def submit_job(self, job_type, settings, path_out, nr_items=1,
batch_size=1, version=DEFAULT_VERSION):
path_out_settings = join(path_out, 'cluster')
makedirs(path_out_settings)
filename_settings = join(path_out_settings, 'settings.conf')
f = file(filename_settings, 'w')
f.write(settings)
f.close()
args = ['-s', filename_settings]
# adjust the number of job items according to the batch size
nr_items = int(math.ceil(float(nr_items)/batch_size))
is_bulk_job = True #if nr_items > 1 else False
jt = self._session.createJobTemplate()
jt = cecog_job_template(jt, path_out, args, version,
batch_size, is_bulk_job)
if is_bulk_job:
job_id = self._session.runBulkJobs(jt, 1, nr_items, 1)
else:
job_id = self._session.runJob(jt)
print job_id
return job_id
def cecog_job_template(jt, path_out, args, version, batch_size=1,
is_bulk_job=False):
job_name = 'CellCognition'
base_path = join(VERSIONS_PATH, version)
batchpy = join(base_path, 'bin', 'cecog_batch.py')
# I want the almost the same environment as for the gateway!
pypath = join(base_path, 'lib', 'python2.7', 'site-packages')
if os.environ.has_key('PYTHONPATH'):
os.environ["PYTHONPATH"] = pypath+os.pathsep+os.environ["PYTHONPATH"]
else:
os.putenv("PYTHONPATH", pypath)
jt.jobName = job_name
jt.workingDirectory = os.environ['HOME']
print jt.workingDirectory
pybin = 'python'
if os.environ.has_key('PYTHON_BIN'):
pybin = os.environ['PYTHON_BIN']
jt.jobEnvironment = os.environ
print jt.jobEnvironment
jt.remoteCommand = pybin
print jt.remoteCommand
jt.args = [batchpy] + args
jt.joinFiles = True
jt.nativeSpecification = os.environ['JOB_PARAMS']
path_out_cluster = join(path_out, 'cluster', 'log')
makedirs(path_out_cluster)
path_out_cluster = ':' + path_out_cluster
if is_bulk_job:
jt.outputPath = path_out_cluster
# FIXME: another DRMAA hack: the PARAMETRIC_INDEX
# is NOT resolved in args!
# workaround for older batch scripts that don't use argparse module
if version >= "1.7":
jt.args += ['--cluster-index', 'SGE_TASK_ID',
'--batch-size', str(batch_size)]
else:
jt.args += ['--cluster_index', 'SGE_TASK_ID',
'--batch_size', str(batch_size)]
else:
jt.outputPath = path_out_cluster
return jt
