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 __init__(self, **kwargs):
self.defaults = {'copyback' : ['*.py',
'*.dat',
'*.eta',
'*.pot',
'*.cfg',
'output'],
'program' : 'SurfDiff',
'configfile' : None,
'cmd_args' : None,
'seed' : 'MDsim'}
PythonScriptAgent.__init__(self, **kwargs)
# creating the precommand
if self.params['configfile'] is not None:
self.params['configfile'] = 'configfile="-i {}"'.format(self.params['configfile'])
self.precmd.add(self.params['configfile'])
cmd_args = self.params['cmd_args']
if cmd_args is None:
flags = ''
else:
flags = ''
for arg, val in cmd_args:
if arg in ['io.seed',
'misc.walltime']:
continue
flags +='--{}="{}" '.format(arg, val)
flags += '--io.seed="{}" '.format(self.params['seed'])
flags += '--misc.walltime="{}"'.format(walltime_sec = get_sec(self._tp_walltime()))
self.precmd.add("flags='{}'".format(flags))
# remove the old command first
self.cmd.remove(-1)
self.cmd.add('$python_bin $pyflags $program $configfile $flags')