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Changes ess_settings to contain a list of servers
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Also renamed it to ess-Settings throughout
Also using levels_ess from settings
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@alongd
alongd committed Mar 28, 2019
1 parent 36641a4 commit c21b4ef
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Showing 3 changed files with 153 additions and 127 deletions.
133 changes: 73 additions & 60 deletions arc/job/job.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
import logging

from arc.settings import arc_path, servers, submit_filename, delete_command, t_max_format,\
input_filename, output_filename, rotor_scan_resolution, list_available_nodes_command
input_filename, output_filename, rotor_scan_resolution, list_available_nodes_command, levels_ess
from arc.job.submit import submit_scripts
from arc.job.inputs import input_files
from arc.job.ssh import SSH_Client
Expand All @@ -24,7 +24,7 @@ class Job(object):
Attribute Type Description
================ =================== ===============================================================================
`project` ``str`` The project's name. Used for naming the directory.
`settings` ``dict`` A dictionary of available servers and software
`ess_settings` ``dict`` A dictionary of available ESS and a corresponding server list
`species_name` ``str`` The species/TS name. Used for naming the directory.
`charge` ``int`` The species net charge. Default is 0
`multiplicity` ``int`` The species multiplicity.
Expand Down Expand Up @@ -77,13 +77,13 @@ class Job(object):
The job ess (electronic structure software calculation) status is in job.job_status[0] and can be
either `initializing` / `running` / `errored: {error type / message}` / `unconverged` / `done`
"""
def __init__(self, project, settings, species_name, xyz, job_type, level_of_theory, multiplicity, project_directory,
def __init__(self, project, ess_settings, species_name, xyz, job_type, level_of_theory, multiplicity, project_directory,
charge=0, conformer=-1, fine=False, shift='', software=None, is_ts=False, scan='', pivots=None,
memory=1500, comments='', trsh='', scan_trsh='', ess_trsh_methods=None, initial_trsh=None, job_num=None,
job_server_name=None, job_name=None, job_id=None, server=None, initial_time=None, occ=None,
max_job_time=120, scan_res=None):
self.project = project
self.settings=settings
self.ess_settings = ess_settings
self.initial_time = initial_time
self.final_time = None
self.run_time = None
Expand Down Expand Up @@ -126,60 +126,72 @@ def __init__(self, project, settings, species_name, xyz, job_type, level_of_theo
self.software = self.software.lower()
else:
if job_type == 'orbitals':
if not 'qchem' in self.settings:
# currently we only have a script to print orbitals on QChem,
# could/should definately be elaborated to additional ESS
if 'qchem' not in self.ess_settings.keys():
logging.debug('Could not find the QChem software to compute molecular orbitals')
self.software = None
self.software = 'qchem'
if job_type == 'composite':
if not self.settings['gaussian']:
else:
self.software = 'qchem'
elif job_type == 'composite':
if not 'gaussian' not in self.ess_settings.keys():
raise JobError('Could not find the Gaussian software to run the composite method {0}'.format(
self.method))
self.software = 'gaussian'
elif job_type in ['conformer', 'opt', 'freq', 'optfreq', 'sp']:
if 'ccs' in self.method or 'cis' in self.method or 'pv' in self.basis_set:
if self.settings['molpro']:
self.software = 'molpro'
elif self.settings['gaussian']:
else:
# use the levels_ess dictionary from settings.py:
for ess, phrase_list in levels_ess.items():
for phrase in phrase_list:
if phrase in self.level_of_theory:
self.software = ess.lower()
if self.software is None:
# otherwise, deduce which software to use base on hard coded heuristics
if job_type in ['conformer', 'opt', 'freq', 'optfreq', 'sp']:
if 'ccs' in self.method or 'cis' in self.method or 'pv' in self.basis_set:
if 'molpro' in self.ess_settings.keys():
self.software = 'molpro'
elif 'gaussian' in self.ess_settings.keys():
self.software = 'gaussian'
elif 'qchem' in self.ess_settings.keys():
self.software = 'qchem'
elif 'b3lyp' in self.method:
if 'gaussian' in self.ess_settings.keys():
self.software = 'gaussian'
elif 'qchem' in self.ess_settings.keys():
self.software = 'qchem'
elif 'molpro' in self.ess_settings.keys():
self.software = 'molpro'
elif 'wb97xd' in self.method:
if not 'gaussian' in self.ess_settings.keys():
raise JobError('Could not find the Gaussian software to run {0}/{1}'.format(
self.method, self.basis_set))
self.software = 'gaussian'
elif self.settings['qchem']:
elif 'b97' in self.method or 'm06-2x' in self.method or 'def2' in self.basis_set:
if not 'qchem' in self.ess_settings.keys():
raise JobError('Could not find the QChem software to run {0}/{1}'.format(
self.method, self.basis_set))
self.software = 'qchem'
elif 'b3lyp' in self.method:
if self.settings['gaussian']:
elif job_type == 'scan':
if 'wb97xd' in self.method:
if not 'gaussian' in self.ess_settings.keys():
raise JobError('Could not find the Gaussian software to run {0}/{1}'.format(
self.method, self.basis_set))
self.software = 'gaussian'
elif self.settings['qchem']:
elif 'b97' in self.method or 'm06-2x' in self.method or 'def2' in self.basis_set:
if not 'qchem' in self.ess_settings.keys():
raise JobError('Could not find the QChem software to run {0}/{1}'.format(
self.method, self.basis_set))
self.software = 'qchem'
elif self.settings['molpro']:
self.software = 'molpro'
elif 'wb97xd' in self.method:
if not self.settings['gaussian']:
raise JobError('Could not find the Gaussian software to run {0}/{1}'.format(
self.method, self.basis_set))
self.software = 'gaussian'
elif 'b97' in self.method or 'm06-2x' in self.method or 'def2' in self.basis_set:
if not self.settings['qchem']:
raise JobError('Could not find the QChem software to run {0}/{1}'.format(
self.method, self.basis_set))
self.software = 'qchem'
elif job_type == 'scan':
if 'wb97xd' in self.method:
if not self.settings['gaussian']:
raise JobError('Could not find the Gaussian software to run {0}/{1}'.format(
self.method, self.basis_set))
self.software = 'gaussian'
elif 'b97' in self.method or 'm06-2x' in self.method or 'def2' in self.basis_set:
if not self.settings['qchem']:
raise JobError('Could not find the QChem software to run {0}/{1}'.format(
self.method, self.basis_set))
self.software = 'qchem'
else:
if self.settings['gaussian']:
self.software = 'gaussian'
else:
self.software = 'qchem'
elif job_type in ['gsm', 'irc']:
if not self.settings['gaussian']:
raise JobError('Could not find the Gaussian software to run {0}'.format(job_type))
if 'gaussian' in self.ess_settings.keys():
self.software = 'gaussian'
else:
self.software = 'qchem'
elif job_type in ['gsm', 'irc']:
if not 'gaussian' in self.ess_settings.keys():
raise JobError('Could not find the Gaussian software to run {0}'.format(job_type))
if self.software is None:
# if still no software was determined, just try by order, if exists: Gaussian > QChem > Molpro
logging.error('job_num: {0}'.format(self.job_num))
logging.error('ess_trsh_methods: {0}'.format(self.ess_trsh_methods))
logging.error('trsh: {0}'.format(self.trsh))
Expand All @@ -190,18 +202,18 @@ def __init__(self, project, settings, species_name, xyz, job_type, level_of_theo
logging.error('method: {0}'.format(self.method))
logging.error('basis_set: {0}'.format(self.basis_set))
logging.error('Could not determine software for job {0}'.format(self.job_name))
if self.settings['gaussian']:
if 'gaussian' in self.ess_settings.keys():
logging.error('Setting it to gaussian')
self.software = 'gaussian'
elif self.settings['qchem']:
elif 'qchem' in self.ess_settings.keys():
logging.error('Setting it to qchem')
self.software = 'qchem'
elif self.settings['molpro']:
elif 'molpro' in self.ess_settings.keys():
logging.error('Setting it to molpro')
self.software = 'molpro'

if self.settings['ssh']:
self.server = server if server is not None else self.settings[self.software]
if self.ess_settings['ssh']:
self.server = server if server is not None else self.ess_settings[self.software][0]
else:
self.server = None

Expand Down Expand Up @@ -370,7 +382,7 @@ def write_submit_script(self):
os.makedirs(self.local_path)
with open(os.path.join(self.local_path, submit_filename[servers[self.server]['cluster_soft']]), 'wb') as f:
f.write(self.submit)
if self.settings['ssh']:
if self.ess_settings['ssh']:
self._upload_submit_file()

def write_input_file(self):
Expand Down Expand Up @@ -464,7 +476,8 @@ def write_input_file(self):
else:
job_type_1 = 'opt'
if 'PRINT_ORBITALS' not in self.trsh:
self.trsh += '\n PRINT_ORBITALS TRUE\n GUI 2'
self.trsh += '\n NBO TRUE\n RUN_NBO6 TRUE\n ' \
'PRINT_ORBITALS TRUE\n GUI 2'

elif self.job_type == 'freq':
if self.software == 'gaussian':
Expand Down Expand Up @@ -600,7 +613,7 @@ def write_input_file(self):
os.makedirs(self.local_path)
with open(os.path.join(self.local_path, input_filename[self.software]), 'wb') as f:
f.write(self.input)
if self.settings['ssh']:
if self.ess_settings['ssh']:
self._upload_input_file()

def _upload_submit_file(self):
Expand Down Expand Up @@ -644,7 +657,7 @@ def run(self):
self.write_submit_script()
logging.debug('writing input file...')
self.write_input_file()
if self.settings['ssh']:
if self.ess_settings['ssh']:
ssh = SSH_Client(self.server)
logging.debug('submitting job...')
# submit_job returns job server status and job server id
Expand All @@ -658,7 +671,7 @@ def run(self):

def delete(self):
logging.debug('Deleting job {name} for {label}'.format(name=self.job_name, label=self.species_name))
if self.settings['ssh']:
if self.ess_settings['ssh']:
ssh = SSH_Client(self.server)
logging.debug('deleting job...')
ssh.delete_job(self.job_id)
Expand Down Expand Up @@ -751,7 +764,7 @@ def _check_job_server_status(self):
"""
Possible statuses: `initializing`, `running`, `errored on node xx`, `done`
"""
if self.settings['ssh']:
if self.ess_settings['ssh']:
ssh = SSH_Client(self.server)
return ssh.check_job_status(self.job_id)

Expand All @@ -764,7 +777,7 @@ def _check_job_ess_status(self):
os.remove(self.local_path_to_output_file)
if os.path.exists(self.local_path_to_orbitals_file):
os.remove(self.local_path_to_orbitals_file)
if self.settings['ssh']:
if self.ess_settings['ssh']:
self._download_output_file()
with open(self.local_path_to_output_file, 'rb') as f:
lines = f.readlines()
Expand Down Expand Up @@ -856,7 +869,7 @@ def _check_job_ess_status(self):
return 'errored: Unknown reason'

def troubleshoot_server(self):
if self.settings['ssh']:
if self.ess_settings['ssh']:
if servers[self.server]['cluster_soft'].lower() == 'oge':
# delete present server run
logging.error('Job {name} has server status "{stat}" on {server}. Troubleshooting by changing node.'.format(
Expand Down
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