def _download_output_file(self):
ssh = SSH_Client(self.server)
remote_file_path = os.path.join(self.remote_path, output_filename[self.software])
local_file_path = os.path.join(self.local_path, 'output.out')
ssh.download_file(remote_file_path=remote_file_path, local_file_path=local_file_path)
if self.job_type == 'orbitals':
remote_file_path = os.path.join(self.remote_path, 'input.FChk')
local_file_path = os.path.join(self.local_path_to_orbitals_file)
ssh.download_file(remote_file_path=remote_file_path, local_file_path=local_file_path)
self.final_time = ssh.get_last_modified_time(remote_file_path=remote_file_path)
self.determine_run_time()
if not os.path.isfile(local_file_path):
raise JobError('output file for {0} was not downloaded properly'.format(self.job_name))
def _get_additional_job_info(self):
"""
Download the additional information of stdout and stderr from the server
"""
lines1, lines2 = list(), list()
content = ''
ssh = SSH_Client(self.server)
cluster_soft = servers[self.server]['cluster_soft'].lower()
if cluster_soft in ['oge', 'sge']:
remote_file_path = os.path.join(self.remote_path, 'out.txt')
local_file_path1 = os.path.join(self.local_path, 'out.txt')
try:
ssh.download_file(remote_file_path=remote_file_path, local_file_path=local_file_path1)
except (TypeError, IOError) as e:
logging.warning('Got the following error when trying to download out.txt for {0}:'.format(self.job_name))
logging.warning(e.message)
remote_file_path = os.path.join(self.remote_path, 'err.txt')
local_file_path2 = os.path.join(self.local_path, 'err.txt')
try:
ssh.download_file(remote_file_path=remote_file_path, local_file_path=local_file_path2)
except (TypeError, IOError) as e:
logging.warning('Got the following error when trying to download err.txt for {0}:'.format(self.job_name))
logging.warning(e.message)
if os.path.isfile(local_file_path1):
with open(local_file_path1, 'r') as f:
lines1 = f.readlines()
if os.path.isfile(local_file_path2):
with open(local_file_path2, 'r') as f:
lines2 = f.readlines()
content += ''.join([line for line in lines1])
content += '\n'
content += ''.join([line for line in lines2])
elif cluster_soft == 'slurm':
respond = ssh.send_command_to_server(command='ls -alF', remote_path=self.remote_path)
files = list()
for line in respond[0][0].splitlines():
files.append(line.split()[-1])
for file in files:
if 'slurm' in file and '.out' in file:
remote_file_path = os.path.join(self.remote_path, file)
local_file_path = os.path.join(self.local_path, file)
try:
ssh.download_file(remote_file_path=remote_file_path, local_file_path=local_file_path)
except (TypeError, IOError) as e:
logging.warning('Got the following error when trying to download {0} for {1}:'.format(
file, self.job_name))
logging.warning(e.message)
if os.path.isfile(local_file_path):
with open(local_file_path, 'r') as f:
lines1 = f.readlines()
content += ''.join([line for line in lines1])
content += '\n'
return content