def __initialize_pilot_data(self, service_url):
# initialize file adaptor
# Pilot Data API for File Management
if service_url.startswith("ssh:"):
logger.debug("Use SSH backend")
try:
from pilot.filemanagement.ssh_adaptor import SSHFileAdaptor
self.__filemanager = SSHFileAdaptor(service_url)
except:
logger.debug("SSH/Paramiko package not found.")
self.__print_traceback()
elif service_url.startswith("http:"):
logger.debug("Use WebHDFS backend")
try:
from pilot.filemanagement.webhdfs_adaptor import WebHDFSFileAdaptor
self.__filemanager = WebHDFSFileAdaptor(service_url)
except:
logger.debug("WebHDFS package not found.")
elif service_url.startswith("go:"):
logger.debug("Use Globus Online backend")
try:
from pilot.filemanagement.globusonline_adaptor import GlobusOnlineFileAdaptor
self.__filemanager = GlobusOnlineFileAdaptor(service_url)
except:
logger.debug("Globus Online package not found.")
self.__print_traceback()
def __initialize_pilot_data(self, service_url):
# initialize file adaptor
# Pilot Data API for File Management
if service_url.startswith("ssh:"):
logger.debug("Use SSH backend")
try:
from pilot.filemanagement.ssh_adaptor import SSHFileAdaptor
self.__filemanager = SSHFileAdaptor(service_url)
except:
logger.debug("SSH package not found.")
self.__print_traceback()
elif service_url.startswith("http:"):
logger.debug("Use WebHDFS backend")
try:
from pilot.filemanagement.webhdfs_adaptor import WebHDFSFileAdaptor
self.__filemanager = WebHDFSFileAdaptor(service_url)
except:
logger.debug("WebHDFS package not found.")
elif service_url.startswith("go:"):
logger.debug("Use Globus Online backend")
try:
from pilot.filemanagement.globusonline_adaptor import GlobusOnlineFileAdaptor
self.__filemanager = GlobusOnlineFileAdaptor(service_url)
except:
logger.debug("Globus Online package not found.")
self.__print_traceback()
def __initialize_pilot_data(self):
if self.pilot_data_description != None:
self.service_url = self.pilot_data_description["service_url"]
if self.pilot_data_description.has_key("size"):
self.size = self.pilot_data_description["size"]
# initialize file adaptor
if self.service_url.startswith("ssh:"):
logger.debug("Use SSH backend")
self.__filemanager = SSHFileAdaptor(
self.service_url, self.security_context,
self.pilot_data_description)
elif self.service_url.startswith("http:"):
logger.debug("Use WebHDFS backend")
self.__filemanager = WebHDFSFileAdaptor(self.service_url)
elif self.service_url.startswith("go:"):
logger.debug("Use Globus Online backend")
self.__filemanager = GlobusOnlineFileAdaptor(self.service_url)
elif self.service_url.startswith("gs:"):
logger.debug("Use Google Cloud Storage backend")
self.__filemanager = GSFileAdaptor(self.service_url,
self.security_context)
elif self.service_url.startswith("irods:"):
logger.debug("Use iRods Storage backend")
self.__filemanager = iRodsFileAdaptor(self.service_url,
self.security_context)
elif self.service_url.startswith("s3:") \
or self.service_url.startswith("walrus:") \
or self.service_url.startswith("swift:"):
logger.debug(
"Use Amazon S3/Eucalyptus Walrus/SWIFT Storage backend")
self.__filemanager = S3FileAdaptor(self.service_url,
self.security_context,
self.pilot_data_description)
else:
raise PilotError("No File Plugin found.")
self.__filemanager.initialize_pilotdata()
self.__filemanager.get_pilotdata_size()
# Update security context
self.security_context = self.__filemanager.get_security_context()
class bigjob(api.base.bigjob):
''' BigJob: Class for managing pilot jobs:
Example:
bj = bigjob("redis://localhost")
bj.start_pilot_job("fork://localhost")
..
bj.cancel()
'''
__APPLICATION_NAME = "bigjob"
def __init__(self,
coordination_url="advert://localhost/?dbtype=sqlite3",
pilot_url=None):
""" Initializes BigJob's coordination system
advert://localhost (SAGA/Advert SQLITE)
advert://advert.cct.lsu.edu:8080 (SAGA/Advert POSTGRESQL)
redis://localhost:6379 (Redis at localhost)
tcp://localhost (ZMQ)
The following formats for pilot_url are supported:
1.) Including root path at distributed coordination service:
redis://localhost/bigjob:bj-1c3816f0-ad5f-11e1-b326-109addae22a3:localhost
This path is returned when call bigjob.get_url()
2.) BigJob unique ID:
bigjob:bj-1c3816f0-ad5f-11e1-b326-109addae22a3:localhost
"""
self.coordination_url = coordination_url
#self.launch_method=""
self.__filemanager = None
# restore existing BJ or initialize new BJ
if pilot_url != None:
logger.debug("Reconnect to BJ: %s" % pilot_url)
if pilot_url.startswith("bigjob:"):
self.pilot_url = pilot_url
else:
self.coordination_url, self.pilot_url = self.__parse_pilot_url(
pilot_url)
self.uuid = self.__get_bj_id(pilot_url)
self.app_url = self.__APPLICATION_NAME + ":" + str(self.uuid)
self.job = None
self.working_directory = None
# Coordination subsystem must be initialized before get_state_detail
self.coordination = self.__init_coordination(self.coordination_url)
self.state = self.get_state_detail()
_pilot_url_dict[self.pilot_url] = self
else:
self.coordination = self.__init_coordination(self.coordination_url)
self.uuid = "bj-" + str(get_uuid())
logger.debug("init BigJob w/: " + coordination_url)
self.app_url = self.__APPLICATION_NAME + ":" + str(self.uuid)
self.state = Unknown
self.pilot_url = ""
self.job = None
self.working_directory = None
logger.debug("initialized BigJob: " + self.app_url)
def start_pilot_job(self,
lrms_url,
number_nodes=1,
queue=None,
project=None,
working_directory=None,
userproxy=None,
walltime=None,
processes_per_node=1,
filetransfers=None,
external_queue="",
pilot_compute_description=None):
""" Start a batch job (using SAGA Job API) at resource manager. Currently, the following resource manager are supported:
fork://localhost/ (Default Job Adaptor
gram://qb1.loni.org/jobmanager-pbs (Globus Adaptor)
pbspro://localhost (PBS Pro Adaptor)
"""
if self.job != None:
raise BigJobError(
"One BigJob already active. Please stop BigJob first.")
return
##############################################################################
# initialization of coordination and communication subsystem
# Communication & Coordination initialization
lrms_saga_url = SAGAUrl(lrms_url)
self.url = lrms_saga_url
self.pilot_url = self.app_url + ":" + lrms_saga_url.host
self.number_nodes = int(number_nodes) * int(processes_per_node)
# Store references to BJ in global dict
_pilot_url_dict[self.pilot_url] = self
_pilot_url_dict[external_queue] = self
logger.debug("create pilot job entry on backend server: " +
self.pilot_url)
self.coordination.set_pilot_state(self.pilot_url, str(Unknown), False)
self.coordination.set_pilot_description(self.pilot_url, filetransfers)
logger.debug("set pilot state to: " + str(Unknown))
##############################################################################
# Create Job Service (Default: SAGA Job Service, alternative Job Services supported)
self.js = None
if lrms_saga_url.scheme == "gce+ssh":
self.js = GCEService(lrms_saga_url, pilot_compute_description)
elif lrms_saga_url.scheme=="ec2+ssh" or lrms_saga_url.scheme=="euca+ssh" \
or lrms_saga_url.scheme=="nova+ssh":
self.js = EC2Service(lrms_saga_url, pilot_compute_description)
else:
self.js = SAGAJobService(lrms_saga_url)
##############################################################################
# create job description
jd = SAGAJobDescription()
# Attempt to create working directory (e.g. in local scenario)
if working_directory != None:
if not os.path.isdir(working_directory) \
and (lrms_saga_url.scheme.startswith("fork") or lrms_saga_url.scheme.startswith("condor")) \
and working_directory.startswith("go:")==False:
os.mkdir(working_directory)
self.working_directory = working_directory
else:
# if no working dir is set assume use home directory
# will fail if home directory is not the same on remote machine
# but this is just a guess to avoid failing
#self.working_directory = os.path.expanduser("~")
self.working_directory = ""
if queue != None:
jd.queue = queue
if project != None:
jd.project = project
if walltime != None:
if is_bliss:
jd.wall_time_limit = int(walltime)
else:
jd.wall_time_limit = str(walltime)
##############################################################################
# File Management and Stage-In
# Determine whether target machine use gsissh or ssh to logon.
# logger.debug("Detect launch method for: " + lrms_saga_url.host)
# self.launch_method = self.__get_launch_method(lrms_saga_url.host,lrms_saga_url.username)
self.bigjob_working_directory_url = ""
if lrms_saga_url.scheme.startswith("gce") or lrms_saga_url.scheme.startswith("ec2")\
or lrms_saga_url.scheme.startswith("euca") or lrms_saga_url.scheme.startswith("nova"):
logger.debug(
"File Staging for Cloud Instances currently not supported.")
elif lrms_saga_url.scheme.startswith("condor") == True:
logger.debug("Using Condor file staging")
else:
# build target url for working directory
# this will also create the remote directory for the BJ
# Fallback if working directory is not a valid URL
if not (self.working_directory.startswith("go:")
or self.working_directory.startswith("ssh://")):
if lrms_saga_url.username != None and lrms_saga_url.username != "":
self.bigjob_working_directory_url = "ssh://" + lrms_saga_url.username + "@" + lrms_saga_url.host + self.__get_bigjob_working_dir(
)
else:
self.bigjob_working_directory_url = "ssh://" + lrms_saga_url.host + self.__get_bigjob_working_dir(
)
elif self.working_directory.startswith("go:"):
self.bigjob_working_directory_url = os.path.join(
self.working_directory, self.uuid)
else:
# working directory is a valid file staging URL
self.bigjob_working_directory_url = self.working_directory
# initialize file manager that takes care of file movement and directory creation
if self.__filemanager == None:
self.__initialize_pilot_data(
self.bigjob_working_directory_url) # determines the url
if self.__filemanager != None and not self.working_directory.startswith(
"/"):
self.working_directory = self.__filemanager.get_path(
self.bigjob_working_directory_url)
# determine working directory of bigjob
# if a remote sandbox can be created via ssh => create a own dir for each bj job id
# otherwise use specified working directory
logger.debug("BigJob working directory: %s" %
self.bigjob_working_directory_url)
if self.__filemanager != None and self.__filemanager.create_remote_directory(
self.bigjob_working_directory_url) == True:
self.working_directory = self.__get_bigjob_working_dir()
self.__stage_files(filetransfers,
self.bigjob_working_directory_url)
else:
logger.warn("No file staging adaptor found.")
logger.debug("BJ Working Directory: %s", self.working_directory)
if lrms_saga_url.scheme.startswith("condor") == False:
jd.working_directory = self.working_directory
else:
jd.working_directory = ""
##############################################################################
# Create and process BJ bootstrap script
bootstrap_script = self.__generate_bootstrap_script(
self.coordination.get_address(),
self.pilot_url, # Queue 1 used by this BJ object
external_queue # Queue 2 used by Pilot Compute Service
# or another external scheduler
)
logger.debug("Adaptor specific modifications: " +
str(lrms_saga_url.scheme))
if is_bliss:
bootstrap_script = self.__escape_bliss(bootstrap_script)
else:
if lrms_saga_url.scheme == "gram":
bootstrap_script = self.__escape_rsl(bootstrap_script)
elif lrms_saga_url.scheme == "pbspro" or lrms_saga_url.scheme == "xt5torque" or lrms_saga_url.scheme == "torque":
bootstrap_script = self.__escape_pbs(bootstrap_script)
elif lrms_saga_url.scheme == "ssh":
bootstrap_script = self.__escape_ssh(bootstrap_script)
logger.debug(bootstrap_script)
# Define Agent Executable in Job description
# in Condor case bootstrap script is staged
# (Python app cannot be passed inline in Condor job description)
if lrms_saga_url.scheme.startswith("condor") == True:
condor_bootstrap_filename = os.path.join(
"/tmp", "bootstrap-" + str(self.uuid))
condor_bootstrap_file = open(condor_bootstrap_filename, "w")
condor_bootstrap_file.write(bootstrap_script)
condor_bootstrap_file.close()
logger.debug("Using Condor - bootstrap file: " +
condor_bootstrap_filename)
jd.executable = "/usr/bin/env"
jd.arguments = [
"python",
os.path.basename(condor_bootstrap_filename)
]
bj_file_transfers = []
file_transfer_spec = condor_bootstrap_filename + " > " + os.path.basename(
condor_bootstrap_filename)
bj_file_transfers.append(file_transfer_spec)
output_file_name = "output-" + str(self.uuid) + ".tar.gz"
output_file_transfer_spec = os.path.join(
self.working_directory,
output_file_name) + " < " + output_file_name
#output_file_transfer_spec = os.path.join(self.working_directory, "output.tar.gz") +" < output.tar.gz"
logger.debug("Output transfer: " + output_file_transfer_spec)
bj_file_transfers.append(output_file_transfer_spec)
if filetransfers != None:
for t in filetransfers:
bj_file_transfers.append(t)
logger.debug("Condor file transfers: " + str(bj_file_transfers))
jd.file_transfer = bj_file_transfers
else:
if is_bliss:
jd.total_cpu_count = int(number_nodes)
else:
jd.number_of_processes = str(number_nodes)
jd.processes_per_host = str(processes_per_node)
jd.spmd_variation = "single"
jd.arguments = ["python", "-c", bootstrap_script]
jd.executable = "/usr/bin/env"
logger.debug("Working directory: " + jd.working_directory)
jd.output = os.path.join(self.working_directory,
"stdout-" + self.uuid + "-agent.txt")
jd.error = os.path.join(self.working_directory,
"stderr-" + self.uuid + "-agent.txt")
##############################################################################
# Create and submit pilot job to job service
logger.debug("Creating pilot job with description: %s" % str(jd))
self.job = self.js.create_job(jd)
logger.debug("Submit pilot job to: " + str(lrms_saga_url))
self.job.run()
return self.pilot_url
def list_subjobs(self):
sj_list = self.coordination.get_jobs_of_pilot(self.pilot_url)
logger.debug(str(sj_list))
subjobs = []
for i in sj_list:
url = i
#if url.find("/")>0:
# url = url[url.find("bigjob"):]
# url = url.replace("/", ":")
#sj = subjob(coordination_url=self.coordination_url, subjob_url=url)
sj = subjob(subjob_url=url)
subjobs.append(sj.get_url())
return subjobs
def get_state(self):
""" duck typing for get_state of saga.job.job
state of saga job that is used to spawn the pilot agent
"""
return self.get_state_detail()
def get_state_detail(self):
""" internal state of BigJob agent """
try:
return self.coordination.get_pilot_state(self.pilot_url)["state"]
except:
return None
def get_url(self):
""" Get unique URL of big-job. This URL can be used to reconnect to BJ later, e.g.:
redis://localhost/bigjob:bj-1c3816f0-ad5f-11e1-b326-109addae22a3:localhost
"""
url = os.path.join(self.coordination.address, self.pilot_url)
if self.coordination.dbtype != "" and self.coordination.dbtype != None:
url = os.path.join(url, "?" + self.coordination.dbtype)
return url
def get_free_nodes(self):
jobs = self.coordination.get_jobs_of_pilot(self.pilot_url)
number_used_nodes = 0
for i in jobs:
job_detail = self.coordination.get_job(i)
if job_detail != None and job_detail.has_key("state") == True\
and job_detail["state"]==str(Running):
job_np = "1"
if (job_detail["NumberOfProcesses"] == True):
job_np = job_detail["NumberOfProcesses"]
number_used_nodes = number_used_nodes + int(job_np)
return (self.number_nodes - number_used_nodes)
def cancel(self):
""" duck typing for cancel of saga.cpr.job and saga.job.job """
logger.debug("Cancel Pilot Job")
try:
if self.url.scheme.startswith("condor") == False:
self.job.cancel()
else:
logger.debug(
"Output files are being transfered to file: outpt.tar.gz. Please wait until transfer is complete."
)
except:
pass
#traceback.print_stack()
try:
self._stop_pilot_job()
logger.debug("delete pilot job: " + str(self.pilot_url))
if _CLEANUP:
self.coordination.delete_pilot(self.pilot_url)
#os.remove(os.path.join("/tmp", "bootstrap-"+str(self.uuid)))
except:
pass
#traceback.print_stack()
logger.debug("Cancel Pilot Job finished")
def wait(self):
""" Waits for completion of all sub-jobs """
while 1:
jobs = self.coordination.get_jobs_of_pilot(self.pilot_url)
finish_counter = 0
result_map = {}
for i in jobs:
# parse job id out of sj url
surl = SAGAUrl(i)
state = self.coordination.get_job_state(surl.path)
#state = job_detail["state"]
if result_map.has_key(state) == False:
result_map[state] = 1
else:
result_map[state] = result_map[state] + 1
if self.__has_finished(state) == True:
finish_counter = finish_counter + 1
logger.debug("Total Jobs: %s States: %s" %
(len(jobs), str(result_map)))
if finish_counter == len(jobs):
break
time.sleep(2)
###########################################################################
# internal and protected methods
def _stop_pilot_job(self):
""" mark in database entry of pilot-job as stopped """
try:
logger.debug("stop pilot job: " + self.pilot_url)
self.coordination.set_pilot_state(self.pilot_url, str(Done), True)
self.job = None
except:
pass
def _delete_subjob(self, job_url):
self.coordination.delete_job(job_url)
def _get_subjob_state(self, job_url):
return self.coordination.get_job_state(job_url)
def _get_subjob_details(self, job_url):
return self.coordination.get_job(job_url)
def _add_subjob(self, queue_url, jd, job_url, job_id):
logger.debug("add subjob to queue of PJ: " + str(queue_url))
for i in range(0, 3):
try:
logger.debug(
"create dictionary for job description. Job-URL: " +
job_url)
# put job description attributes to Coordination Service
job_dict = {}
# to accomendate current bug in bliss (Number of processes is not returned from list attributes)
job_dict["NumberOfProcesses"] = "1"
attributes = jd.list_attributes()
logger.debug("SJ Attributes: " + str(jd))
for i in attributes:
if jd.attribute_is_vector(i):
vector_attr = []
for j in jd.get_vector_attribute(i):
vector_attr.append(j)
job_dict[i] = vector_attr
else:
#logger.debug("Add attribute: " + str(i) + " Value: " + jd.get_attribute(i))
job_dict[i] = jd.get_attribute(i)
# Other pilot state information
job_dict["state"] = str(Unknown)
job_dict["job-id"] = str(job_id)
logger.debug("job dict: " + str(job_dict))
if job_dict.has_key("FileTransfer"):
files = job_dict["FileTransfer"]
sj_work_dir = self.__get_subjob_working_dir(job_id)
self.__stage_files(files, sj_work_dir)
#logger.debug("update job description at communication & coordination sub-system")
self.coordination.set_job(job_url, job_dict)
self.coordination.queue_job(queue_url, job_url)
break
except:
self.__print_traceback()
time.sleep(2)
def _get_subjob_url(self, subjob_url):
""" Get unique URL for a sub-job. This URL can be used to reconnect to SJ later, e.g.:
redis://localhost/bigjob:bj-9a9ba4d8-b162-11e1-9c42-109addae22a3:localhost:jobs:sj-6f44da6e-b178-11e1-bc99-109addae22a3
"""
url = subjob_url
if subjob_url.find("bigjob") == 0:
url = os.path.join(self.coordination.address, subjob_url)
if self.coordination.dbtype != "" and self.coordination.dbtype != None:
url = os.path.join(url, "?" + self.coordination.dbtype)
return url
def __generate_bootstrap_script(self,
coordination_host,
coordination_namespace,
external_coordination_namespace=""):
script = textwrap.dedent("""import sys
import os
import urllib
import sys
import time
start_time = time.time()
home = os.environ.get("HOME")
#print "Home: " + home
if home==None: home = os.getcwd()
BIGJOB_AGENT_DIR= os.path.join(home, ".bigjob")
if not os.path.exists(BIGJOB_AGENT_DIR): os.mkdir (BIGJOB_AGENT_DIR)
BIGJOB_PYTHON_DIR=BIGJOB_AGENT_DIR+"/python/"
if not os.path.exists(BIGJOB_PYTHON_DIR): os.mkdir(BIGJOB_PYTHON_DIR)
BOOTSTRAP_URL="https://raw.github.com/saga-project/BigJob/master/bootstrap/bigjob-bootstrap.py"
BOOTSTRAP_FILE=BIGJOB_AGENT_DIR+"/bigjob-bootstrap.py"
#ensure that BJ in .bigjob is upfront in sys.path
sys.path.insert(0, os.getcwd() + "/../")
#sys.path.insert(0, /User/luckow/.bigjob/python/lib")
#sys.path.insert(0, os.getcwd() + "/../../")
p = list()
for i in sys.path:
if i.find(\".bigjob/python\")>1:
p.insert(0, i)
for i in p: sys.path.insert(0, i)
print "Python path: " + str(sys.path)
print "Python version: " + str(sys.version_info)
try: import saga
except: print "SAGA and SAGA Python Bindings not found: BigJob only work w/ non-SAGA backends e.g. Redis, ZMQ.";
try: import bigjob.bigjob_agent
except:
print "BigJob not installed. Attempt to install it.";
opener = urllib.FancyURLopener({});
opener.retrieve(BOOTSTRAP_URL, BOOTSTRAP_FILE);
print "Execute: " + "python " + BOOTSTRAP_FILE + " " + BIGJOB_PYTHON_DIR
os.system("/usr/bin/env")
try:
os.system("python " + BOOTSTRAP_FILE + " " + BIGJOB_PYTHON_DIR);
activate_this = BIGJOB_PYTHON_DIR+'bin/activate_this.py';
execfile(activate_this, dict(__file__=activate_this))
except:
print "BJ installation failed. Trying system-level python (/usr/bin/python)";
os.system("/usr/bin/python " + BOOTSTRAP_FILE + " " + BIGJOB_PYTHON_DIR);
activate_this = BIGJOB_PYTHON_DIR+'bin/activate_this.py';
execfile(activate_this, dict(__file__=activate_this))
#try to import BJ once again
import bigjob.bigjob_agent
# execute bj agent
args = list()
args.append("bigjob_agent.py")
args.append(\"%s\")
args.append(\"%s\")
args.append(\"%s\")
print "Bootstrap time: " + str(time.time()-start_time)
print "Starting BigJob Agents with following args: " + str(args)
bigjob_agent = bigjob.bigjob_agent.bigjob_agent(args)
""" % (coordination_host, coordination_namespace,
external_coordination_namespace))
return script
def __escape_rsl(self, bootstrap_script):
logger.debug("Escape RSL")
bootstrap_script = bootstrap_script.replace("\"", "\"\"")
return bootstrap_script
def __escape_pbs(self, bootstrap_script):
logger.debug("Escape PBS")
bootstrap_script = "\'" + bootstrap_script + "\'"
return bootstrap_script
def __escape_ssh(self, bootstrap_script):
logger.debug("Escape SSH")
bootstrap_script = bootstrap_script.replace("\"", "\\\"")
bootstrap_script = bootstrap_script.replace("\'", "\\\"")
bootstrap_script = "\"" + bootstrap_script + "\""
return bootstrap_script
def __escape_bliss(self, bootstrap_script):
logger.debug("Escape Bliss")
#bootstrap_script = bootstrap_script.replace("\'", "\"")
#bootstrap_script = "\'" + bootstrap_script+ "\'"
bootstrap_script = bootstrap_script.replace('"', '\\"')
bootstrap_script = '"' + bootstrap_script + '"'
return bootstrap_script
def __parse_pilot_url(self, pilot_url):
#pdb.set_trace()
pilot_saga_url = SAGAUrl(pilot_url)
dbtype = pilot_saga_url.query
coordination = pilot_url[:pilot_url.index("bigjob")]
if dbtype != None:
coordination = os.path.join(coordination, "?" + dbtype)
pilot_url = pilot_saga_url.path[1:]
#dbtype = None
#coordination = pilot_url[:pilot_url.index("bigjob")]
#pilot_url = pilot_url[pilot_url.find("bigjob"):]
#if pilot_url.find("/") > 0:
# comp = pilot_url.split("/")
# pilot_url = comp[0]
# if comp[1].find("dbtype")>0:
# dbtype=comp[1][comp[1].find("dbtype"):]
#if dbtype!=None:
# coordination = os.path.join(coordination, "?"+dbtype)
logger.debug("Parsed URL - Coordination: %s Pilot: %s" %
(coordination, pilot_url))
return coordination, pilot_url
def __has_finished(self, state):
state = state.lower()
if state == "done" or state == "failed" or state == "canceled":
return True
else:
return False
def __parse_url(self, url):
try:
surl = SAGAUrl(url)
host = surl.host
port = surl.port
username = surl.username
password = surl.password
query = surl.query
if query != None and query.endswith("/"):
query = query[:-1]
scheme = "%s://" % surl.scheme
except:
""" Fallback URL parser based on Python urlparse library """
logger.error("URL %s could not be parsed" % (url))
traceback.print_exc(file=sys.stderr)
result = urlparse.urlparse(url)
logger.debug("Result: " + str(result))
host = result.hostname
#host = None
port = result.port
username = result.username
password = result.password
scheme = "%s://" % result.scheme
if host == None:
logger.debug("Python 2.6 fallback")
if url.find("/", len(scheme)) > 0:
host = url[len(scheme):url.find("/", len(scheme))]
else:
host = url[len(scheme):]
if host.find(":") > 1:
logger.debug(host)
comp = host.split(":")
host = comp[0]
port = int(comp[1])
if url.find("?") > 0:
query = url[url.find("?") + 1:]
else:
query = None
logger.debug("%s %s %s" % (scheme, host, port))
return scheme, username, password, host, port, query
def __get_bj_id(self, pilot_url):
start = pilot_url.index("bj-")
end = pilot_url.index(":", start)
return pilot_url[start:end]
def __init_coordination(self, coordination_url):
if (coordination_url.startswith("advert://")
or coordination_url.startswith("sqlasyncadvert://")):
try:
from coordination.bigjob_coordination_advert import bigjob_coordination
logger.debug("Utilizing ADVERT Backend")
except:
logger.error("Advert Backend could not be loaded")
elif (coordination_url.startswith("redis://")):
try:
from coordination.bigjob_coordination_redis import bigjob_coordination
logger.debug("Utilizing Redis Backend")
except:
logger.error("Error loading pyredis.")
elif (coordination_url.startswith("tcp://")):
try:
from coordination.bigjob_coordination_zmq import bigjob_coordination
logger.debug("Utilizing ZMQ Backend")
except:
logger.error(
"ZMQ Backend not found. Please install ZeroMQ (http://www.zeromq.org/intro:get-the-software) and "
+ "PYZMQ (http://zeromq.github.com/pyzmq/)")
else:
logger.error("No suitable coordination backend found.")
logger.debug("Parsing URL: " + coordination_url)
scheme, username, password, host, port, dbtype = self.__parse_url(
coordination_url)
if port == -1:
port = None
coordination = bigjob_coordination(server=host,
server_port=port,
username=username,
password=password,
dbtype=dbtype,
url_prefix=scheme)
return coordination
def __get_bigjob_working_dir(self):
if self.working_directory.find(
self.uuid) != -1: # working directory already contains BJ id
return self.working_directory
else:
return os.path.join(self.working_directory, self.uuid)
def __get_subjob_working_dir(self, sj_id):
base_url = self.bigjob_working_directory_url
url = os.path.join(base_url, sj_id)
return url
###########################################################################
# File Management
def __initialize_pilot_data(self, service_url):
# initialize file adaptor
# Pilot Data API for File Management
if service_url.startswith("ssh:"):
logger.debug("Use SSH backend")
try:
from pilot.filemanagement.ssh_adaptor import SSHFileAdaptor
self.__filemanager = SSHFileAdaptor(service_url)
except:
logger.debug("SSH/Paramiko package not found.")
self.__print_traceback()
elif service_url.startswith("http:"):
logger.debug("Use WebHDFS backend")
try:
from pilot.filemanagement.webhdfs_adaptor import WebHDFSFileAdaptor
self.__filemanager = WebHDFSFileAdaptor(service_url)
except:
logger.debug("WebHDFS package not found.")
elif service_url.startswith("go:"):
logger.debug("Use Globus Online backend")
try:
from pilot.filemanagement.globusonline_adaptor import GlobusOnlineFileAdaptor
self.__filemanager = GlobusOnlineFileAdaptor(service_url)
except:
logger.debug("Globus Online package not found.")
self.__print_traceback()
def __stage_files(self, filetransfers, target_url):
logger.debug("Stage: %s to %s" % (filetransfers, target_url))
if filetransfers == None:
return
if self.__filemanager:
self.__filemanager.create_remote_directory(target_url)
for i in filetransfers:
source_file = i
if i.find(">") > 0:
source_file = i[:i.find(">")].strip()
if source_file.startswith(
"ssh://") == False and source_file.startswith(
"go://") == False:
logger.error(
"Staging of file: %s not supported. Please use URL in form ssh://<filename>"
% source_file)
continue
target_url_full = os.path.join(target_url,
os.path.basename(source_file))
logger.debug("Stage: %s to %s" % (source_file, target_url_full))
#self.__third_party_transfer(source_file, target_url_full)
if self.__filemanager:
self.__filemanager.transfer(source_file, target_url_full)
def __get_launch_method(self, hostname, user=None):
""" returns desired execution method: ssh, aprun """
if user == None: user = self.__discover_ssh_user(hostname)
host = ""
if user != None and user != "":
logger.debug("discovered user: "******"@" + hostname
else:
host = hostname
gsissh_available = False
try:
cmd = "gsissh " + host + " /bin/date"
logger.debug("Execute: " + cmd)
gsissh_available = (subprocess.call(cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE) == 0)
except:
pass
ssh_available = False
try:
cmd = "ssh " + host + " /bin/date"
logger.debug("Execute: " + cmd)
ssh_available = (subprocess.call(cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE) == 0)
except:
pass
launch_method = "ssh"
if ssh_available == False and gsissh_available == True:
launch_method = "gsissh"
else:
launch_method = "ssh"
logger.info("SSH: %r GSISSH: %r Use: %s" %
(ssh_available, gsissh_available, launch_method))
return launch_method
def __discover_ssh_user(self, hostname):
# discover username
user = None
ssh_config = os.path.join(os.path.expanduser("~"), ".ssh/config")
ssh_config_file = open(ssh_config, "r")
lines = ssh_config_file.readlines()
for i in range(0, len(lines)):
line = lines[i]
if line.find(hostname) > 0:
for k in range(i + 1, len(lines)):
sub_line = lines[k]
if sub_line.startswith(
" ") == True and sub_line.startswith("\t") == True:
break # configuration for next host
elif sub_line.find("User") != -1:
stripped_sub_line = sub_line.strip()
user = stripped_sub_line.split()[1]
break
ssh_config_file.close()
return user
def __print_traceback(self):
exc_type, exc_value, exc_traceback = sys.exc_info()
logger.debug("*** print_exception:",
exc_info=(exc_type, exc_value, exc_traceback))
#traceback.print_exception(exc_type, exc_value, exc_traceback,
# limit=2, file=sys.stdout)
def __repr__(self):
return self.pilot_url
def __del__(self):
""" BJ is not cancelled when object terminates
Application can reconnect to BJ via pilot url later on"""
pass
class bigjob(api.base.bigjob):
''' BigJob: Class for managing pilot jobs:
Example:
bj = bigjob("redis://localhost")
bj.start_pilot_job("fork://localhost")
..
bj.cancel()
'''
__APPLICATION_NAME="bigjob"
def __init__(self,
coordination_url="advert://localhost/?dbtype=sqlite3",
pilot_url=None):
""" Initializes BigJob's coordination system
advert://localhost (SAGA/Advert SQLITE)
advert://advert.cct.lsu.edu:8080 (SAGA/Advert POSTGRESQL)
redis://localhost:6379 (Redis at localhost)
tcp://localhost (ZMQ)
The following formats for pilot_url are supported:
1.) Including root path at distributed coordination service:
redis://localhost/bigjob:bj-1c3816f0-ad5f-11e1-b326-109addae22a3:localhost
This path is returned when call bigjob.get_url()
2.) BigJob unique ID:
bigjob:bj-1c3816f0-ad5f-11e1-b326-109addae22a3:localhost
"""
self.coordination_url = coordination_url
if self.coordination_url==None:
logger.error("Coordination URL not set. Exiting BigJob.")
#self.launch_method=""
self.__filemanager=None
# restore existing BJ or initialize new BJ
if pilot_url!=None:
logger.debug("Reconnect to BJ: %s"%pilot_url)
if pilot_url.startswith("bigjob:"):
self.pilot_url=pilot_url
else:
self.coordination_url, self.pilot_url = self.__parse_pilot_url(pilot_url)
self.uuid = self.__get_bj_id(pilot_url)
self.app_url = self.__APPLICATION_NAME +":" + str(self.uuid)
self.job = None
self.working_directory = None
# Coordination subsystem must be initialized before get_state_detail
self.coordination = self.__init_coordination(self.coordination_url)
self.state=self.get_state_detail()
_pilot_url_dict[self.pilot_url]=self
else:
self.coordination = self.__init_coordination(self.coordination_url)
self.uuid = "bj-" + str(get_uuid())
logger.debug("init BigJob w/: " + coordination_url)
self.app_url =self. __APPLICATION_NAME +":" + str(self.uuid)
self.state=Unknown
self.pilot_url=""
self.job = None
self.working_directory = None
logger.debug("initialized BigJob: " + self.app_url)
def start_pilot_job(self,
lrms_url,
number_nodes=1,
queue=None,
project=None,
working_directory=None,
userproxy=None,
walltime=None,
processes_per_node=1,
filetransfers=None,
external_queue="",
pilot_compute_description=None):
""" Start a batch job (using SAGA Job API) at resource manager. Currently, the following resource manager are supported:
fork://localhost/ (Default Job Adaptor
gram://qb1.loni.org/jobmanager-pbs (Globus Adaptor)
pbspro://localhost (PBS Pro Adaptor)
"""
if self.job != None:
raise BigJobError("One BigJob already active. Please stop BigJob first.")
return
##############################################################################
# initialization of coordination and communication subsystem
# Communication & Coordination initialization
lrms_saga_url = SAGAUrl(lrms_url)
self.url = lrms_saga_url
self.pilot_url = self.app_url + ":" + lrms_saga_url.host
self.number_nodes=int(number_nodes)*int(processes_per_node)
# Store references to BJ in global dict
_pilot_url_dict[self.pilot_url]=self
_pilot_url_dict[external_queue]=self
logger.debug("create pilot job entry on backend server: " + self.pilot_url)
self.coordination.set_pilot_state(self.pilot_url, str(Unknown), False)
if pilot_compute_description==None:
pilot_compute_description={"service_url": lrms_url,
"number_of_processes": number_nodes,
"processes_per_node": processes_per_node,
"working_directory": working_directory}
self.coordination.set_pilot_description(self.pilot_url, pilot_compute_description)
logger.debug("set pilot state to: " + str(Unknown))
# Create Job Service (Default: SAGA Job Service, alternative Job Services supported)
self.js =None
if lrms_saga_url.scheme=="gce+ssh":
self.js = GCEService(lrms_saga_url, pilot_compute_description)
elif lrms_saga_url.scheme=="ec2+ssh" or lrms_saga_url.scheme=="euca+ssh" \
or lrms_saga_url.scheme=="nova+ssh":
self.js = EC2Service(lrms_saga_url, pilot_compute_description)
elif lrms_saga_url.scheme=="slurm+ssh":
self.js = SlurmService(lrms_saga_url, pilot_compute_description)
else:
self.js = SAGAJobService(lrms_saga_url)
##############################################################################
# create job description
jd = SAGAJobDescription()
# Attempt to create working directory (e.g. in local scenario)
if working_directory != None:
if not os.path.isdir(working_directory) \
and (lrms_saga_url.scheme.startswith("fork") or lrms_saga_url.scheme.startswith("condor")) \
and working_directory.startswith("go:")==False:
os.mkdir(working_directory)
self.working_directory = working_directory
else:
# if no working dir is set assume use home directory
# will fail if home directory is not the same on remote machine
# but this is just a guess to avoid failing
#self.working_directory = os.path.expanduser("~")
self.working_directory = ""
if queue != None:
jd.queue = queue
if project !=None:
jd.project=project
if walltime!=None:
logger.debug("setting walltime to: " + str(walltime))
if is_bliss:
jd.wall_time_limit=int(walltime)
else:
jd.wall_time_limit=str(walltime)
##############################################################################
# File Management and Stage-In
# Determine whether target machine use gsissh or ssh to logon.
# logger.debug("Detect launch method for: " + lrms_saga_url.host)
# self.launch_method = self.__get_launch_method(lrms_saga_url.host,lrms_saga_url.username)
self.bigjob_working_directory_url=""
if lrms_saga_url.scheme.startswith("gce") or lrms_saga_url.scheme.startswith("ec2")\
or lrms_saga_url.scheme.startswith("euca") or lrms_saga_url.scheme.startswith("nova"):
logger.debug("File Staging for Cloud Instances currently not supported.")
elif lrms_saga_url.scheme.startswith("condor") == True:
logger.debug("Using Condor file staging")
else:
# build target url for working directory
# this will also create the remote directory for the BJ
# Fallback if working directory is not a valid URL
if not (self.working_directory.startswith("go:") or self.working_directory.startswith("ssh://")):
if lrms_saga_url.username!=None and lrms_saga_url.username!="":
self.bigjob_working_directory_url = "ssh://" + lrms_saga_url.username + "@" + lrms_saga_url.host + "/" + self.__get_bigjob_working_dir()
else:
self.bigjob_working_directory_url = "ssh://" + lrms_saga_url.host + "/" + self.__get_bigjob_working_dir()
elif self.working_directory.startswith("go:"):
self.bigjob_working_directory_url=os.path.join(self.working_directory, self.uuid)
else:
# working directory is a valid file staging URL
self.bigjob_working_directory_url=self.working_directory
# initialize file manager that takes care of file movement and directory creation
if self.__filemanager==None:
self.__initialize_pilot_data(self.bigjob_working_directory_url) # determines the url
if self.__filemanager != None and not self.working_directory.startswith("/"):
self.working_directory = self.__filemanager.get_path(self.bigjob_working_directory_url)
# determine working directory of bigjob
# if a remote sandbox can be created via ssh => create a own dir for each bj job id
# otherwise use specified working directory
logger.debug("BigJob working directory: %s"%self.bigjob_working_directory_url)
if self.__filemanager!=None and self.__filemanager.create_remote_directory(self.bigjob_working_directory_url)==True:
self.working_directory = self.__get_bigjob_working_dir()
self.__stage_files(filetransfers, self.bigjob_working_directory_url)
else:
logger.warn("No file staging adaptor found.")
logger.debug("BJ Working Directory: %s", self.working_directory)
if lrms_saga_url.scheme.startswith("condor")==False:
jd.working_directory = self.working_directory
else:
jd.working_directory=""
##############################################################################
# Create and process BJ bootstrap script
bootstrap_script = self.__generate_bootstrap_script(
self.coordination.get_address(),
self.pilot_url, # Queue 1 used by this BJ object
external_queue # Queue 2 used by Pilot Compute Service
# or another external scheduler
)
logger.debug("Adaptor specific modifications: " + str(lrms_saga_url.scheme))
if is_bliss and lrms_saga_url.scheme.startswith("condor")==False:
bootstrap_script = self.__escape_bliss(bootstrap_script)
else:
if lrms_saga_url.scheme == "gram":
bootstrap_script = self.__escape_rsl(bootstrap_script)
elif lrms_saga_url.scheme == "pbspro" or lrms_saga_url.scheme=="xt5torque" or lrms_saga_url.scheme=="torque":
bootstrap_script = self.__escape_pbs(bootstrap_script)
elif lrms_saga_url.scheme == "ssh" and lrms_saga_url.scheme == "slurm+ssh":
bootstrap_script = self.__escape_ssh(bootstrap_script)
logger.debug(bootstrap_script)
# Define Agent Executable in Job description
# in Condor case bootstrap script is staged
# (Python app cannot be passed inline in Condor job description)
if lrms_saga_url.scheme.startswith("condor")==True:
bootstrap_script = self.__generate_bootstrap_script_from_binary(
self.coordination.get_address(),
self.pilot_url, # Queue 1 used by this BJ object
external_queue # Queue 2 used by Pilot Compute Service
# or another external scheduler
)
condor_bootstrap_filename = os.path.join("/tmp", "bootstrap-"+str(self.uuid))
condor_bootstrap_file = open(condor_bootstrap_filename, "w")
condor_bootstrap_file.write(bootstrap_script)
condor_bootstrap_file.close()
logger.debug("Using Condor - bootstrap file: " + condor_bootstrap_filename)
jd.executable = "/usr/bin/env"
jd.arguments = ["python", os.path.basename(condor_bootstrap_filename)]
if pilot_compute_description.has_key("candidate_hosts"):
jd.candidate_hosts = pilot_compute_description["candidate_hosts"]
bj_file_transfers = []
file_transfer_spec = condor_bootstrap_filename + " > " + os.path.basename(condor_bootstrap_filename)
bj_file_transfers.append(file_transfer_spec)
output_file_name = "output-" + str(self.uuid) + ".tar.gz"
#output_file_transfer_spec = os.path.join(self.working_directory, output_file_name) +" < " + output_file_name
output_file_transfer_spec = output_file_name +" < " + output_file_name
#output_file_transfer_spec = os.path.join(self.working_directory, "output.tar.gz") +" < output.tar.gz"
#logger.debug("Output transfer: " + output_file_transfer_spec)
#bj_file_transfers.append(output_file_transfer_spec)
if filetransfers != None:
for t in filetransfers:
bj_file_transfers.append(t)
logger.debug("Condor file transfers: " + str(bj_file_transfers))
jd.file_transfer = bj_file_transfers
else:
if is_bliss:
jd.total_cpu_count=int(number_nodes)
else:
jd.number_of_processes=str(number_nodes)
jd.processes_per_host=str(processes_per_node)
jd.spmd_variation = "single"
if pilot_compute_description!=None and pilot_compute_description.has_key("spmd_variation"):
jd.spmd_variation=pilot_compute_description["spmd_variation"]
jd.arguments = ["python", "-c", bootstrap_script]
jd.executable = "/usr/bin/env"
logger.debug("Working directory: " + jd.working_directory + " Job Description: " + str(jd))
jd.output = os.path.join(self.working_directory, "stdout-" + self.uuid + "-agent.txt")
jd.error = os.path.join(self.working_directory, "stderr-" + self.uuid + "-agent.txt")
##############################################################################
# Create and submit pilot job to job service
logger.debug("Creating pilot job with description: %s" % str(jd))
self.job = self.js.create_job(jd)
logger.debug("Submit pilot job to: " + str(lrms_saga_url))
self.job.run()
return self.pilot_url
def list_subjobs(self):
sj_list = self.coordination.get_jobs_of_pilot(self.pilot_url)
logger.debug(str(sj_list))
subjobs = []
for i in sj_list:
url = i
#if url.find("/")>0:
# url = url[url.find("bigjob"):]
# url = url.replace("/", ":")
#sj = subjob(coordination_url=self.coordination_url, subjob_url=url)
sj = subjob(subjob_url=url)
subjobs.append(sj.get_url())
return subjobs
def get_state(self):
""" duck typing for get_state of saga.job.job
state of saga job that is used to spawn the pilot agent
"""
return self.get_state_detail()
def get_state_detail(self):
""" internal state of BigJob agent """
try:
return self.coordination.get_pilot_state(self.pilot_url)["state"]
except:
return None
def get_url(self):
""" Get unique URL of big-job. This URL can be used to reconnect to BJ later, e.g.:
redis://localhost/bigjob:bj-1c3816f0-ad5f-11e1-b326-109addae22a3:localhost
"""
url = os.path.join(self.coordination.address,
self.pilot_url)
if self.coordination.dbtype!="" and self.coordination.dbtype!=None:
url = os.path.join(url, "?" + self.coordination.dbtype)
return url
def get_free_nodes(self):
jobs = self.coordination.get_jobs_of_pilot(self.pilot_url)
number_used_nodes=0
for i in jobs:
job_detail = self.coordination.get_job(i)
if job_detail != None and job_detail.has_key("state") == True\
and job_detail["state"]==str(Running):
job_np = "1"
if (job_detail["NumberOfProcesses"] == True):
job_np = job_detail["NumberOfProcesses"]
number_used_nodes=number_used_nodes + int(job_np)
return (self.number_nodes - number_used_nodes)
def cancel(self):
""" duck typing for cancel of saga.cpr.job and saga.job.job """
logger.debug("Cancel Pilot Job")
try:
if self.url.scheme.startswith("condor")==False:
self.job.cancel()
else:
pass
#logger.debug("Output files are being transfered to file: outpt.tar.gz. Please wait until transfer is complete.")
except:
pass
#traceback.print_stack()
try:
self._stop_pilot_job()
logger.debug("delete pilot job: " + str(self.pilot_url))
if _CLEANUP:
self.coordination.delete_pilot(self.pilot_url)
#os.remove(os.path.join("/tmp", "bootstrap-"+str(self.uuid)))
except:
pass
#traceback.print_stack()
logger.debug("Cancel Pilot Job finished")
def wait(self):
""" Waits for completion of all sub-jobs """
while 1:
jobs = self.coordination.get_jobs_of_pilot(self.pilot_url)
finish_counter=0
result_map = {}
for i in jobs:
# parse job id out of sj url
surl = SAGAUrl(i)
sj_id = surl.path
if sj_id.startswith("/"): sj_id = sj_id[1:]
state = str(self.coordination.get_job_state(sj_id))
#logger.debug("SJ: %s : State: %s"%(sj_id, str(state)))
#state = job_detail["state"]
if result_map.has_key(state)==False:
result_map[state]=1
else:
result_map[state] = result_map[state]+1
if self.__has_finished(state)==True:
finish_counter = finish_counter + 1
logger.debug("Total Jobs: %s States: %s"%(len(jobs), str(result_map)))
if finish_counter == len(jobs):
break
time.sleep(2)
###########################################################################
# internal and protected methods
def _stop_pilot_job(self):
""" mark in database entry of pilot-job as stopped """
try:
logger.debug("stop pilot job: " + self.pilot_url)
self.coordination.set_pilot_state(self.pilot_url, str(Done), True)
self.job=None
except:
pass
def _delete_subjob(self, job_url):
self.coordination.delete_job(job_url)
def _get_subjob_state(self, job_url):
logger.debug("Get subjob state: " + str(job_url))
return self.coordination.get_job_state(job_url)
def _get_subjob_details(self, job_url):
return self.coordination.get_job(job_url)
def _add_subjob(self, queue_url, jd, job_url, job_id):
logger.debug("add subjob to queue of PJ: " + str(queue_url))
for i in range(0,3):
try:
logger.debug("create dictionary for job description. Job-URL: " + job_url)
# put job description attributes to Coordination Service
job_dict = {}
# to accomendate current bug in bliss (Number of processes is not returned from list attributes)
job_dict["NumberOfProcesses"] = "1"
attributes = jd.list_attributes()
logger.debug("SJ Attributes: " + str(jd))
for i in attributes:
if jd.attribute_is_vector(i):
vector_attr = []
for j in jd.get_vector_attribute(i):
vector_attr.append(j)
job_dict[i]=vector_attr
else:
#logger.debug("Add attribute: " + str(i) + " Value: " + jd.get_attribute(i))
job_dict[i] = jd.get_attribute(i)
# Other pilot state information
job_dict["state"] = str(Unknown)
job_dict["job-id"] = str(job_id)
logger.debug("job dict: " + str(job_dict))
if job_dict.has_key("FileTransfer"):
files = job_dict["FileTransfer"]
sj_work_dir = self.__get_subjob_working_dir(job_id)
self.__stage_files(files, sj_work_dir)
#logger.debug("update job description at communication & coordination sub-system")
self.coordination.set_job(job_url, job_dict)
self.coordination.queue_job(queue_url, job_url)
break
except:
self.__print_traceback()
time.sleep(2)
def _get_subjob_url(self, subjob_url):
""" Get unique URL for a sub-job. This URL can be used to reconnect to SJ later, e.g.:
redis://localhost/bigjob:bj-9a9ba4d8-b162-11e1-9c42-109addae22a3:localhost:jobs:sj-6f44da6e-b178-11e1-bc99-109addae22a3
"""
url = subjob_url
if subjob_url.find("bigjob")==0:
url = os.path.join(self.coordination.address,
subjob_url)
if self.coordination.dbtype!="" and self.coordination.dbtype!=None:
url = os.path.join(url, "?" + self.coordination.dbtype)
return url
def __generate_bootstrap_script(self, coordination_host, coordination_namespace, external_coordination_namespace="", bigjob_home=None):
script = textwrap.dedent("""import sys
import os
import urllib
import sys
import time
start_time = time.time()
home = os.environ.get("HOME")
#print "Home: " + home
if home==None: home = os.getcwd()
BIGJOB_AGENT_DIR= os.path.join(home, ".bigjob")
if not os.path.exists(BIGJOB_AGENT_DIR): os.mkdir (BIGJOB_AGENT_DIR)
BIGJOB_PYTHON_DIR=BIGJOB_AGENT_DIR+"/python/"
if not os.path.exists(BIGJOB_PYTHON_DIR): os.mkdir(BIGJOB_PYTHON_DIR)
BOOTSTRAP_URL="https://raw.github.com/saga-project/BigJob/master/bootstrap/bigjob-bootstrap.py"
BOOTSTRAP_FILE=BIGJOB_AGENT_DIR+"/bigjob-bootstrap.py"
#ensure that BJ in .bigjob is upfront in sys.path
sys.path.insert(0, os.getcwd() + "/../")
p = list()
for i in sys.path:
if i.find(\".bigjob/python\")>1:
p.insert(0, i)
for i in p: sys.path.insert(0, i)
print "Python path: " + str(sys.path)
print "Python version: " + str(sys.version_info)
try: import saga
except: print "SAGA and SAGA Python Bindings not found.";
try: import bigjob.bigjob_agent
except:
print "BigJob not installed. Attempt to install it.";
opener = urllib.FancyURLopener({});
opener.retrieve(BOOTSTRAP_URL, BOOTSTRAP_FILE);
print "Execute: " + "python " + BOOTSTRAP_FILE + " " + BIGJOB_PYTHON_DIR
os.system("/usr/bin/env")
try:
os.system("python " + BOOTSTRAP_FILE + " " + BIGJOB_PYTHON_DIR);
activate_this = os.path.join(BIGJOB_PYTHON_DIR, "bin/activate_this.py");
execfile(activate_this, dict(__file__=activate_this))
except:
print "BJ installation failed. Trying system-level python (/usr/bin/python)";
os.system("/usr/bin/python " + BOOTSTRAP_FILE + " " + BIGJOB_PYTHON_DIR);
activate_this = os.path.join(BIGJOB_PYTHON_DIR, "bin/activate_this.py");
execfile(activate_this, dict(__file__=activate_this))
#try to import BJ once again
import bigjob.bigjob_agent
# execute bj agent
args = list()
args.append("bigjob_agent.py")
args.append(\"%s\")
args.append(\"%s\")
args.append(\"%s\")
print "Bootstrap time: " + str(time.time()-start_time)
print "Starting BigJob Agents with following args: " + str(args)
bigjob_agent = bigjob.bigjob_agent.bigjob_agent(args)
""" % (coordination_host, coordination_namespace, external_coordination_namespace))
return script
def __generate_bootstrap_script_from_binary(self, coordination_host, coordination_namespace,
external_coordination_namespace="",
bigjob_home=None):
script = textwrap.dedent("""import sys
import os
import urllib
import sys
import time
start_time = time.time()
home = os.environ.get("HOME")
#print "Home: " + home
if home==None: home = os.getcwd()
BIGJOB_AGENT_DIR= os.path.join(home, ".bigjob")
if not os.path.exists(BIGJOB_AGENT_DIR): os.mkdir (BIGJOB_AGENT_DIR)
BIGJOB_PYTHON_DIR=BIGJOB_AGENT_DIR+"/python/"
if not os.path.exists(BIGJOB_PYTHON_DIR): os.mkdir(BIGJOB_PYTHON_DIR)
BOOTSTRAP_URL="http://s3.amazonaws.com/bigjob/bigjob-Linux-x86_64.tar.gz"
BOOTSTRAP_FILE="bigjob-Linux-x86_64.tar.gz"
#ensure that BJ in .bigjob is upfront in sys.path
sys.path.insert(0, os.getcwd() + "/../")
#sys.path.insert(0, /User/luckow/.bigjob/python/lib")
#sys.path.insert(0, os.getcwd() + "/../../")
p = list()
for i in sys.path:
if i.find(\".bigjob/python\")>1:
p.insert(0, i)
for i in p: sys.path.insert(0, i)
print "Python path: " + str(sys.path)
print "Python version: " + str(sys.version_info)
try: import saga
except: print "SAGA and SAGA Python Bindings not found.";
try: import bigjob.bigjob_agent
except:
print "BigJob not installed. Attempt to install it.";
#opener = urllib.FancyURLopener({});
#ret = opener.retrieve(BOOTSTRAP_URL, BOOTSTRAP_FILE);
print "Download via wget"
os.system("wget " + BOOTSTRAP_URL)
os.system("rm -rf .bigjob")
print "Execute: " + "tar -xzf " + BOOTSTRAP_FILE
os.system("ls -lta")
try:
os.system("tar -xzf " + BOOTSTRAP_FILE);
os.system("ls -lta")
os.system(".bigjob/python/bin/python -c 'import bigjob; import bigjob.bigjob_agent; print bigjob.version; bigjob.bigjob_agent.bigjob_agent([\\"bigjob_agent.py\\", \\"%s\\", \\"%s\\", \\"%s\\"])'")
except:
print "BJ installation failed!";
""" % (coordination_host, coordination_namespace, external_coordination_namespace))
return script
def __escape_rsl(self, bootstrap_script):
logger.debug("Escape RSL")
bootstrap_script = bootstrap_script.replace("\"", "\"\"")
return bootstrap_script
def __escape_pbs(self, bootstrap_script):
logger.debug("Escape PBS")
bootstrap_script = "\'" + bootstrap_script+ "\'"
return bootstrap_script
def __escape_ssh(self, bootstrap_script):
logger.debug("Escape SSH")
bootstrap_script = bootstrap_script.replace("\"", "\\\"")
bootstrap_script = bootstrap_script.replace("\'", "\\\"")
bootstrap_script = "\"" + bootstrap_script+ "\""
return bootstrap_script
def __escape_bliss(self, bootstrap_script):
logger.debug("Escape Bliss")
#bootstrap_script = bootstrap_script.replace("\'", "\"")
#bootstrap_script = "\'" + bootstrap_script+ "\'"
bootstrap_script = bootstrap_script.replace('"','\\"')
bootstrap_script = '"' + bootstrap_script+ '"'
return bootstrap_script
def __parse_pilot_url(self, pilot_url):
#pdb.set_trace()
pilot_saga_url = SAGAUrl(pilot_url)
dbtype = pilot_saga_url.query
coordination = pilot_url[:pilot_url.index("bigjob")]
if dbtype!=None:
coordination = os.path.join(coordination, "?"+dbtype)
pilot_url = pilot_saga_url.path[1:]
#dbtype = None
#coordination = pilot_url[:pilot_url.index("bigjob")]
#pilot_url = pilot_url[pilot_url.find("bigjob"):]
#if pilot_url.find("/") > 0:
# comp = pilot_url.split("/")
# pilot_url = comp[0]
# if comp[1].find("dbtype")>0:
# dbtype=comp[1][comp[1].find("dbtype"):]
#if dbtype!=None:
# coordination = os.path.join(coordination, "?"+dbtype)
logger.debug("Parsed URL - Coordination: %s Pilot: %s"%(coordination, pilot_url))
return coordination, pilot_url
def __has_finished(self, state):
state = state.lower()
if state=="done" or state=="failed" or state=="canceled":
return True
else:
return False
def __parse_url(self, url):
try:
surl = SAGAUrl(url)
host = surl.host
port = surl.port
username = surl.username
password = surl.password
query = surl.query
if query!=None and query.endswith("/"):
query = query[:-1]
scheme = "%s://"%surl.scheme
except:
""" Fallback URL parser based on Python urlparse library """
logger.error("URL %s could not be parsed"%(url))
traceback.print_exc(file=sys.stderr)
result = urlparse.urlparse(url)
logger.debug("Result: " + str(result))
host = result.hostname
#host = None
port = result.port
username = result.username
password = result.password
scheme = "%s://"%result.scheme
if host==None:
logger.debug("Python 2.6 fallback")
if url.find("/", len(scheme)) > 0:
host = url[len(scheme):url.find("/", len(scheme))]
else:
host = url[len(scheme):]
if host.find(":")>1:
logger.debug(host)
comp = host.split(":")
host = comp[0]
port = int(comp[1])
if url.find("?")>0:
query = url[url.find("?")+1:]
else:
query = None
logger.debug("%s %s %s"%(scheme, host, port))
return scheme, username, password, host, port, query
def __get_bj_id(self, pilot_url):
start = pilot_url.index("bj-")
end =pilot_url.index(":", start)
return pilot_url[start:end]
def __init_coordination(self, coordination_url):
if(coordination_url.startswith("advert://") or coordination_url.startswith("sqlasyncadvert://")):
try:
from coordination.bigjob_coordination_advert import bigjob_coordination
logger.debug("Utilizing ADVERT Backend")
except:
logger.error("Advert Backend could not be loaded")
elif (coordination_url.startswith("redis://")):
try:
from coordination.bigjob_coordination_redis import bigjob_coordination
logger.debug("Utilizing Redis Backend")
except:
logger.error("Error loading pyredis.")
elif (coordination_url.startswith("tcp://")):
try:
from coordination.bigjob_coordination_zmq import bigjob_coordination
logger.debug("Utilizing ZMQ Backend")
except:
logger.error("ZMQ Backend not found. Please install ZeroMQ (http://www.zeromq.org/intro:get-the-software) and "
+"PYZMQ (http://zeromq.github.com/pyzmq/)")
else:
logger.error("No suitable coordination backend found.")
logger.debug("Parsing URL: " + coordination_url)
scheme, username, password, host, port, dbtype = self.__parse_url(coordination_url)
if port == -1:
port = None
coordination = bigjob_coordination(server=host, server_port=port, username=username,
password=password, dbtype=dbtype, url_prefix=scheme)
return coordination
def __get_bigjob_working_dir(self):
self.working_directory = os.path.abspath(self.working_directory)
if self.working_directory.find(self.uuid)!=-1: # working directory already contains BJ id
return self.working_directory
else:
return os.path.join(self.working_directory, self.uuid)
def __get_subjob_working_dir(self, sj_id):
base_url = self.bigjob_working_directory_url
url = os.path.join(base_url, sj_id)
return url
###########################################################################
# File Management
def __initialize_pilot_data(self, service_url):
# initialize file adaptor
# Pilot Data API for File Management
if service_url.startswith("ssh:"):
logger.debug("Use SSH backend")
try:
from pilot.filemanagement.ssh_adaptor import SSHFileAdaptor
self.__filemanager = SSHFileAdaptor(service_url)
except:
logger.debug("SSH package not found.")
self.__print_traceback()
elif service_url.startswith("http:"):
logger.debug("Use WebHDFS backend")
try:
from pilot.filemanagement.webhdfs_adaptor import WebHDFSFileAdaptor
self.__filemanager = WebHDFSFileAdaptor(service_url)
except:
logger.debug("WebHDFS package not found.")
elif service_url.startswith("go:"):
logger.debug("Use Globus Online backend")
try:
from pilot.filemanagement.globusonline_adaptor import GlobusOnlineFileAdaptor
self.__filemanager = GlobusOnlineFileAdaptor(service_url)
except:
logger.debug("Globus Online package not found.")
self.__print_traceback()
def __stage_files(self, filetransfers, target_url):
logger.debug("Stage: %s to %s"%(filetransfers, target_url))
if filetransfers==None:
return
if self.__filemanager:
self.__filemanager.create_remote_directory(target_url)
for i in filetransfers:
source_file=i
if i.find(">")>0:
source_file = i[:i.find(">")].strip()
if source_file.startswith("ssh://")==False and source_file.startswith("go://")==False:
logger.error("Staging of file: %s not supported. Please use URL in form ssh://<filename>"%source_file)
continue
target_url_full = os.path.join(target_url, os.path.basename(source_file))
logger.debug("Stage: %s to %s"%(source_file, target_url_full))
#self.__third_party_transfer(source_file, target_url_full)
if self.__filemanager:
self.__filemanager.transfer(source_file, target_url_full)
def __get_launch_method(self, hostname, user=None):
""" returns desired execution method: ssh, aprun """
if user == None: user = self.__discover_ssh_user(hostname)
host = ""
if user!=None and user!="":
logger.debug("discovered user: "******"@" + hostname
else:
host = hostname
gsissh_available = False
try:
cmd = "gsissh " + host + " /bin/date"
logger.debug("Execute: " + cmd)
gsissh_available = (subprocess.call(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)==0)
except:
pass
ssh_available = False
try:
cmd = "ssh " + host + " /bin/date"
logger.debug("Execute: " + cmd)
ssh_available = (subprocess.call(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)==0)
except:
pass
launch_method = "ssh"
if ssh_available == False and gsissh_available == True:
launch_method="gsissh"
else:
launch_method="ssh"
logger.info("SSH: %r GSISSH: %r Use: %s"%(ssh_available, gsissh_available, launch_method))
return launch_method
def __discover_ssh_user(self, hostname):
# discover username
user = None
ssh_config = os.path.join(os.path.expanduser("~"), ".ssh/config")
ssh_config_file = open(ssh_config, "r")
lines = ssh_config_file.readlines()
for i in range(0, len(lines)):
line = lines[i]
if line.find(hostname)>0:
for k in range(i + 1, len(lines)):
sub_line = lines[k]
if sub_line.startswith(" ")==True and sub_line.startswith("\t")==True:
break # configuration for next host
elif sub_line.find("User")!=-1:
stripped_sub_line = sub_line.strip()
user = stripped_sub_line.split()[1]
break
ssh_config_file.close()
return user
def __print_traceback(self):
exc_type, exc_value, exc_traceback = sys.exc_info()
logger.debug("*** print_exception:",
exc_info=(exc_type, exc_value, exc_traceback))
#traceback.print_exception(exc_type, exc_value, exc_traceback,
# limit=2, file=sys.stdout)
def __repr__(self):
return self.pilot_url
def __del__(self):
""" BJ is not cancelled when object terminates
Application can reconnect to BJ via pilot url later on"""
pass