def check_postproc(self):
"""check for input completeness"""
# additionally check for the postprogram
postprogram = self._tp_postprogram()
# check if the program is executable
if not which(postprogram):
# check all additional paths specified
if all([
which(postprogram, path=str(path)) is None
for path in self.environment.values()
]):
raise Warning(
'Cannot find <postprogram> by invoking `which()`. If you did not do fancy bash aliasing, your job will crash!'
)
def check_consistency(self):
"""check for input completeness"""
if self.params['aims_outfile'] is None:
self.params['aims_outfile'] = self.params['job_name'] + '.out'
# make sure that we copy back the outfile
if not self.params['aims_outfile'] in self.params['copyback']:
self.params['copyback'] += [self.params['aims_outfile']]
program = self._tp_program()
walltime_sec = get_sec(self._tp_walltime())
# check if the program is executable
if not which(program):
# check all additional paths specified
if all([
which(program, path=str(path)) is None
for path in self.environment.values()
]):
raise Warning(
'Cannot find <program> by invoking `which()`. If you did not do fancy bash aliasing, your job will crash!'
)
control_path = os.path.join(self.params['job_dir'], "control.in")
geometry_path = os.path.join(self.params['job_dir'], "geometry.in")
if not os.path.exists(geometry_path):
raise Warning('No geometry.in in <job_dir>. Your job will crash!')
if not os.path.exists(control_path):
raise Warning('No control.in in <job_dir>. Your job will crash!')
else:
# check for runtime flag
with open(control_path, 'r') as controlfile:
found = False
for line in controlfile:
if 'walltime' in line.lower():
found = True
if not found:
with open(control_path, 'a') as controlfile:
# down-scale walltime limit to make sure that
# the job + ensuing IO can finish.
if walltime_sec < 24 * 60 * 60:
scale = .9
else:
scale = .95
controlfile.write(
'\nwalltime {} # added by submit script'.format(
int(walltime_sec * scale)))
def check_consistency(self):
"""check for input completeness"""
program = self._tp_program()
# check if the program is executable
if not which(program):
# check all additional paths specified
if all([
which(program, path=str(path)) is None
for path in self.environment.values()
]):
raise Warning(
'Cannot find <program> by invoking `which()`. If you did not do fancy bash aliasing, your job will crash!'
)
walltime_sec = get_sec(self._tp_walltime())
seed = self.params['seed']
cellfile_path = os.path.join(self.params['job_dir'], seed + '.cell')
if not os.path.exists(cellfile_path):
raise Warning('No cellfile in <job_dir>. Your job will crash!')
paramfile_path = os.path.join(self.params['job_dir'], seed + '.param')
if not os.path.exists(paramfile_path):
raise Warning('No paramfile in <job_dir>. Your job will crash!')
else:
# check for runtime flag
with open(paramfile_path, 'r') as paramfile:
found = False
for line in paramfile:
if 'run_time' in line.lower():
found = True
if not found:
with open(paramfile_path, 'a') as paramfile:
# down-scale walltime limit to make sure that
# the job + ensuing IO can finish.
if walltime_sec < 24 * 60 * 60:
scale = .9
else:
scale = .95
paramfile.write(
'\nRUN_TIME : {} # added by submit script'.format(
int(walltime_sec * scale)))
def check_consistency(self):
"""check for input completeness"""
program = self._tp_program()
# check if the program is executable
if not which(program):
# check all additional paths specified
if all([
which(program, path=str(path)) is None
for path in self.environment.values()
]):
raise Warning(
'Cannot find <program> by invoking `which()`. If you did not do fancy bash aliasing, your job will crash!'
)
seed = self.params['seed']
cellfile_path = os.path.join(self.params['job_dir'], seed + '.cell')
if not os.path.exists(cellfile_path):
raise Warning('No cellfile in <job_dir>. Your job will crash!')
paramfile_path = os.path.join(self.params['job_dir'], seed + '.param')
if not os.path.exists(paramfile_path):
raise Warning('No paramfile in <job_dir>. Your job will crash!')
import os
import unittest
import shutil
import tempfile
from rtools.submitagents.workstation import castep, WorkstationAgent
try:
from rtools.filesys import which
castep_installed = True
program = 'castep'
if not which(program):
castep_installed = False
else:
castep_installed = True
except ImportError:
castep_installed = False
class TestBaseArthurAgent(unittest.TestCase):
"""
Test some functionality of the base agent class.
"""
def setUp(self):
self.tmpdir = tempfile.mkdtemp()
self.foldername = os.path.basename(self.tmpdir)
def test_check_arg_works_for_nonexisting_arg(self):
with self.assertRaises(RuntimeError):
WorkstationAgent(job_dir=self.tmpdir, pbsnamee='myjob')
class TestCastepAgent(unittest.TestCase):
"""