orqal 0.0.12

Orchestration of Algorithm on docker cluster

Orqal for [ORQ]chestration of [AL]gorithms is a simple batch scheduler for docker cluster which can be used remotly and without overhead in scientific experiment.

📐 Design

Overview

Orqal claim to be and stay as simple as possible. 

• We use the docker api to manage docker nodes, which means that there is no configuration on node except open the api port.
• HTTP/REST API enable to schedule jobs and retrieve data.
• A dashboard is provided to monitor load average per nodes, jobs scheduling and redoc api.

Wrapper

The glue between docker image and orqal need to be implemented in python with the ArbstractWorker class in order to :

• get command to execute
• set the result if necessary

Here is a simple example using radare2

class Rabin2(AbstractWorker):
    docker_url = "radare/radare2"
    volumes = {'/database': {'bind': '/database', 'mode': 'ro'}}
    threads = 1
    memory_in_gb = 1
	
    def get_cmd(self, params):
        return "rabin2 -I %s" % self.job.input
	
    def set_result(self, job):
        r = {l.split()[0].replace('.', '_'): l.split()[1] for l in job.stdout if len(l.split()) == 2}
        job.set_result(r)

Install

pip3 install orqal 

Run

Start the web worker :

orqal-worker

Start the web interface :

orqal-web

NB: In a production mode, use gunicorn, in orqal dir :

gunicorn3 web:app --bind 0.0.0.0:5001 --worker-class aiohttp.GunicornWebWorker --workers 8 --timeout 120

user

Configuration

In order to establish a DB connection, process will search the following environment variable :

ORQAL_MONGO_URI

By default : 'mongodb://localhost/'

Other settings will be loaded from the conf collection, using the request : active=True

Here is a example :

NB : The first run will initiate it if necessary

    {
        "_id" : ObjectId("5d1a78eca307b20dd5a660ce"),
        "active" : true,
        "mongourl" : "mongodb://localhost/",
        "docker_hosts" : [ 
            "192.168.100.51:2376", 
            .....
            "192.168.100.64:2376"
        ],
        "docker_api_version" : "1.37",
        "mongo_replicaset" : "madlabReplSet",
        "registry_auth_config" : {
            "password" : "65sX2-9sSXSp-hs-XeZ8",
            "username" : "test"
        },
        "services" : "/home/madlab/services.py",
        "nb_disp_jobs" : 30,
        "contact" : "[e-mail]",
        "jobs_dir" : "/scratch/jobs"
    }

Services

The python module is defined in the configuration (see services above)

Here is a example :

import json
import logging
import conf
import os
from orqal.abstract import AbstractWrapper

class TestProd(AbstractWrapper):
    docker_url = "madlab:5000/test_module"

    def get_cmd(self, params):
        return "python3 simple_job.py %s %s %s" % (params['echo'], params['time'], params['exit_code'])

    def set_result(self, job):
        job.set_result("My results")


class AngrExtraction(AbstractWrapper):
    docker_url = "madlab:5000/scdg/madlab-v2"
    threads = 1
    memory_in_gb = 10
    create_dir = True

    def get_cmd(self, params):
        return "python /code/src/interfaces/cli.py %s params.json -o calls.json" % self.job.input

    def set_result(self, job):
        return os.path.join(self.job.wd, "calls.json")

DB tuning : log collection in Mongo

Process use a mongo logging handler, in order to provide it in the web interface, you can customize parameters like that :

use orqal
db.createCollection('log', {capped:true, size:10000000}) 
db.log.createIndex( { "time": 1 }, { expireAfterSeconds: 86400 } )

Cache :

use orqal
db.jobs.createIndex( { input: 1 } )
db.jobs.createIndex( { params: 1 } )
db.jobs.createIndex( { app: 1 } )

Distribution

   python setup.py bdist
   python3 setup.py sdist
   twine upload dist/*

Licence

GNU AFFERO GENERAL PUBLIC LICENSE https://www.gnu.org/licenses/agpl-3.0.txt

Credits

• Dashboard template : https://github.com/puikinsh/sufee-admin-dashboard
• Font : https://fonts.google.com/specimen/Righteous

FAQ

How to open api port on docker ?

Add in file /etc/systemd/system/docker.service.d/override.conf

[Service]
ExecStart=
ExecStart=/usr/bin/docker daemon -H fd://  -H tcp://0.0.0.0:2376 -s overlay --insecure-registry orqal:5000

Then flush changes by executing :

systemctl daemon-reload

verify that the configuration has been loaded:

systemctl show --property=ExecStart docker

restart docker:

systemctl restart docker

Clean old jobs

Add a index (7 days here):

db.jobs.createIndex( { "ctime": 1 }, { expireAfterSeconds: 604800 } )

And call http:///api/clean/old periodically in order to delete old job directories.