def sub_jobs_submit( jd_executable, job_type, affinity , subjobs_start, number_of_jobs, jd_number_of_processes):
jd = saga.job.description()
for i in range(subjobs_start, int(number_of_jobs) + int(subjobs_start) ):
#pick the executble different for preparing read files
if jd_executable == "bfast":
jd_executable_use = bfast_exe[affinity] + "/bfast"
elif jd_executable == "solid2fastq":
jd_executable_use = bfast_exe[affinity] + "/solid2fastq"
else:
jd_executable_use = jd_executable
# create job description
uowd = troy.uow_description()
print jd_executable_use
uowd.set_attribute('Executable', jd_executable_use)
uowd.set_attribute('NumberOfProcesses', str(jd_number_of_processes))
uowd.set_attribute('SPMDVariation', 'single')
# choose the job arguments based on type of job
if job_type == "reads":
uowd.set_vector_attribute('Arguments', \
["-n", "%s" %(bfast_reads_num[affinity]),
"-o", "%s/%s.%s" %(bfast_reads_dir[affinity],shortreads_name ,dare_uuid),
"%s/*.csfasta"%(bfast_raw_reads_dir[affinity]),
"%s/*.qual" %(bfast_raw_reads_dir[affinity])])
elif job_type == "count":
uowd.set_vector_attribute('Arguments', \
[" -altr" , "%s/%s.%s.*" %(bfast_reads_dir[affinity],shortreads_name ,dare_uuid),
"|", "/usr/bin/wc", "-l" ,
">", "%s/out.%s.txt"%(bfast_raw_reads_dir[affinity], dare_uuid)])
elif job_type == "matches":
uowd.set_vector_attribute('Arguments', \
["match",
"-f", "%s/%s.fa" %( bfast_ref_genome_dir[affinity], refgenome) ,
"-A", encoding_space,
"-r", "%s/%s.%s.fastq"%(bfast_reads_dir[affinity], shortreads_name,i+1),
"-n" ,str(jd_number_of_processes) ,
"-T" , "%s" %(bfast_tmp_dir[affinity]),
">" , "%s/bfast.matches.file.%s.%s.%s.bmf" %(bfast_matches_dir[affinity],dare_uuid,refgenome,i+1)])
elif job_type == "localalign":
uowd.set_vector_attribute('Arguments', \
["localalign",
"-f", "%s/%s.fa"%(bfast_ref_genome_dir[affinity], refgenome),
"-A", encoding_space,
"-m", "%s/bfast.matches.file.%s.%s.%s.bmf"%(bfast_matches_dir[affinity],dare_uuid,refgenome,i+1),
">", "%s/bfast.aligned.file.%s.%s.%s.baf" %(bfast_localalign_dir[affinity],dare_uuid,refgenome,i+1)])
elif job_type == "postprocess":
uowd.set_vector_attribute('Arguments', \
["postprocess",
"-f", "%s/%s.fa" %(bfast_ref_genome_dir[affinity], refgenome),
"-A", encoding_space,
"-i", "%s/bfast.aligned.file.%s.%s.%s.baf" %(bfast_localalign_dir[affinity],dare_uuid,refgenome,i+1),
">", "%s/bfast.postprocess.file.%s.%s.%s.sam" %(bfast_postprocess_dir[affinity],dare_uuid,refgenome,i+1)])
elif job_type == "hostname":
uowd.set_vector_attribute('Arguments', \
['-f', '>', 'hostname%s.txt'%i, ';', '/bin/sleep', '15'])
else:
uowd.set_vector_attribute('Arguments', [""])
#jd.environment = ["affinity=affinity%s"%(affinity)]
print "affinity%s"%(affinity)
uowd.set_attribute('WorkingDirectory', work_dir[affinity])
uowd.set_attribute('Output', os.path.join(work_dir[affinity], "stdout_" + job_type + \
"-"+ str(dare_uuid)+"-"+ str(i) + ".txt"))
uowd.set_attribute('Error', os.path.join(work_dir[affinity], "stderr_"+ job_type + \
"-"+str(dare_uuid)+ "-"+str(i) + ".txt"))
uows.append(bj.assign_uow(uowd))
print "Submited sub-job " + "%d"%i + "."
logger.info( job_type + "subjob " + str(i))
logger.info( "jd.number_of_processes " + str(jd_number_of_processes))
print "jd.arguments"
logger.info("affinity%s"%(affinity))
logger.info( "jd exec " + jd_executable_use)
def sub_jobs_submit(jd_executable, job_type, affinity, subjobs_start,
number_of_jobs, jd_number_of_processes):
jd = saga.job.description()
for i in range(subjobs_start, int(number_of_jobs) + int(subjobs_start)):
#pick the executble different for preparing read files
if jd_executable == "bfast":
jd_executable_use = bfast_exe[affinity] + "/bfast"
elif jd_executable == "solid2fastq":
jd_executable_use = bfast_exe[affinity] + "/solid2fastq"
else:
jd_executable_use = jd_executable
# create job description
uowd = troy.uow_description()
print(jd_executable_use)
uowd.set_attribute('Executable', jd_executable_use)
uowd.set_attribute('NumberOfProcesses', str(jd_number_of_processes))
uowd.set_attribute('SPMDVariation', 'single')
# choose the job arguments based on type of job
if job_type == "reads":
uowd.set_vector_attribute('Arguments', \
["-n", "%s" %(bfast_reads_num[affinity]),
"-o", "%s/%s.%s" %(bfast_reads_dir[affinity],shortreads_name ,dare_uuid),
"%s/*.csfasta"%(bfast_raw_reads_dir[affinity]),
"%s/*.qual" %(bfast_raw_reads_dir[affinity])])
elif job_type == "count":
uowd.set_vector_attribute('Arguments', \
[" -altr" , "%s/%s.%s.*" %(bfast_reads_dir[affinity],shortreads_name ,dare_uuid),
"|", "/usr/bin/wc", "-l" ,
">", "%s/out.%s.txt"%(bfast_raw_reads_dir[affinity], dare_uuid)])
elif job_type == "matches":
uowd.set_vector_attribute('Arguments', \
["match",
"-f", "%s/%s.fa" %( bfast_ref_genome_dir[affinity], refgenome) ,
"-A", encoding_space,
"-r", "%s/%s.%s.fastq"%(bfast_reads_dir[affinity], shortreads_name,i+1),
"-n" ,str(jd_number_of_processes) ,
"-T" , "%s" %(bfast_tmp_dir[affinity]),
">" , "%s/bfast.matches.file.%s.%s.%s.bmf" %(bfast_matches_dir[affinity],dare_uuid,refgenome,i+1)])
elif job_type == "localalign":
uowd.set_vector_attribute('Arguments', \
["localalign",
"-f", "%s/%s.fa"%(bfast_ref_genome_dir[affinity], refgenome),
"-A", encoding_space,
"-m", "%s/bfast.matches.file.%s.%s.%s.bmf"%(bfast_matches_dir[affinity],dare_uuid,refgenome,i+1),
">", "%s/bfast.aligned.file.%s.%s.%s.baf" %(bfast_localalign_dir[affinity],dare_uuid,refgenome,i+1)])
elif job_type == "postprocess":
uowd.set_vector_attribute('Arguments', \
["postprocess",
"-f", "%s/%s.fa" %(bfast_ref_genome_dir[affinity], refgenome),
"-A", encoding_space,
"-i", "%s/bfast.aligned.file.%s.%s.%s.baf" %(bfast_localalign_dir[affinity],dare_uuid,refgenome,i+1),
">", "%s/bfast.postprocess.file.%s.%s.%s.sam" %(bfast_postprocess_dir[affinity],dare_uuid,refgenome,i+1)])
elif job_type == "hostname":
uowd.set_vector_attribute('Arguments', \
['-f', '>', 'hostname%s.txt'%i, ';', '/bin/sleep', '15'])
else:
uowd.set_vector_attribute('Arguments', [""])
#jd.environment = ["affinity=affinity%s"%(affinity)]
print("affinity%s" % (affinity))
uowd.set_attribute('WorkingDirectory', work_dir[affinity])
uowd.set_attribute('Output', os.path.join(work_dir[affinity], "stdout_" + job_type + \
"-"+ str(dare_uuid)+"-"+ str(i) + ".txt"))
uowd.set_attribute('Error', os.path.join(work_dir[affinity], "stderr_"+ job_type + \
"-"+str(dare_uuid)+ "-"+str(i) + ".txt"))
uows.append(bj.assign_uow(uowd))
print("Submited sub-job " + "%d" % i + ".")
logger.info(job_type + "subjob " + str(i))
logger.info("jd.number_of_processes " + str(jd_number_of_processes))
print("jd.arguments")
logger.info("affinity%s" % (affinity))
logger.info("jd exec " + jd_executable_use)
jd.set_attribute('ProcessesPerHost', '1') # Ignored?
jd.set_attribute('Queue', 'workq')
jd.set_vector_attribute('JobProject', ['randomstring'])
jd.set_attribute('WorkingDirectory', DEPLOYMENT_LOCATION)
jd.set_attribute('WallTimeLimit', '12')
bj.add_resource(troy.bigjob_type.SAGA, RESOURCE_URL, jd)
print "Pilot Job/BigJob URL: ", bj.list_resources()
#######################################################################
# Submit UoW through BigJob
uows = []
WORKING_DIRECTORY = '/work/marksant/saga'
for i in range (15):
uowd = troy.uow_description()
uowd.set_attribute('Executable', '/bin/hostname')
uowd.set_attribute('NumberOfProcesses', '1')
uowd.set_attribute('SPMDVariation', 'single')
uowd.set_attribute('WorkingDirectory', WORKING_DIRECTORY)
uowd.set_attribute('Output', 'stdout.txt')
uowd.set_attribute('Error', 'stderr.txt')
uowd.set_vector_attribute('Arguments', \
['-f', '>', 'hostname%s.txt'%i, ';', '/bin/sleep', '60'])
uows.append(bj.assign_uow(uowd))
# busy wait for completion
while 1:
uow_states = set()
for i in range(len(uows)):
