def get_queues_info(self):
logging.debug("Parsing tree of %s" % self.sge_file)
fileutils.check_empty_file(self.sge_file)
tree, root = self.sge_stat_maker.tree, self.sge_stat_maker.root
qstatq_list = self._extract_queues('queue_info/Queue-List', root)
total_running_jobs = sum([d['run'] for d in qstatq_list])
logging.info('Total running jobs found: %s' % total_running_jobs)
for d in qstatq_list:
d['run'] = str(d['run'])
d['queued'] = str(d['queued'])
total_queued_jobs = self._get_total_queued_jobs(
'job_info/job_list', root)
qstatq_list.append({
'run': '0',
'queued': total_queued_jobs,
'queue_name': 'Pending',
'state': 'Q',
'lm': '0'
})
logging.debug('qstatq_list contains %s elements' % len(qstatq_list))
# TODO: check validity. 'state' shouldnt just be 'Q'!
logging.debug("Closing %s" % self.sge_file)
return total_running_jobs, int(eval(
str(total_queued_jobs))), qstatq_list
def extract_qstat(self, orig_file):
try:
fileutils.check_empty_file(orig_file)
except fileutils.FileEmptyError:
all_qstat_values = []
else:
all_qstat_values = list()
with open(orig_file, 'r') as fin:
_ = fin.readline() # header
fin.readline()
line = fin.readline()
re_match_positions = ('job_id', 'user', 'state', 'queue_name'
) # was: (1, 5, 7, 8), (1, 4, 5, 8)
try: # first qstat line determines which format qstat follows.
re_search = self.user_q_search
qstat_values = self._process_qstat_line(
re_search, line, re_match_positions)
all_qstat_values.append(qstat_values)
# unused: _job_nr, _ce_name, _name, _time_use = m.group(2), m.group(3), m.group(4), m.group(6)
except AttributeError: # this means 'prior' exists in qstat, it's another format
re_search = self.user_q_search_prior
qstat_values = self._process_qstat_line(
re_search, line, re_match_positions)
all_qstat_values.append(qstat_values)
# unused: _prior, _name, _submit, _start_at, _queue_domain, _slots, _ja_taskID =
# m.group(2), m.group(3), m.group(6), m.group(7), m.group(9), m.group(10), m.group(11)
# hence the rest of the lines should follow either try's or except's same format
for line in fin:
qstat_values = self._process_qstat_line(
re_search, line, re_match_positions)
all_qstat_values.append(qstat_values)
return all_qstat_values
def extract_qstat(self, orig_file):
try:
fileutils.check_empty_file(orig_file)
except fileutils.FileEmptyError:
logging.error('File %s seems to be empty.' % orig_file)
all_qstat_values = []
else:
all_qstat_values = list()
with open(orig_file, 'r') as fin:
_ = fin.readline() # header
fin.readline()
line = fin.readline()
re_match_positions = ('job_id', 'user', 'state', 'queue_name') # was: (1, 5, 7, 8), (1, 4, 5, 8)
try: # first qstat line determines which format qstat follows.
re_search = self.user_q_search
qstat_values = self._process_qstat_line(re_search, line, re_match_positions)
# unused: _job_nr, _ce_name, _name, _time_use = m.group(2), m.group(3), m.group(4), m.group(6)
except AttributeError: # this means 'prior' exists in qstat, it's another format
re_search = self.user_q_search_prior
qstat_values = self._process_qstat_line(re_search, line, re_match_positions)
# unused: _prior, _name, _submit, _start_at, _queue_domain, _slots, _ja_taskID =
# m.group(2), m.group(3), m.group(6), m.group(7), m.group(9), m.group(10), m.group(11)
finally:
all_qstat_values.append(qstat_values)
# hence the rest of the lines should follow either try's or except's same format
for line in fin:
qstat_values = self._process_qstat_line(re_search, line, re_match_positions)
all_qstat_values.append(qstat_values)
return all_qstat_values
def extract_qstat(self, orig_file):
try:
fileutils.check_empty_file(orig_file)
except fileutils.FileEmptyError:
logging.error('File %s seems to be empty.' % orig_file)
all_qstat_values = []
else:
all_qstat_values = list()
with open(orig_file, 'r') as fin:
_ = fin.readline() # header
fin.readline()
line = fin.readline()
re_match_positions = ('job_id', 'user', 'state', 'queue_name'
) # was: (1, 5, 7, 8), (1, 4, 5, 8)
re_search = self.user_q_search
qstat_values = self._process_qstat_line(
re_search, line, re_match_positions)
all_qstat_values.append(qstat_values)
# hence the rest of the lines should follow either try's or except's same format
for line in fin:
qstat_values = self._process_qstat_line(
re_search, line, re_match_positions)
all_qstat_values.append(qstat_values)
return all_qstat_values
def extract_qstatq(self, orig_file):
"""
reads QSTATQ_ORIG_FN sequentially and returns useful data
Searches for lines in the following format:
biomed -- -- 72:00:00 -- 31 0 -- E R
(except for the last line, which contains two sums and is parsed separately)
"""
try:
fileutils.check_empty_file(orig_file)
except fileutils.FileEmptyError:
all_values = []
else:
anonymize = self.anonymize_func()
queue_search = r'^(?P<queue_name>[\w.-]+)\s+' \
r'(?:--|[0-9]+[mgtkp]b[a-z]*)\s+' \
r'(?:--|\d+:\d+:?\d*:?)\s+' \
r'(?:--|\d+:\d+:?\d+:?)\s+(--)\s+' \
r'(?P<run>\d+)\s+' \
r'(?P<queued>\d+)\s+' \
r'(?P<lm>--|\d+)\s+' \
r'(?P<state>[DE] R)'
run_qd_search = '^\s*(?P<tot_run>\d+)\s+(?P<tot_queued>\d+)' # this picks up the last line contents
all_values = list()
with open(orig_file, 'r') as fin:
fin.next()
fin.next()
# server_name = fin.next().split(': ')[1].strip()
fin.next()
fin.next().strip() # the headers line should later define the keys in temp_dict, should they be different
fin.next()
for line in fin:
line = line.strip()
m = re.search(queue_search, line)
n = re.search(run_qd_search, line)
temp_dict = {}
try:
queue_name = m.group('queue_name') if not self.options.ANONYMIZE else anonymize(m.group('queue_name'), 'qs')
run, queued, lm, state = m.group('run'), m.group('queued'), m.group('lm'), m.group('state')
except AttributeError:
try:
total_running_jobs, total_queued_jobs = n.group('tot_run'), n.group('tot_queued')
except AttributeError:
continue
else:
for key, value in [('queue_name', queue_name),
('run', run),
('queued', queued),
('lm', lm),
('state', state)]:
temp_dict[key] = value
all_values.append(temp_dict)
all_values.append({'Total_running': total_running_jobs, 'Total_queued': total_queued_jobs})
finally:
return all_values
def get_worker_nodes(self, job_ids, job_queues, options):
try:
fileutils.check_empty_file(self.pbsnodes_file)
except fileutils.FileEmptyError:
all_pbs_values = []
return all_pbs_values
raw_blocks = self._read_all_blocks(self.pbsnodes_file)
all_pbs_values = []
anonymize = self.qstat_maker.anonymize_func()
for block in raw_blocks:
pbs_values = dict()
pbs_values['domainname'] = block[
'domainname'] if not self.options.ANONYMIZE else anonymize(
block['domainname'], 'wns')
nextchar = block['state'][0]
state = (nextchar == 'f') and "-" or nextchar
pbs_values['state'] = state
try:
pbs_values['np'] = block['np']
except KeyError:
pbs_values['np'] = block[
'pcpus'] # handle torque cases # todo : to check
if block.get('gpus') > 0: # this should be rare.
pbs_values['gpus'] = block['gpus']
try: # this should turn up more often, hence the try/except.
_ = block['jobs']
except KeyError:
pbs_values['core_job_map'] = dict(
) # change of behaviour: all entries should contain the key even if no value
else:
# jobs = re.split(r'(?<=[A-Za-z0-9]),\s?', block['jobs'])
jobs = re.findall(r'[0-9][0-9,-]*/[^,]+', block['jobs'])
pbs_values['core_job_map'] = dict(
(core, job) for job, core in self._get_jobs_cores(jobs))
finally:
all_pbs_values.append(pbs_values)
all_pbs_values = self.ensure_worker_nodes_have_qnames(
all_pbs_values, job_ids, job_queues)
return all_pbs_values
def get_worker_nodes(self, job_ids, job_queues, options):
try:
fileutils.check_empty_file(self.pbsnodes_file)
except fileutils.FileEmptyError:
all_pbs_values = []
return all_pbs_values
raw_blocks = self._read_all_blocks(self.pbsnodes_file)
all_pbs_values = []
anonymize = self.qstat_maker.anonymize_func()
for block in raw_blocks:
pbs_values = dict()
pbs_values['domainname'] = block['domainname'] if not self.options.ANONYMIZE else anonymize(block['domainname'], 'wns')
nextchar = block['state'][0]
state = (nextchar == 'f') and "-" or nextchar
pbs_values['state'] = state
try:
pbs_values['np'] = block['np']
except KeyError:
pbs_values['np'] = block['pcpus'] # handle torque cases # todo : to check
if block.get('gpus') > 0: # this should be rare.
pbs_values['gpus'] = block['gpus']
try: # this should turn up more often, hence the try/except.
_ = block['jobs']
except KeyError:
pbs_values['core_job_map'] = dict() # change of behaviour: all entries should contain the key even if no value
else:
# jobs = re.split(r'(?<=[A-Za-z0-9]),\s?', block['jobs'])
jobs = re.findall(r'[0-9][0-9,-]*/[^,]+', block['jobs'])
pbs_values['core_job_map'] = dict((core, job) for job, core in self._get_jobs_cores(jobs))
finally:
all_pbs_values.append(pbs_values)
all_pbs_values = self.ensure_worker_nodes_have_qnames(all_pbs_values, job_ids, job_queues)
return all_pbs_values
def get_queues_info(self):
logging.debug("Parsing tree of %s" % self.sge_file)
fileutils.check_empty_file(self.sge_file)
tree, root = self.sge_stat_maker.tree, self.sge_stat_maker.root
qstatq_list = self._extract_queues('queue_info/Queue-List', root)
total_running_jobs = sum([d['run'] for d in qstatq_list])
logging.info('Total running jobs found: %s' % total_running_jobs)
for d in qstatq_list:
d['run'] = str(d['run'])
d['queued'] = str(d['queued'])
total_queued_jobs = self._get_total_queued_jobs('job_info/job_list', root)
qstatq_list.append({'run': '0', 'queued': total_queued_jobs, 'queue_name': 'Pending', 'state': 'Q', 'lm': '0'})
logging.debug('qstatq_list contains %s elements' % len(qstatq_list))
# TODO: check validity. 'state' shouldnt just be 'Q'!
logging.debug("Closing %s" % self.sge_file)
return total_running_jobs, int(eval(str(total_queued_jobs))), qstatq_list
def extract_qstatq(self, orig_file):
"""
reads QSTATQ_ORIG_FN sequentially and returns useful data
Searches for lines in the following format:
biomed -- -- 72:00:00 -- 31 0 -- E R
(except for the last line, which contains two sums and is parsed separately)
"""
try:
fileutils.check_empty_file(orig_file)
except fileutils.FileEmptyError:
all_values = []
else:
anonymize = self.anonymize_func()
queue_search = r'^(?P<queue_name>[\w.-]+)\s+' \
r'(?:--|[0-9]+[mgtkp]b[a-z]*)\s+' \
r'(?:--|\d+:\d+:?\d*:?)\s+' \
r'(?:--|\d+:\d+:?\d+:?)\s+(--)\s+' \
r'(?P<run>\d+)\s+' \
r'(?P<queued>\d+)\s+' \
r'(?P<lm>--|\d+)\s+' \
r'(?P<state>[DE] R)'
run_qd_search = '^\s*(?P<tot_run>\d+)\s+(?P<tot_queued>\d+)' # this picks up the last line contents
all_values = list()
with open(orig_file, 'r') as fin:
fin.next()
fin.next()
# server_name = fin.next().split(': ')[1].strip()
fin.next()
fin.next().strip(
) # the headers line should later define the keys in temp_dict, should they be different
fin.next()
for line in fin:
line = line.strip()
m = re.search(queue_search, line)
n = re.search(run_qd_search, line)
temp_dict = {}
try:
queue_name = m.group(
'queue_name'
) if not self.options.ANONYMIZE else anonymize(
m.group('queue_name'), 'qs')
run, queued, lm, state = m.group('run'), m.group(
'queued'), m.group('lm'), m.group('state')
except AttributeError:
try:
total_running_jobs, total_queued_jobs = n.group(
'tot_run'), n.group('tot_queued')
except AttributeError:
continue
else:
for key, value in [('queue_name', queue_name),
('run', run), ('queued', queued),
('lm', lm), ('state', state)]:
temp_dict[key] = value
all_values.append(temp_dict)
all_values.append({
'Total_running': total_running_jobs,
'Total_queued': total_queued_jobs
})
finally:
return all_values