def launch_resources_agents(self,resource_list, resources_used_info):
try:
# submit via mj abstraction
## start the big job agents
resource_list = []
i =0
print all_resources_used[resource]["resource_url"]
for resource in resources_used:
num_nodes= calculate_nodes(resources_used_info[resource]["cores_per_node"],\
resources_job_count[i],\
resources_app[resource][cores])
resource_list.append({ \
"resource_url" : resources_used_info[resource]["resource_url"] , \
"walltime": resources_used_info[resource]["walltime"] , \
"number_nodes" : str(1), \
"cores_per_node" : resources_used_info[resource]["cores_per_node"], \
"allocation" : resources_used_info[resource]["allocation"], \
"queue" : resources_used_info[resource]["queue"], \
"bigjob_agent": resources_used_info[resource]["bigjob_agent"], \
"userproxy": resources_used_info[resource]["proxy"], \
"working_directory": resources_used_info[resource]["work_dir"],\
"affinity" : resources_used_info[resource]["affinity"} \
)
logger.info("resource_url" + resources_url[i])
logger.info("affinity%s"%(i))
print "Create manyjob service "
#create multiple manyjobs should be changed by bfast affinity implementation
i = i+1
#decide type of bigjob to use here
resources_service = many_job_affinity.many_job_service(resource_list, \
DARE_ADVERT_HOST)
except:
traceback.print_exc(file=sys.stdout)
terminate_resources_agents(resources_service)
return resources_service
def terminate_resources_agents(self,resource_service):
try:
resource_service.cancel()
except:
pass
class subjob_handler(api.base.subjob_handler):
def __init__():
pass
def has_finished(state):
state = state.lower()
if state=="done" or state=="failed" or state=="canceled":
return True
else:
return False
def create_subjob( job_description, jd_arguments, affinity, handler_resource):
# create job description
jd = saga.job.description()
jd.executable = str(job_description["jd_executable"]
jd.number_of_processes = str(job_description["jd_number_of_processes"]
jd.spmd_variation = job_description["jd_spmd_variation"]
# choose the job arguments based on type of job
jd.arguments = jd_arguments
jd.environment = ["affinity=%s"%(affinity)]
jd.working_directory = job_description["jd_work_dir"]
jd.output = job_description["jd_output"]
jd.error = job_description["jd_error"]
logger.info( "subjob " + str(i))
logger.info( "jd.number_of_processes " + str(jd.number_of_processes))
for item in jd.arguments:
logger.info( "jd.arguments" + item)
logger.info("%s"%(affinity))
logger.info( "jd exec" + jd.executable)
return jd
def submit_subjob(jd, handler_resource):
try:
subjob = handler_resource.create_job(jd)
subjob.run()
print "Submited sub-job " + "%d"%i + "."
return subjob
except:
traceback.print_exc(file=sys.stdout)
try:
handler_resource.cancel()
except:
pass
def add_subjob_to_list(subjob):
jobs.append(subjob)
job_start_times[subjob]=time.time()
job_states[subjob] = subjob.get_state()
def monitor_subjobs(number_of_jobs):
logger.info("********All Jobs submitted********" + str(number_of_jobs))
while 1:
finish_counter=0
result_map = {}
for i in range(0, number_of_jobs):
old_state = job_states[jobs[i]]
state = jobs[i].get_state()
if result_map.has_key(state) == False:
result_map[state]=0
result_map[state] = result_map[state]+1
#print "counter: " + str(i) + " job: " + str(jobs[i]) + " state: " + state
if old_state != state:
logger.info("Job " + str(jobs[i]) + " changed from: " + old_state + \
" to " + state)
if old_state != state and has_finished(state)==True:
logger.info("Job: " + str(jobs[i]) + " Runtime: " + \
str(time.time()-job_start_times[jobs[i]]) + " s.")
if has_finished(state)==True:
finish_counter = finish_counter + 1
job_states[jobs[i]]=state
logger.info("Current states: " + str(result_map))
time.sleep(5)
logger.info("Current states: " + str(result_map))
if finish_counter == number_of_jobs:
break
class file_handler(api.base.file_handler)
def file_stager(source_url, dest_url):
logger.info("Now I am tranferring the files from %s to %s"%(source_url, dest_url))
#fgeuca for clouds
if dest_url.startswith("fgeuca"):
try:
#for cloud files
cmd = "scp -r -i /path/to/smaddi2.private %s %s"%(source_url, dest_url)
os.system(cmd)
except saga.exception, e:
error_msg = "File stage in failed : from "+ source_url + " to "+ dest_url
else:
try:
cmd = "globus-url-copy -cd %s %s"%(source_url, dest_url)
os.system(cmd)
except saga.exception, e:
error_msg = "File stage in failed : from "+ source_url + " to "+ dest_url
return None
if __name__ == "__main__":
config = {}
#define app name
DARE_APP_NAME="BFAST"
DARE_UUID = uuid.uuid1()
DARE_ADVERT_HOST = "advert.cct.lsu.edu"
# parse options
parser = optparse.OptionParser()
parser.add_option("-j", "--job-conf", dest="job_conf", help="job configuration file")
(options, args) = parser.parse_args()
#read job conf file
job_info = read_job_conf(options.job_conf)
job_id = job_info['job_id']
resources_used = []
resources_used = job_info['resources_use'].replace(' ','').split(',')
resources_used_job_count = job_info['resources_job_count'].replace(' ','').split(',')
resources_used_walltime = job_info['resources_walltime'].replace(' ','').split(',')
#read resource_info conf file
resources_used_info = read_conf(job_info['resources_info_filename'],resources_used)
#read resource_app_info conf file
resources_used_app_info = read_conf(job_info['resources_app_info_filename'],resources_used)
#get the current working directory
cwd = os.getcwd()
#define log filename
logger = set_logger(DARE_APP_NAME, LOG_FILENAME)
logger.info("Reading conf files is done ")
logger.info("Job id is " + str(job_id) )
logger.info("Machine used are ")
for i in ranger(resource_used):
logger.info("resources_used[i]")
#launch manyjob affinity
job_service = launch_manyjob(self,resource_list)
#create subjob description
jd = create_subjob("/bin/date" , 1, "single", [""], "LONI", \
"/work/smaddi2/", "/work/smaddi2/stdout-1-now.out", \
"/work/smaddi2/stderr-1-now.out")
#submit subjob
submit_subjob(jd,job_service)
# wait for submitted subjobs to get to state done
wait_for_subjobs(1)
terminate_resource_agents(job_service)
def add_resources(self,resource_list, resources_used_info):
try:
# submit via mj abstraction
## start the big job agents
resource_list = []
i =0
print all_resources_used[resource]["resource_url"]
for resource in resources_used:
num_nodes= calculate_nodes(resources_used_info[resource]["cores_per_node"],\
resources_job_count[i],\
resources_app[resource][cores])
resource_list.append({ \
"resource_url" : resources_used_info[resource]["resource_url"] , \
"walltime": resources_used_info[resource]["walltime"] , \
"number_nodes" : str(1), \
"cores_per_node" : resources_used_info[resource]["cores_per_node"], \
"allocation" : resources_used_info[resource]["allocation"], \
"queue" : resources_used_info[resource]["queue"], \
"bigjob_agent": resources_used_info[resource]["bigjob_agent"], \
"userproxy": resources_used_info[resource]["proxy"], \
"working_directory": resources_used_info[resource]["work_dir"],\
"affinity" : resources_used_info[resource]["affinity"} \
)
logger.info("resource_url" + resources_url[i])
logger.info("affinity%s"%(i))
print "Create manyjob service "
#create multiple manyjobs should be changed by bfast affinity implementation
i = i+1
#decide type of bigjob to use here
resources_service = many_job_affinity.many_job_service(resource_list, \
DARE_ADVERT_HOST)
except:
traceback.print_exc(file=sys.stdout)
terminate_resources_agents(resources_service)
return resources_service
def terminate_resources(self,resource_service):
try:
resource_service.cancel()
except:
pass
class subjob_handler(api.base.subjob_handler):
def __init__():
pass
def has_finished(state):
state = state.lower()
if state=="done" or state=="failed" or state=="canceled":
return True
else:
return False
def create_subjob( job_description, jd_arguments, affinity, handler_resource):
# create job description
jd = saga.job.description()
jd.executable = str(job_description["jd_executable"]
jd.number_of_processes = str(job_description["jd_number_of_processes"]
jd.spmd_variation = job_description["jd_spmd_variation"]
# choose the job arguments based on type of job
jd.arguments = jd_arguments
jd.environment = ["affinity=%s"%(affinity)]
jd.working_directory = job_description["jd_work_dir"]
jd.output = job_description["jd_output"]
jd.error = job_description["jd_error"]
logger.info( "subjob " + str(i))
logger.info( "jd.number_of_processes " + str(jd.number_of_processes))
for item in jd.arguments:
logger.info( "jd.arguments" + item)
logger.info("%s"%(affinity))
logger.info( "jd exec" + jd.executable)
return jd
def submit_subjob(jd, handler_resource):
try:
subjob = handler_resource.create_job(jd)
subjob.run()
print "Submited sub-job " + "%d"%i + "."
return subjob
except:
traceback.print_exc(file=sys.stdout)
try:
handler_resource.cancel()
except:
pass
def add_subjob_to_list(subjob):
jobs.append(subjob)
job_start_times[subjob]=time.time()
job_states[subjob] = subjob.get_state()
def monitor_subjobs(number_of_jobs):
logger.info("********All Jobs submitted********" + str(number_of_jobs))
while 1:
finish_counter=0
result_map = {}
for i in range(0, number_of_jobs):
old_state = job_states[jobs[i]]
state = jobs[i].get_state()
if result_map.has_key(state) == False:
result_map[state]=0
result_map[state] = result_map[state]+1
#print "counter: " + str(i) + " job: " + str(jobs[i]) + " state: " + state
if old_state != state:
logger.info("Job " + str(jobs[i]) + " changed from: " + old_state + \
" to " + state)
if old_state != state and has_finished(state)==True:
logger.info("Job: " + str(jobs[i]) + " Runtime: " + \
str(time.time()-job_start_times[jobs[i]]) + " s.")
if has_finished(state)==True:
finish_counter = finish_counter + 1
job_states[jobs[i]]=state
logger.info("Current states: " + str(result_map))
time.sleep(5)
logger.info("Current states: " + str(result_map))
if finish_counter == number_of_jobs:
break
class file_handler(api.base.file_handler)
def file_stager(source_url, dest_url):
logger.info("Now I am tranferring the files from %s to %s"%(source_url, dest_url))
#fgeuca for clouds
if dest_url.startswith("fgeuca"):
try:
#for cloud files
cmd = "scp -r -i /path/to/smaddi2.private %s %s"%(source_url, dest_url)
os.system(cmd)
except saga.exception, e:
error_msg = "File stage in failed : from "+ source_url + " to "+ dest_url
else:
try:
cmd = "globus-url-copy -cd %s %s"%(source_url, dest_url)
os.system(cmd)
except saga.exception, e:
error_msg = "File stage in failed : from "+ source_url + " to "+ dest_url
return None
