xqute 0.5.7

A job management system for python

xqute

A job management system for python

Features

• Written in async
• Plugin system
• Scheduler adaptor
• Job retrying/pipeline halting when failed

Installation

pip install xqute

A toy example

import asyncio
from xqute import Xqute

async def main():
    # 3 jobs allowed to run at the same time
    xqute = Xqute(scheduler_forks=3)
    for _ in range(10):
        await xqute.put('sleep 1')
    await xqute.run_until_complete()

if __name__ == '__main__':
    asyncio.run(main())

API

https://pwwang.github.io/xqute/

Usage

Xqute object

An xqute is initialized by:

xqute = Xqute(...)

Available arguments are:

• scheduler: The scheduler class or name
• plugins: The plugins to enable/disable for this session
• job_metadir: The job meta directory (Default: ./.xqute/)
• job_error_strategy: The strategy when there is error happened
• job_num_retries: Max number of retries when job_error_strategy is retry
• job_submission_batch: The number of consumers to submit jobs
• scheduler_forks: Max number of job forks
• **scheduler_opts: Additional keyword arguments for scheduler

Note that the producer must be initialized in an event loop.

To push a job into the queue:

await xqute.put(['echo', 1])

Using SGE scheduler

xqute = Xqute(
    'sge',
    scheduler_forks=100,
    qsub='path to qsub',
    qdel='path to qdel',
    qstat='path to qstat',
    sge_q='1-day',  # or qsub_q='1-day'
    ...
)

Keyword-arguments with names starting with sge_ will be interpreted as qsub options. list or tuple option values will be expanded. For example: sge_l=['h_vmem=2G', 'gpu=1'] will be expanded in wrapped script like this:

# ...

#$ -l h_vmem=2G
#$ -l gpu=1

# ...

Using Slurm scheduler

xqute = Xqute(
    'slurm',
    scheduler_forks=100,
    sbatch='path to sbatch',
    scancel='path to scancel',
    squeue='path to squeue',
    sbatch_partition='1-day',  # or slurm_partition='1-day'
    sbatch_time='01:00:00',
    ...
)

Using ssh scheduler

xqute = Xqute(
    'ssh',
    scheduler_forks=100,
    ssh='path to ssh',
    ssh_servers={
        "server1": {
            "user": ...,
            "port": 22,
            "keyfile": ...,
            # How long to keep the ssh connection alive
            "ctrl_persist": 600,
            # Where to store the control socket
            "ctrl_dir": "/tmp",
        },
        ...
    }
    ...
)

SSH servers must share the same filesystem and using keyfile authentication.

Plugins

To write a plugin for xqute, you will need to implement the following hooks:

• def on_init(scheduler): Right after scheduler object is initialized
• def on_shutdown(scheduler, sig): When scheduler is shutting down
• async def on_job_init(scheduler, job): When the job is initialized
• async def on_job_queued(scheduler, job): When the job is queued
• async def on_job_submitted(scheduler, job): When the job is submitted
• async def on_job_started(scheduler, job): When the job is started (when status changed to running)
• async def on_job_polling(scheduler, job): When job status is being polled
• async def on_job_killing(scheduler, job): When the job is being killed
• async def on_job_killed(scheduler, job): When the job is killed
• async def on_job_failed(scheduler, job): When the job is failed
• async def on_job_succeeded(scheduler, job): When the job is succeeded
• def on_jobcmd_init(scheduler, job) -> str: When the job command wrapper script is initialized before the prescript is run. This will replace the placeholder #![jobcmd_init] in the wrapper script.
• def on_jobcmd_prep(scheduler, job) -> str: When the job command is right about to run in the wrapper script. This will replace the placeholder #![jobcmd_prep] in the wrapper script.
• def on_jobcmd_end(scheduler, job) -> str: When the job command wrapper script is about to end and after the postscript is run. This will replace the placeholder #![jobcmd_end] in the wrapper script.

Note that all hooks are corotines except on_init and on_shutdown, that means you should also implement them as corotines (sync implementations are allowed but will be warned).

To implement a hook, you have to fetch the plugin manager:

from simplug import Simplug
pm = Simplug('xqute')

# or
from xqute import simplug as pm

and then use the decorator pm.impl:

@pm.impl
def on_init(scheduler):
    ...

Implementing a scheduler

Currently there are only 2 builtin schedulers: local and sge.

One can implement a scheduler by subclassing the Scheduler abstract class. There are three abstract methods that have to be implemented in the subclass:

from xqute import Scheduer

class MyScheduler(Scheduler):
    name = 'my'
    job_class: MyJob

    async def submit_job(self, job):
        """How to submit a job, return a unique id in the scheduler system
        (the pid for local scheduler for example)
        """

    async def kill_job(self, job):
        """How to kill a job"""

    async def job_is_running(self, job):
        """Check if a job is running"""

As you may see, we may also need to implement a job class before MyScheduler. The only abstract method to be implemented is wrap_cmd:

from xqute import Job

class MyJob(Job):

    def shebang(self, scheduler: Scheduler) -> str:
        """The shebang and the options for the job script"""