def write_batch_script(self, n):
"""Instantiate and write the batch script to the work_dir."""
self.context['n'] = n
self.context['queue'] = self.queue
print self.context
# first priority is batch_template if set
if self.batch_template_file and not self.batch_template:
# second priority is batch_template_file
with open(self.batch_template_file) as f:
self.batch_template = f.read()
if not self.batch_template:
# third (last) priority is default_template
self.batch_template = self.default_template
regex = re.compile(self.job_array_regexp)
# print regex.search(self.batch_template)
if not regex.search(self.batch_template):
self.log.info("adding job array settings to batch script")
firstline, rest = self.batch_template.split('\n',1)
self.batch_template = u'\n'.join([firstline, self.job_array_template, rest])
regex = re.compile(self.queue_regexp)
# print regex.search(self.batch_template)
if self.queue and not regex.search(self.batch_template):
self.log.info("adding PBS queue settings to batch script")
firstline, rest = self.batch_template.split('\n',1)
self.batch_template = u'\n'.join([firstline, self.queue_template, rest])
script_as_string = Itpl.itplns(self.batch_template, self.context)
self.log.info('Writing instantiated batch script: %s' % self.batch_file)
with open(self.batch_file, 'w') as f:
f.write(script_as_string)
os.chmod(self.batch_file, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR)
def write_batch_script(self, n):
"""Instantiate and write the batch script to the work_dir."""
self.context['n'] = n
script_as_string = Itpl.itplns(self.batch_template, self.context)
log.msg('Writing instantiated batch script: %s' % self.batch_file)
f = open(self.batch_file, 'w')
f.write(script_as_string)
f.close()
def write_batch_script(self, n):
"""Instantiate and write the batch script to the work_dir."""
self.context['n'] = n
script_as_string = Itpl.itplns(self.batch_template, self.context)
log.msg('Writing instantiated batch script: %s' % self.batch_file)
f = open(self.batch_file, 'w')
f.write(script_as_string)
f.close()
def write_batch_script(self, n):
self.context['n'] = n
template = open(self.template_file, 'r').read()
log.msg('Using template for batch script: %s' % self.template_file)
script_as_string = Itpl.itplns(template, self.context)
log.msg('Writing instantiated batch script: %s' % self.batch_file)
f = open(self.batch_file,'w')
f.write(script_as_string)
f.close()
def write_batch_script(self, n):
self.context['n'] = n
template = open(self.template_file, 'r').read()
log.msg('Using template for batch script: %s' % self.template_file)
script_as_string = Itpl.itplns(template, self.context)
log.msg('Writing instantiated batch script: %s' % self.batch_file)
f = open(self.batch_file, 'w')
f.write(script_as_string)
f.close()
def write_batch_script(self, n):
"""Instantiate and write the batch script to the work_dir."""
self.context['n'] = n
self.context['queue'] = self.queue
print self.context
# first priority is batch_template if set
if self.batch_template_file and not self.batch_template:
# second priority is batch_template_file
with open(self.batch_template_file) as f:
self.batch_template = f.read()
if not self.batch_template:
# third (last) priority is default_template
self.batch_template = self.default_template
regex = re.compile(self.job_array_regexp)
# print regex.search(self.batch_template)
if not regex.search(self.batch_template):
self.log.info("adding job array settings to batch script")
firstline, rest = self.batch_template.split('\n', 1)
self.batch_template = u'\n'.join(
[firstline, self.job_array_template, rest])
regex = re.compile(self.queue_regexp)
# print regex.search(self.batch_template)
if self.queue and not regex.search(self.batch_template):
self.log.info("adding PBS queue settings to batch script")
firstline, rest = self.batch_template.split('\n', 1)
self.batch_template = u'\n'.join(
[firstline, self.queue_template, rest])
script_as_string = Itpl.itplns(self.batch_template, self.context)
self.log.info('Writing instantiated batch script: %s' %
self.batch_file)
with open(self.batch_file, 'w') as f:
f.write(script_as_string)
os.chmod(self.batch_file, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR)
