = p.stdout.decode("utf-8")
# err = p.stderr.decode('utf-8')
if out:
status = extract_slurm_status(out)
self.job_status = JOB_STATUS_DIC[status]
else:
self.job_status = "finished"
return self.job_status
def cancel(self, bypass_statuses: Container[str] = ("finished", "failed")) -> None:
"""Cancel the execution."""
if self.update_status() not in bypass_statuses:
log.info(f"Canceling {self.job_fname.name} - {self.job_id}")
cmd = f"scancel {self.job_id}"
_ = subprocess.run(shlex.split(cmd), capture_output=True)
class HPCScheduler:
"""Schedules tasks to run in HPC."""
def __init__(
self,
task_list: list[CNSJob],
target_queue: str = HPCWorker_QUEUE_DEFAULT,
queue_limit: int = HPCWorker_QUEUE_LIMIT_DEFAULT,
concat: int = HPCScheduler_CONCAT_DEFAULT,
) -> None:
self.num_tasks = len(task_list)
self.queue_limit = queue_limit
self.concat = concat
# split tasks according to concat level
if concat > 1:
log.info(
f"Concatenating, each .job will produce {concat} " "(or less) models"
)
job_list = [task_list[i : i + concat] for i in range(0, len(task_list), concat)]
self.worker_list = [HPCWorker(t, j) for j, t in enumerate(job_list, start=1)]
# set the queue
# (this is outside the comprehension for clarity)
if target_queue:
for worker in self.worker_list:
worker.queue = target_queue
log.debug(f"{self.num_tasks} HPC tasks ready.")
def run(self) -> None:
"""Run tasks in the Queue."""
# split by maximum number of submission so we do it in batches
batch = [
self.worker_list[i : i + self.queue_limit]
for i in range(0, len(self.worker_list), self.queue_limit)
]
total_batches = len(batch)
try:
for batch_num, worker_list in enumerate(batch, start=1):
log.info(f"> Running batch {batch_num}/{total_batches}")
start = time.time()
for worker in worker_list:
worker.run()
# check if those finished
completed: bool = False
elapsed: float = 0.0
while not completed:
# Initiate count of terminated jobs
terminated_count: int = 0
# Loop over workers
for worker in worker_list:
worker.update_status()
# Log status if not finished
if worker.job_status != "finished":
log.info(
f">> {worker.job_fname.name}" f" {worker.job_status}"
)
# Increment number of terminated works
if worker.job_status in TERMINATED_STATUS:
terminated_count += 1
# Check if all terminated
if terminated_count == len(worker_list):
# Set while loop condition
completed = True
end = time.time()
elapsed = end - start
else:
# use pre-defined waits
if len(worker_list) < 10:
sleep_timer = 10
elif len(worker_list) < 50:
sleep_timer = 30
else:
sleep_timer = 60
log.info(f">> Waiting... ({sleep_timer:.2f}s)")
time.sleep(sleep_timer)
per = (float(batch_num) / float(total_batches)) * 100
log.info(
f">> Batch {batch_num}/{total_batches} took "
f"{elapsed:.2f}s to finish, {per:.2f}% complete"
)
except KeyboardInterrupt as err:
self.terminate()
raise err
def terminate(self) -> None:
"""Terminate all jobs in the queue in a controlled way."""
log.info("Terminate signal received, removing jobs from the queue...")
for worker in self.worker_list:
worker.cancel()
log.info("The jobs in the queue were terminated in a controlled way")
def create_slurm_header(
job_name: FilePath = "haddock3_slurm_job",
work_dir: FilePath = ".",
stdout_path: FilePath = "haddock3_job.out",
stderr_path: FilePath = "haddock3_job.err",
queue: Optional[str] = None,
ncores: int = 48,
) -> str:
"""
Create HADDOCK3 Slurm Batch job file.
Parameters
----------
job_name : str
The name of the job.
work_dir : pathlib.Path
The working dir of the example. That is, the directory where
`input`, `jobs`, and `logs` reside. Injected in `create_job_header`.
time : int
Time in minutes before job reach TIMEOUT status.
**job_params
According to `job_setup`.
Return
------
str
Slurm-based job file for HADDOCK3.
"""
header = f"#!/usr/bin/env bash{os.linesep}"
header += f"#SBATCH -J {job_name}{os.linesep}"
if queue:
header += f"#SBATCH -p {queue}{os.linesep}"
header += f"#SBATCH --nodes=1{os.linesep}"
header += f"#SBATCH --tasks-per-node={str(ncores)}{os.linesep}"
header += f"#SBATCH --output={stdout_path}{os.linesep}"
header += f"#SBATCH --error={stderr_path}{os.linesep}"
# commenting the workdir option (not supported by all versions of slurm)
# header += f"#SBATCH --workdir={work_dir}{os.linesep}"
return header
def create_torque_header(
job_name: FilePath = "haddock3_slurm_job",
work_dir: FilePath = ".",
stdout_path: FilePath = "haddock3_job.out",
stderr_path: FilePath = "haddock3_job.err",
queue: Optional[str] = None,
ncores: int = 48,
) -> str:
"""
Create HADDOCK3 Alcazar job file.
Parameters
----------
job_name : str
The name of the job.
work_dir : pathlib.Path
The working dir of the example. That is, the directory where
`input`, `jobs`, and `logs` reside. Injected in `create_job_header`.
**job_params
According to `job_setup`.
Return
------
str
Torque-based job file for HADDOCK3 benchmarking.
"""
header = f"#!/usr/bin/env tcsh{os.linesep}"
header += f"#PBS -N {job_name}{os.linesep}"
if queue:
header += f"#PBS -q {queue}{os.linesep}"
header += f"#PBS -l nodes=1:ppn={str(ncores)}{os.linesep}"
header += f"#PBS -S /bin/tcsh{os.linesep}"
header += f"#PBS -o {stdout_path}{os.linesep}"
header += f"#PBS -e {stderr_path}{os.linesep}"
header += f"#PBS -wd {work_dir}{os.linesep}"
return header
def to_torque_time(time: int) -> str:
"""Convert time in minutes to the form hh:mm:ss.
Parameters
----------
time : int
Time in minutes.
Return
------
hh_mm_ss : str
Time in the form for HH:MM:SS
"""
hours = time // 60
remain_mins = time - (hours * 60)
# Convert to hh:mm:ss string
hh_mm_ss_l = [hours, remain_mins, 0]
# Make sure hours contain at least 2 characters
hh_mm_ss = "{0:02d}:{1:02d}:{2:02d}".format(*hh_mm_ss_l)
return hh_mm_ss
def extract_slurm_status(slurm_out: str) -> str:
"""Extract job status from slurm scontrol stdout.
Parameters
----------
slurm_out : str
StdOut of `scontrol show jobid -dd {job_id}` command.
Return
------
status : str
Status of the slurm job.
May also return `error`, when job do not exists.
"""
try:
# https://regex101.com/r/M2vbAc/1
status = re.findall(STATE_REGEX, slurm_out)[0]
except IndexError:
status = "FAILED"
return status
def create_CNS_export_envvars(**envvars: Any) -> str:
"""Create a string exporting envvars needed for CNS.
Parameters
----------
envvars : dict
A dictionary containing envvariables where keys are var names
and values are the values.
Returns
-------
str
In the form of:
export VAR1=VALUE1
export VAR2=VALUE2
export VAR3=VALUE3
"""
exports = os.linesep.join(
f"export {key.upper()}={value}" for key, value in envvars.items()
)
return exports + os.linesep + os.linesep
# the different job submission queues
create_job_header_funcs = {
"torque": create_torque_header,
"slurm": create_slurm_header,
}
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