def parse_sacct(job_info, log=None):
try:
job_info2 = job_info.copy()
if job_info2['State'] in FAILED_STATES + PENDING_STATES:
job_info2['exit_status'] = None
else:
job_info2['exit_status'] = int(job_info2['ExitCode'].split(":")[0])
job_info2['cpu_time'] = int(job_info2['CPUTimeRAW'])
job_info2['wall_time'] = parse_slurm_time(job_info2['Elapsed'])
job_info2['percent_cpu'] = div(float(job_info2['cpu_time']),
float(job_info2['wall_time']))
job_info2['avg_rss_mem'] = convert_size_to_kb(
job_info2['AveRSS']) if job_info2['AveRSS'] != '' else None
job_info2['max_rss_mem'] = convert_size_to_kb(
job_info2['MaxRSS']) if job_info2['MaxRSS'] != '' else None
job_info2['avg_vms_mem'] = convert_size_to_kb(
job_info2['AveVMSize']) if job_info2['AveVMSize'] != '' else None
job_info2['max_vms_mem'] = convert_size_to_kb(
job_info2['MaxVMSize']) if job_info2['MaxVMSize'] != '' else None
except Exception as e:
if log:
log.info('Error Parsing: %s' % pformat(job_info2))
raise e
return job_info2
def parse_sacct(job_info, log=None):
try:
job_info2 = job_info.copy()
if job_info2["State"] in FAILED_STATES + PENDING_STATES:
job_info2["exit_status"] = None
else:
job_info2["exit_status"] = int(job_info2["ExitCode"].split(":")[0])
job_info2["cpu_time"] = int(job_info2["CPUTimeRAW"])
job_info2["wall_time"] = parse_slurm_time(job_info2["Elapsed"])
job_info2["percent_cpu"] = div(float(job_info2["cpu_time"]),
float(job_info2["wall_time"]))
job_info2["avg_rss_mem"] = (convert_size_to_kb(job_info2["AveRSS"])
if job_info2["AveRSS"] != "" else None)
job_info2["max_rss_mem"] = (convert_size_to_kb(job_info2["MaxRSS"])
if job_info2["MaxRSS"] != "" else None)
job_info2["avg_vms_mem"] = (convert_size_to_kb(job_info2["AveVMSize"])
if job_info2["AveVMSize"] != "" else None)
job_info2["max_vms_mem"] = (convert_size_to_kb(job_info2["MaxVMSize"])
if job_info2["MaxVMSize"] != "" else None)
except Exception as e:
if log:
log.info("Error Parsing: %s" % pformat(job_info2))
raise e
return job_info2
def parse_drmaa_jobinfo(drmaa_jobinfo):
d = drmaa_jobinfo['resourceUsage']
cosmos_jobinfo = dict(
exit_status=int(drmaa_jobinfo.get('exitStatus', os.EX_UNAVAILABLE)),
percent_cpu=div(float(d.get('cpu', 0)), float(d.get('ru_wallclock',
0))),
wall_time=float(d.get('ru_wallclock', 0)),
cpu_time=float(d.get('cpu', 0)),
user_time=float(d.get('ru_utime', 0)),
system_time=float(d.get('ru_stime', 0)),
# TODO should we be calling convert_size_to_kb() for avg_rss_mem?
avg_rss_mem=d.get('ru_ixrss', "0"),
max_rss_mem_kb=convert_size_to_kb(d.get('ru_maxrss', "0")),
avg_vms_mem_kb=None,
max_vms_mem_kb=convert_size_to_kb(d.get('maxvmem', "0")),
io_read_count=int(float(d.get('ru_inblock', 0))),
io_write_count=int(float(d.get('ru_oublock', 0))),
io_wait=float(d.get('iow', 0)),
io_read_kb=float(d.get('io', 0)),
io_write_kb=float(d.get('io', 0)),
ctx_switch_voluntary=int(float(d.get('ru_nvcsw', 0))),
ctx_switch_involuntary=int(float(d.get('ru_nivcsw', 0))),
avg_num_threads=None,
max_num_threads=None,
avg_num_fds=None,
max_num_fds=None,
memory=float(d.get('mem', 0)),
)
#
# Wait, what? drmaa has two exit status fields? Of course, they don't always
# agree when an error occurs. Worse, sometimes drmaa doesn't set exit_status
# when a job is killed. We may not be able to get the exact exit code, but
# at least we can guarantee it will be non-zero for any job that shows signs
# of terminating in error.
#
if int(drmaa_jobinfo['exitStatus']) != 0 or \
drmaa_jobinfo['hasSignal'] or \
drmaa_jobinfo['wasAborted'] or \
not drmaa_jobinfo['hasExited']:
if cosmos_jobinfo['exit_status'] == 0:
try:
cosmos_jobinfo['exit_status'] = int(
float(drmaa_jobinfo['resourceUsage']['exit_status']))
except KeyError:
cosmos_jobinfo['exit_status'] = os.EX_UNAVAILABLE
if cosmos_jobinfo['exit_status'] == 0:
cosmos_jobinfo['exit_status'] = os.EX_SOFTWARE
cosmos_jobinfo['successful'] = False
else:
cosmos_jobinfo['successful'] = True
return cosmos_jobinfo
def _get_task_return_data(self, task):
"""
Convert raw qacct job data into Cosmos's more portable format.
Returns a 2-tuple comprising:
[0] a dictionary of job metadata,
[1] a boolean indicating whether the metadata in [0] are affected by an
SGE bug that causes qacct to occasionally return corrupt results.
"""
d = self.task_qacct(task)
job_failed = d['failed'][0] != '0'
data_are_corrupt = is_corrupt(d)
if job_failed or data_are_corrupt:
task.workflow.log.warn('%s SGE (qacct -j %s) reports %s:\n%s' %
(task, task.drm_jobID,
'corrupt data' if data_are_corrupt else 'job failure',
json.dumps(d, indent=4, sort_keys=True)))
processed_data = dict(
exit_status=int(d['exit_status']) if not job_failed else int(re.search(r'^(\d+)', d['failed']).group(1)),
percent_cpu=div(float(d['cpu']), float(d['ru_wallclock'])),
wall_time=float(d['ru_wallclock']),
cpu_time=float(d['cpu']),
user_time=float(d['ru_utime']),
system_time=float(d['ru_stime']),
avg_rss_mem=d['ru_ixrss'],
max_rss_mem_kb=convert_size_to_kb(d['maxrss']),
avg_vms_mem_kb=None,
max_vms_mem_kb=convert_size_to_kb(d['maxvmem']),
io_read_count=int(d['ru_inblock']),
io_write_count=int(d['ru_oublock']),
io_wait=float(d['iow']),
io_read_kb=convert_size_to_kb("%fG" % float(d['io'])),
io_write_kb=convert_size_to_kb("%fG" % float(d['io'])),
ctx_switch_voluntary=int(d['ru_nvcsw']),
ctx_switch_involuntary=int(d['ru_nivcsw']),
avg_num_threads=None,
max_num_threads=None,
avg_num_fds=None,
max_num_fds=None,
memory=float(d['mem']),
)
return processed_data, data_are_corrupt
def parse_sacct(job_info, log=None):
try:
job_info2 = job_info.copy()
if job_info2['State'] in FAILED_STATES + PENDING_STATES:
job_info2['exit_status'] = None
else:
job_info2['exit_status'] = int(job_info2['ExitCode'].split(":")[0])
job_info2['cpu_time'] = int(job_info2['CPUTimeRAW'])
job_info2['wall_time'] = parse_slurm_time(job_info2['Elapsed'])
job_info2['percent_cpu'] = div(float(job_info2['cpu_time']), float(job_info2['wall_time']))
job_info2['avg_rss_mem'] = convert_size_to_kb(job_info2['AveRSS']) if job_info2['AveRSS'] != '' else None
job_info2['max_rss_mem'] = convert_size_to_kb(job_info2['MaxRSS']) if job_info2['MaxRSS'] != '' else None
job_info2['avg_vms_mem'] = convert_size_to_kb(job_info2['AveVMSize']) if job_info2['AveVMSize'] != '' else None
job_info2['max_vms_mem'] = convert_size_to_kb(job_info2['MaxVMSize']) if job_info2['MaxVMSize'] != '' else None
except Exception as e:
if log:
log.info('Error Parsing: %s' % pformat(job_info2))
raise e
return job_info2