def __init__(self, out_path, exe_path, params, time=10080,
priority=1, connection=None, verbose=False,
test=False, env='BaseTrial.yml'):
self._connection = None
if connection:
self.connection = connection
self.test = test
self.verbose = verbose
self.out_path = out_path
self.exe_path = exe_path
self.id_ = None
self.priority = priority
self.time = time
if isinstance(params, dict):
params = sorted(list(params.iteritems()))
self.params = sorted(params)
if verbose:
print self.params
sha1 = hashlib.sha1(str((self.exe_path, self.params)))
self.hash_path = path(sha1.hexdigest())
env_file = path('./environments') / path(env)
self.wrap_path = path('./')
if env_file.isfile():
env = yaml.load(open(env_file))
self.env = env
resolve_env_vars(env)
if self.verbose:
print 'outpath before sub ', self.out_path
self.out_path = resolve(env, self.out_path)
self.wrap_path = resolve(env, Trial.MANAGER)
self.python_path = resolve(env, Trial.WORK) / 'local/bin/python'
elif verbose:
print 'No Enviroment path found'
if self.verbose:
print 'exe path, out path, ', self.exe_path, self.out_path
def submit(self):
# set the PATH environment
dir_ = self.out_path / self.hash_path
if self.test:
test = '--test '
else:
test = ''
if test:
print 'setting time to 60 mins for test'
self.time = 60
work_path = resolve(self.env, Trial.WORK)
if self.verbose:
print 'work path = ', work_path
command = "LD_LIBRARY_PATH=%s/local/lib PATH=%s\n sqsub %s -r %d -o %s %s %s %s" % (
work_path,
SharcNetTrial.PATH + ":/home/%s/bin" %self.connection.get_username(),
test, self.time, str(dir_/path(Trial.LOG)),
self.python_path,
str(self.wrap_path / path(Trial.WRAPPER)), str(dir_))
if self.verbose:
print 'Command = ', command
stdin, stdout, stderr = self.connection.exec_command(command)
output = [line for line in stdout]
errors = [line for line in stderr]
for line in output:
match = re.search(pattern='jobid\s+(?P<job>\d+)', string=line)
if match:
self.id_ = int(match.groupdict()['job'])
if self.verbose:
print 'self.id = ', self.id_
return output, errors