def start(self,jid):
"""start running a job by creating a new process"""
global p, jobs
myjobs = []
db = DAL(config.uri, auto_import=True, migrate=False,
folder=config.dbdir)
user = db.jobs(jid).user
app = db.jobs(jid).app
cid = db.jobs(jid).cid
np = db.jobs(jid).np
if np > 1: # use mpi
command = db.apps(name=app).command
command = config.mpirun + " -np " + str(np) + " " + command
else: # dont use mpi
command = db.apps(name=app).command
exe = os.path.join(config.apps_dir,app,app)
outfn = app + ".out"
cmd = command + ' >& ' + outfn
run_dir = os.path.join(config.user_dir,user,app,cid)
# if number procs available fork new process with command
for i in range(np):
self.sem.acquire()
p = Process(target=self.start_job, args=(run_dir,cmd,app,jid,np,))
myjobs.append(p)
print len(myjobs), myjobs
p.start()
for i in range(np):
self.sem.release()
def start(self,jid):
"""start running a job by creating a new process"""
db = DAL(config.uri, auto_import=True, migrate=False, folder=config.dbdir)
uid = db.jobs(jid).uid
user = db.users(uid).user
app = db.jobs(jid).app
cid = db.jobs(jid).cid
np = db.jobs(jid).np
if np > 1: # use mpi
command = db.jobs(jid).command
command = config.mpirun + " -np " + str(np) + " " + command
else: # dont use mpi
command = db.jobs(jid).command
# redirect output to appname.out file
outfn = app + ".out"
cmd = command + ' > ' + outfn + ' 2>&1 '
print "cmd:", cmd
run_dir = os.path.join(user_dir, user, app, cid)
# if number procs available fork new process with command
for i in range(np):
self.sem.acquire()
p = Process(target=self.start_job, args=(run_dir,cmd,app,jid,np,myjobs))
p.start()
for i in range(np):
self.sem.release()
def qdel(self,jid):
"""delete job jid from the queue"""
#try:
db = DAL(config.uri, auto_import=True, migrate=False,
folder=config.dbdir)
del db.jobs[jid]
db.commit()
db.close()
def _set_state(self,jid,state):
"""update state of job"""
self.mutex.acquire()
db = DAL(config.uri, auto_import=True, migrate=False, folder=config.dbdir)
db.jobs[jid] = dict(state=state)
db.commit()
db.close()
self.mutex.release()
def qsub(self,app,cid,user,np,pry,desc=""):
"""queue job ... really just set state to 'Q'."""
db = DAL(config.uri, auto_import=True, migrate=False,
folder=config.dbdir)
jid = db.jobs.insert(user=user, app=app, cid=cid, state=STATE_QUEUED,
description=desc, time_submit=time.asctime(), np=np, priority=pry)
db.commit()
db.close()
return str(jid)
def qfront(self):
"""pop the top job off of the queue that is in a queued 'Q' state"""
db = DAL(config.uri, auto_import=True, migrate=False, folder=config.dbdir)
myorder = db.jobs.priority
#myorder = db.jobs.priority | db.jobs.id
row = db(db.jobs.state==STATE_QUEUED).select(orderby=myorder).first()
db.close()
if row: return row.id
else: return None
def __init__(self):
# if any jobs marked in run state when scheduler starts
# replace their state with X to mark that they have been shutdown
db = DAL(config.uri, auto_import=True, migrate=False,
folder=config.dbdir)
myset = db(db.jobs.state == 'R')
myset.update(state='X')
db.commit()
self.sem = BoundedSemaphore(config.np)
self.mutex = Lock()
def __init__(self):
# if any jobs marked in run state when scheduler starts
# replace their state with X to mark that they have been shutdown
db = DAL(config.uri, auto_import=True, migrate=False, folder=config.dbdir)
myset = db(db.jobs.state == STATE_RUN)
myset.update(state=STATE_STOPPED)
db.commit()
self.sem = BoundedSemaphore(config.np)
self.mutex = Lock()
# set time zone
try:
os.environ['TZ'] = config.time_zone
time.tzset()
except: pass
def stop_expired_jobs(self):
"""shutdown jobs that exceed their time limit"""
db = DAL(config.uri, auto_import=True, migrate=False, folder=config.dbdir)
rows = db(db.jobs.state==STATE_RUN).select()
for row in rows:
if row:
walltime = int(row.walltime)
time_submit = time.mktime(datetime.datetime.strptime(
row.time_submit, "%a %b %d %H:%M:%S %Y").timetuple())
now = time.mktime(datetime.datetime.now().timetuple())
runtime = now - time_submit
if runtime > walltime:
print "INFO: scheduler stopped job", row.id, "REASON: reached timeout"
self.stop(row.id)
db.close()
from gluino import DAL, Field
import config
#db = DAL(config.uri, auto_import=True, migrate=False, folder=config.dbdir)
db = DAL(config.uri, migrate=False, folder=config.dbdir)
users = db.define_table('users', Field('id', 'integer'),
Field('user', 'string'), Field('passwd', 'string'),
Field('email', 'string'), Field('priority', 'integer'))
# this is also defined in scheduler.py
# need to fix in the future
apps = db.define_table('apps', Field('id', 'integer'), Field('name', 'string'),
Field('description', 'string'),
Field('category',
'string'), Field('language', 'string'),
Field('input_format', 'string'),
Field('command', 'string'),
Field('preprocess', 'string'),
Field('postprocess', 'string'), Field('uid', 'integer'))
# this is also defined in scheduler.py
# need to fix in the future
jobs = db.define_table('jobs', Field('id', 'integer'), Field('user', 'string'),
Field('app', 'string'), Field('cid', 'string'),
Field('state', 'string'), Field('time_submit',
'string'),
Field('description', 'string'), Field('np', 'integer'),
Field('priority', 'integer'), Field('shared', 'string'))
plots = db.define_table('plots', Field('id', 'integer'),
Field('appid', db.apps), Field('ptype', 'string'),
Field('title', 'string'), Field('options', 'string'),
def __init__(self, uri=config.uri, migrate=False):
#self.db = DAL(uri, auto_import=True, migrate=migrate, folder=config.dbdir)
self.db = DAL(uri, migrate=migrate, folder=config.dbdir)
# must define these here because need to use the db instance
self.users = self.db.define_table('users', Field('id', 'integer'),
Field('user', 'string'),
Field('passwd', 'string'),
Field('email', 'string'),
Field('priority', 'integer'))
self.apps = self.db.define_table('apps', Field('id', 'integer'),
Field('name', 'string'),
Field('description', 'string'),
Field('category', 'string'),
Field('language', 'string'),
Field('input_format', 'string'),
Field('command', 'string'),
Field('preprocess', 'string'),
Field('postprocess', 'string'),
Field('uid', 'integer'))
self.jobs = self.db.define_table('jobs', Field('id', 'integer'),
Field('user', 'string'),
Field('app', 'string'),
Field('cid', 'string'),
Field('state', 'string'),
Field('time_submit', 'string'),
Field('description', 'string'),
Field('np', 'integer'),
Field('priority', 'integer'),
Field('shared', 'string'))
self.plots = self.db.define_table('plots', Field('id', 'integer'),
Field('appid', self.db.apps),
Field('ptype', 'string'),
Field('title', 'string'),
Field('options', 'string'),
Field('datadef', 'string'))
self.datasource = self.db.define_table('datasource',
Field('id', 'integer'),
Field('pltid', 'integer'),
Field('label', 'string'),
Field('ptype', 'string'),
Field('color', 'string'),
Field('filename', 'string'),
Field('cols', 'string'),
Field('line_range', 'string'))
self.aws_creds = self.db.define_table('aws_creds',
Field('id', 'integer'),
Field('key', 'string'),
Field('secret', 'string'),
Field('account_id', 'string'),
Field('uid', 'integer'))
self.aws_instances = self.db.define_table('aws_instances',
Field('id', 'integer'),
Field('region', 'string'),
Field('instance', 'string'),
Field('itype', 'string'),
Field('rate', 'double'),
Field('uid', 'integer'))
self.containers = self.db.define_table('containers',
Field('id', 'integer'),
Field('containerid', 'string'),
Field('image', 'string'),
Field('command', 'string'),
Field('uid', 'integer'))
self.disciplines = self.db.define_table('disciplines', Field('name'))
import tornado.ioloop
import tornado.web
from gluino import wrapper, DAL, Field, SQLFORM, cache, IS_NOT_EMPTY
import time
# configure the gluino wrapper
wrapper.debug = True
wrapper.http = lambda code, message: tornado.web.HTTPError(code)
wrapper.redirect = lambda status, url: tornado.web.RequestHandler.redirect(url)
# create database and table
db = DAL('sqlite://storage.sqlite')
db.define_table('person', Field('name', requires=IS_NOT_EMPTY()))
# define action
def index(request):
vars = wrapper.extract_vars(request.arguments)
form = SQLFORM(db.person)
if form.accepts(vars):
message = 'hello %s' % form.vars.name
else:
message = 'hello anonymous'
people = db(db.person).select()
now = cache.ram('time', lambda: time.ctime(), 10)
return locals()
class MainHandler(tornado.web.RequestHandler):
@wrapper(view='templates/index.html', dbs=[db])
def get(self):
def __init__(self, uri=config.uri, migrate=False):
self.db = DAL(uri, migrate=migrate, folder=config.dbdir)
# must define these here because need to use the db instance
self.groups = self.db.define_table('groups', Field('id', 'integer'),
Field('name', 'string'))
self.users = self.db.define_table('users', Field('id', 'integer'),
Field('user', 'string'),
Field('passwd', 'string'),
Field('email', 'string'),
Field('new_shared_jobs', 'integer'),
Field('priority', 'integer'),
Field('gid', self.db.groups, ondelete="SET NULL"))
self.user_meta = self.db.define_table('user_meta', Field('id', 'integer'),
Field('uid', self.db.users),
Field('new_shared_jobs', 'integer'),
Field('theme', 'string'))
self.apps = self.db.define_table('apps', Field('id', 'integer'),
Field('name', 'string'),
Field('description', 'string'),
Field('category', 'string'),
Field('language', 'string'),
Field('input_format', 'string'),
Field('command', 'string'),
Field('assets', 'string'),
Field('preprocess', 'string'),
Field('postprocess', 'string'))
self.app_user = self.db.define_table('app_user', Field('id', 'integer'),
Field('appid', 'integer'),
Field('uid', 'integer'))
self.jobs = self.db.define_table('jobs', Field('id', 'integer'),
Field('uid', self.db.users),
Field('app', 'string'),
Field('cid', 'string'),
Field('gid', self.db.groups),
Field('command', 'string'),
Field('state', 'string'),
Field('time_submit', 'string'),
Field('walltime', 'string'),
Field('description', 'string'),
Field('np', 'integer'),
Field('priority', 'integer'),
Field('starred', 'string'),
Field('shared', 'string'))
self.plots = self.db.define_table('plots', Field('id', 'integer'),
# need to turn on unique in the future, but will cause migration probs for old DBs
# this is needed for running "spc update" b/c primary keys are not specified in spc.json
Field('appid', self.db.apps), # unique=True),
Field('ptype', 'string'),
Field('title', 'string'),
Field('options', 'string'))
self.datasource = self.db.define_table('datasource', Field('id', 'integer'),
Field('label', 'string'), # unique=True),
Field('pltid', self.db.plots),
Field('filename', 'string'),
Field('cols', 'string'),
Field('line_range', 'string'),
Field('data_def', 'string'))
self.aws_creds = self.db.define_table('aws_creds', Field('id', 'integer'),
Field('key', 'string'),
Field('secret', 'string'),
Field('account_id', 'string'),
Field('uid', self.db.users))
self.aws_instances = self.db.define_table('aws_instances',
Field('id', 'integer'),
Field('region', 'string'),
Field('instance', 'string'),
Field('itype', 'string'),
Field('rate', 'double'),
Field('uid', self.db.users))
self.disciplines = self.db.define_table('disciplines', Field('name'))
#!/usr/bin/env python
import threading, time, os
import config
from gluino import DAL, Field
import subprocess, signal
#inspired from:
#http://taher-zadeh.com/a-simple-and-dirty-batch-job-scheduler-daemon-in-python/
db = DAL(config.uri, auto_import=False, migrate=False, folder=config.dbdir)
apps = db.define_table('apps', Field('id','integer'),
Field('name','string'),
Field('description','string'),
Field('category','string'),
Field('language','string'),
Field('input_format','string'),
Field('command','string'))
jobs = db.define_table('jobs', Field('id','integer'),
Field('user','string'),
Field('app','string'),
Field('cid','string'),
Field('state','string'),
Field('time_submit','string'),
Field('description','string'),
Field('priority','integer'),
Field('np','integer'))
class scheduler(object):
"""simple single process scheduler"""
def __init__(self):
def qstat(self):
"""return the number of jobs in a queued 'Q' state"""
db = DAL(config.uri, auto_import=True, migrate=False,
folder=config.dbdir)
return db(db.jobs.state==STATE_QUEUED).count()
db.close()