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Source code for galaxy.jobs.runners.univa

Job control via the DRMAA API / qstat and qacct.

Known to work on the UNIVA grid engine.

known bugs/problems:
- if a job runs longer than the time limits of the queue two things happen
  1. at the soft limit (s_rt) SIGUSR1 is sent to the job
  2. at the hard limit (h_rt) SIGKILL is sent to the job
  The second case is covered by the runner -- it's the same mechanism that
  kills a job when the job time limit is reached. The first case is currently
  not covered. The good thing is that most programs ignore SIGUSR1.
  For the second case it seems that jobs are marked as failed (killed by the DRM)
  at random.

  Possible solutions:
  - configure the job destinations such that the queue limits are never reached.
    the time limits can be determined with
    `for i in `qconf -sql`; do qconf -sq $i | grep -E '(h|s)_rt'; done`

  - extend the job runner to cover s_rt cases (some ideas):
    * I'm unsure if the programs reaction to SIGUSR1 can be determined easily
      because it depends on the program. It seems that exit code is in most
      cases 10.
    * The sheduler logs contains quite useful information.
import logging
import re
import signal
import time

from galaxy.jobs.runners.drmaa import DRMAAJobRunner
from galaxy.util import (

log = logging.getLogger(__name__)

__all__ = ('UnivaJobRunner',)

MEMORY_LIMIT_SCAN_SIZE = 1024 * 1024  # 1MB

class DRMAAWaitUnusable(Exception):

[docs]class UnivaJobRunner(DRMAAJobRunner): runner_name = "UnivaJobRunner" # restrict job name length as in the DRMAAJobRunner # restrict_job_name_length = 15
[docs] def check_watched_item(self, ajs, new_watched): """ get state with job_status/qstat since qstat returns undetermined for finished jobs we return DONE here """ state = self._get_drmaa_state(ajs.job_id, self.ds, False) # log.debug("UnivaJobRunner:check_watched_item ({jobid}) -> state {state}".format(jobid=ajs.job_id, state=self.drmaa_job_state_strings[state])) if state == self.drmaa.JobState.UNDETERMINED: return self.drmaa.JobState.DONE return state
def _complete_terminal_job(self, ajs, drmaa_state, **kwargs): extinfo = dict() # get state with job_info/qstat + wait/qacct state = self._get_drmaa_state(ajs.job_id, self.ds, True, extinfo) # log.debug("UnivaJobRunner:_complete_terminal_job ({jobid}) -> state {state} info {info}".format(jobid=ajs.job_id, state=self.drmaa_job_state_strings[state], info=extinfo)) # for any job that is finished (regardless of successful or failed) check if there # were memory or time deletions or if the job was deleted if state in [self.drmaa.JobState.DONE, self.drmaa.JobState.FAILED]: # get configured job destination job_destination = ajs.job_wrapper.job_destination native_spec = job_destination.params.get('nativeSpecification', None) # determine time and memory that was granted for the job time_granted, mem_granted = _parse_native_specs(ajs.job_id, native_spec) time_wasted = extinfo["time_wasted"] mem_wasted = extinfo["memory_wasted"] slots = extinfo["slots"] # log.debug("UnivaJobRunner:_complete_terminal_job ({jobid}) memviolation {mv}".format(jobid=ajs.job_id, mv=memviolation)) # check job for run time or memory violation if "deleted" in extinfo and extinfo["deleted"]: log.info('(%s/%s) Job was cancelled (e.g. with qdel)', ajs.job_wrapper.get_id_tag(), ajs.job_id) ajs.fail_message = "This job failed because it was cancelled." drmaa_state = self.drmaa.JobState.FAILED elif ("signal" in extinfo and extinfo["signal"] == "SIGKILL") and time_wasted > time_granted: log.error('({tag}/{jobid}) Job hit walltime'.format(tag=ajs.job_wrapper.get_id_tag(), jobid=ajs.job_id)) ajs.fail_message = "This job was terminated because it ran longer than the maximum allowed job run time." ajs.runner_state = ajs.runner_states.WALLTIME_REACHED drmaa_state = self.drmaa.JobState.FAILED # test wasted>granted memory only if failed != 0 and exit_status != 0, ie if marked as failed elif state == self.drmaa.JobState.FAILED and mem_wasted > mem_granted * slots: log.error('({idtag}/{jobid}) Job hit memory limit ({used}>{limit})'.format(idtag=ajs.job_wrapper.get_id_tag(), jobid=ajs.job_id, used=mem_wasted, limit=mem_granted)) ajs.fail_message = "This job was terminated because it used more than the maximum allowed memory." ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED drmaa_state = self.drmaa_job_states.FAILED elif state in [self.drmaa.JobState.QUEUED_ACTIVE, self.drmaa.JobState.SYSTEM_ON_HOLD, self.drmaa.JobState.USER_ON_HOLD, self.drmaa.JobState.USER_SYSTEM_ON_HOLD, self.drmaa.JobState.RUNNING, self.drmaa.JobState.SYSTEM_SUSPENDED, self.drmaa.JobState.USER_SUSPENDED]: log.warning('({tag}/{jobid}) Job is {state}, returning to monitor queue'.format(tag=ajs.job_wrapper.get_id_tag(), jobid=ajs.job_id, state=self.drmaa_job_state_strings[state])) # TODO return True? return True # job was not actually terminal elif state == self.drmaa.JobState.UNDETERMINED: log.warning('({tag}/{jobid}) Job state could not be determined'.format(tag=ajs.job_wrapper.get_id_tag(), jobid=ajs.job_id)) drmaa_state = self.drmaa_job_states.FAILED else: log.error("DRMAAUniva: job {job_id} determined unknown state {state}".format(job_id=ajs.job_id, state=state)) drmaa_state = self.drmaa_job_states.FAILED # by default, finish the job with the state from drmaa return super()._complete_terminal_job(ajs, drmaa_state=drmaa_state) def _drmaa_state_is_refined(self, statep, staten): """ check if staten is more 'severe' than statep """ # definition of the severity of job states, the hex codes are # from the drmaa C library which seem to define a useful order drmaa_job_state_order = { self.drmaa.JobState.UNDETERMINED: 0x00, self.drmaa.JobState.QUEUED_ACTIVE: 0x10, self.drmaa.JobState.SYSTEM_ON_HOLD: 0x11, self.drmaa.JobState.USER_ON_HOLD: 0x12, self.drmaa.JobState.USER_SYSTEM_ON_HOLD: 0x13, self.drmaa.JobState.RUNNING: 0x20, self.drmaa.JobState.SYSTEM_SUSPENDED: 0x21, self.drmaa.JobState.USER_SUSPENDED: 0x22, self.drmaa.JobState.DONE: 0x30, self.drmaa.JobState.FAILED: 0x40, } return drmaa_job_state_order[staten] > drmaa_job_state_order[statep] def _get_drmaa_state_qstat(self, job_id, extinfo): """ get a (drmaa) job state with qstat. qstat only returns infos for jobs that are queued, suspended, ..., or just finished (i.e. jobs are still in the system). information on finished jobs can only be found by qacct. Hence if qstat does not contain information on the job the state is assumed as UNDETERMINED job_id the job id extinfo a set that additional information can be stored in, i.e., "deleted" returns the drmaa state """ # log.debug("UnivaJobRunner._get_drmaa_state_qstat ({jobid})".format(jobid=job_id)) # using -u "*" is the simplest way to query the jobs of all users which # allows to treat the case where jobs are submitted as real user it would # be more efficient to specify the user (or in case that the galaxy user # submits the job -> to ommit the -u option) # note that, this is preferred over using `qstat -j JOBID` which returns a non-zero # exit code in case of error as well as if the jobid is not found (if job is finished). # even if this could be disambiguated by the stderr message the `qstat -u "*"` # way seems more generic cmd = ['qstat', '-u', '"*"'] try: stdout = commands.execute(cmd).strip() except commands.CommandLineException as e: log.error(unicodify(e)) raise self.drmaa.InternalException() state = self.drmaa.JobState.UNDETERMINED for line in stdout.split('\n'): line = line.split() if len(line) >= 5 and line[0] == str(job_id): state = self._map_qstat_drmaa_states(job_id, line[5], extinfo) break # log.debug("UnivaJobRunner._get_drmaa_state_qstat ({jobid}) -> {state}".format(jobid=job_id, state=self.drmaa_job_state_strings[state])) return state def _get_drmaa_state_qacct(self, job_id, extinfo): ''' get the job (drmaa) state with qacct. extinfo: dict where signal, exit_status, deleted = True, time_wasted, and memory_wasted can be stored: - signal signal as reported in exit state from qstat (see below) - exit_status set to exit status if returned (ie if qstat returns an exits state larger 0 and less 129 (for exit states > 128 signal is set) in any case (exit state > 0) state FAILED is returned - deleted set to true if the job was deleted (otherwise not set at all), - time_wasted time used in seconds (taken from wallclock) - memory_wasted memory used by the program in byte (taken from maxvmem) return state - first initalised with UNDETERMINED and changed in the following case - DONE if exit state == 0 - FAILED if exit state != 0 - RUNNING if failed in 24,25 - FAILED if failed not in [0,24,25,100] ''' # log.debug("UnivaJobRunner._get_drmaa_state_qacct ({jobid})".format(jobid=job_id)) signals = {k: v for v, k in reversed(sorted(signal.__dict__.items())) if v.startswith('SIG') and not v.startswith('SIG_')} cmd = ['qacct', '-j', job_id] slp = 1 # run qacct -j JOBID (since the accounting data for the job might not be # available immediately a simple retry mechanism is implemented .. # max wait is approx 1min) while True: try: stdout = commands.execute(cmd).strip() except commands.CommandLineException as e: if slp <= 32 and "job id {jobid} not found".format(jobid=job_id) in e.stderr: time.sleep(slp) slp *= 2 continue else: log.error(unicodify(e)) return self.drmaa.JobState.UNDETERMINED else: break qacct = dict() for line in stdout.split("\n"): # remove header if line.startswith("=") or line == "": continue line = line.split() qacct[line[0]] = " ".join(line[1:]) # qacct has three fields of interest: failed, exit_status, deleted_by # experiments # failed exit_status deleted_by # BASH ------------------------------------ # time-limit 100 137 # mem-limit 0 2 # python -------------------------------------------------------------- # time-limit # mem-limit 0 1 # C ------------------------------------------------------------------- # time-limit # mem-limit 0 C programm either have segfault (139) or allocated memory is checked for NULL (then a programmer defined message/exit code is given) # note that max_vmem might not be reliable, since the program never gets the memory. # C++ ----------------------------------------------------------------- # time-limit # mem-limit 0 same as for C programs # JAVA ---------------------------------------------------------------- # time-limit # mem-limit # perl ---------------------------------------------------------------- # time-limit # mem-limit # bash other tests ---------------------------------------------------- # qdel 100 137 user@mail extinfo["time_wasted"] = _parse_time(qacct["wallclock"]) extinfo["memory_wasted"] = size_to_bytes(qacct["maxvmem"]) extinfo["slots"] = int(qacct["slots"]) # deleted_by # If the job (the array task) has been deleted via qdel, "<username>@<hostname>", else # "NONE". If qdel was called multiple times, every invocation is recorded in a comma # separated list. if "deleted_by" in qacct and qacct["deleted_by"] != "NONE": log.info("DRMAAUniva: job {job_id} was aborted by {culprit}".format(job_id=job_id, culprit=qacct["deleted_by"])) extinfo["deleted"] = True return self.drmaa.JobState.FAILED state = self.drmaa.JobState.UNDETERMINED # exit_status # Exit status of the job script (or Univa Grid Engine specific status in case of certain # error conditions). The exit status is determined by following the normal shell conventions # If the command terminates normally the value of the command is its exit status. # However, in the case that the command exits abnormally, a value of 0200 (octal), 128 # (decimal) is added to the value of the command to make up the exit status. # For example: If a job dies through signal 9 (SIGKILL) then the exit status # becomes 128 + 9 = 137. if "exit_status" in qacct: qacct["exit_status"] = int(qacct["exit_status"]) if qacct["exit_status"] < 1: log.error("DRMAAUniva: job {job_id} has exit status {status}".format(job_id=job_id, status=qacct["exit_status"])) state = self.drmaa.JobState.DONE elif 0 < qacct["exit_status"] < 129: log.error("DRMAAUniva: job {job_id} has exit status {status}".format(job_id=job_id, status=qacct["exit_status"])) extinfo['exit_status'] = qacct["exit_status"] state = self.drmaa.JobState.FAILED else: log.error("DRMAAUniva: job {job_id} was killed by signal {signal}".format(job_id=job_id, signal=qacct["exit_status"] - 128)) state = self.drmaa.JobState.FAILED extinfo["signal"] = signals[qacct["exit_status"] - 128] # failed # Indicates the problem which occurred in case a job could not be started on the execution # host (e.g. because the owner of the job did not have a valid account on that # machine). If Univa Grid Engine tries to start a job multiple times, this may lead to # multiple entries in the accounting file corresponding to the same job ID. # for the codes see https://docs.oracle.com/cd/E19957-01/820-0699/chp11-2/index.html if "failed" in qacct: code = int(qacct["failed"].split()[0]) # this happens in case of no error or exit_code!=0 (0) or a signal (100). # both cases are covered already if code in [0, 100]: pass # these seem to be OK as well elif code in [24, 25]: state = self.drmaa.JobState.RUNNING else: log.error("DRMAAUniva: job {job_id} failed with failure {failure}".format(job_id=job_id, failure=qacct["failed"])) state = self.drmaa.JobState.FAILED # log.debug("UnivaJobRunner._get_drmaa_state_qacct ({jobid}) -> {state}".format(jobid=job_id, state=self.drmaa_job_state_strings[state])) return state def _get_drmaa_state_wait(self, job_id, ds, extinfo): ''' get the (drmaa) job state with the python-drmaa wait function this function will not work if the job was started as real user since the external runner uses a different drmaa session. the advantage over the qacct based method is speed (in particular if the accounting data is stored in a huge file) jobid: the jobid ds: drmaa session extinfo dict where signal, exit_status, deleted = True, time_wasted, and memory_wasted can be stored ''' # log.debug("UnivaJobRunner._get_drmaa_state_wait ({jobid})".format(jobid=job_id)) # experiments # exitStatus coreDump hasExited hasSignal Signal wasAborted # BASH ---------------------------------------------------------------- # time-limit 0 0 0 1 SIGKILL 0 # mem-limit 2 0 1 0 0 with creating a large array and dd into variable # python -------------------------------------------------------------- # time-limit 0 0 0 1 SIGKILL 0 # mem-limit 1 0 1 0 0 # C ------------------------------------------------------------------- # time-limit 0 0 0 1 SIGKILL 0 # mem-limit 0 1 0 1 SIGSEGV 0 SegFault when accessing unallocated memory # C++ ----------------------------------------------------------------- # time-limit 0 0 0 1 SIGKILL 0 # mem-limit 0 1 0 1 SIGABRT 0 because of memory # JAVA ---------------------------------------------------------------- # time-limit 0 0 0 1 SIGKILL 0 # mem-limit 1 0 1 0 0 # perl ---------------------------------------------------------------- # time-limit 0 0 0 0 SIGKILL 0 # mem-limit 1 0 1 0 0 # bash other tests ---------------------------------------------------- # no exit 0 0 1 0 0 # qdel 0 0 0 0 1 # TODO just return 0 if external runner is used # TODO do not run for running jobs try: # Note: drmaa refers to the parent galaxy module which has a global # variable drmaa which is the drmaa python library rv = ds.session.wait(job_id, self.drmaa.session.Session.TIMEOUT_NO_WAIT) except self.drmaa.errors.DrmaaException: # log.exception("could not determine status of job {jobid} using drmaa.wait error was {error}".format(jobid=job_id, error=str(e))) raise DRMAAWaitUnusable() # documentation of the variables adapted from the drmaa C library documentation at # https://linux.die.net/man/3/drmaa_wait # currently not used are # - rv.jobId # - rv.resourceUsage (which contains info on runtime and memory usage) # - rv.hasSignal (since we test the terminatedSignal anyway, and the meaning # of hasSignal=0 could be anything from success to failure) # - hasExited # ** wasAborted** # wasAborted is a non-zero value for a job that ended before entering the running state. # Note: seems to be non-zero also if it is already running # **exitStatus** # If hasExited is a non-zero value, the exitStatus variable gives the # exit code that the job passed to exit or the value that the child # process returned from main. # **hasCoreDump** # If hasSignal is a non-zero value, hasCoreDump is a non-zero value if a core image # of the terminated job was created. # **hasExited** # non-zero value for a job that terminated normally. A zero value can also indicate # that although the job has terminated normally, an exit status is not available, # or that it is not known whether the job terminated normally. # In both cases exitStatus will not provide exit status information. # A non-zero value returned in exited indicates more detailed diagnosis can be # provided by means of hasSignal, terminatedSignal and hasCoreDump. # **hasSignal** # non-zero integer for a job that terminated due to the receipt of a signal. # A zero value can also indicate that although the job has terminated due to the # receipt of a signal, the signal is not available, or it is not known whether # the job terminated due to the receipt of a signal. # In both cases terminatedSignal will not provide signal information. # A non-zero value returned in signaled indicates signal information can be # retrieved from terminatedSignal. # **terminatedSignal** # If hasSignal is a non-zero value, the terminatedSignal is a # a string representation of the signal that caused the termination # of the job. For signals declared by POSIX.1, the symbolic names # are returned (e.g., SIGABRT, SIGALRM). # For signals not declared by POSIX, any other string may be returned. # check if job was aborted # get the used time and memory extinfo["time_wasted"] = float(rv.resourceUsage['wallclock']) extinfo["memory_wasted"] = float(rv.resourceUsage['maxvmem']) # TODO unsure if the resourceUsage key is really slots -> test in submit as galaxy user setting extinfo["slots"] = float(rv.resourceUsage['slots']) # log.debug("wait -> \texitStatus {0}\thasCoreDump {1}\thasExited {2}\thasSignal {3}\tjobId {4}\t\tterminatedSignal {5}\twasAborted {6}\tresourceUsage {7}".format(rv.exitStatus, rv.hasCoreDump, rv.hasExited, rv.hasSignal, rv.jobId, rv.terminatedSignal, rv.wasAborted, rv.resourceUsage)) if rv.wasAborted: log.error("DRMAAUniva: job {job_id} was aborted according to wait()".format(job_id=job_id)) extinfo["deleted"] = True return self.drmaa.JobState.FAILED # determine if something went wrong. this could be application errors # but also violation of scheduler constraints state = self.drmaa.JobState.DONE if rv.exitStatus != 0: log.error("DRMAAUniva: job {job_id} has exit status {status}".format(job_id=job_id, status=rv.exitStatus)) extinfo["state"] = self.drmaa.JobState.FAILED if not rv.hasExited or rv.hasSignal: if rv.hasCoreDump != 0: log.error("DRMAAUniva: job {job_id} has core dump".format(job_id=job_id)) extinfo["state"] = self.drmaa.JobState.FAILED elif len(rv.terminatedSignal) > 0: log.error("DRMAAUniva: job {job_id} was kill by signal {signal}".format(job_id=job_id, signal=rv.terminatedSignal)) state = self.drmaa.JobState.FAILED extinfo["signal"] = rv.terminatedSignal elif rv.wasAborted == 0: log.error("DRMAAUniva: job {job_id} has finished in unclear condition".format(job_id=job_id)) state = self.drmaa.JobState.FAILED # log.debug("UnivaJobRunner._get_drmaa_state_wait ({jobid}) -> {state}".format(jobid=job_id, state=self.drmaa_job_state_strings[state])) return state def _get_drmaa_state(self, job_id, ds, waitqacct, extinfo=None): """ get the state using drmaa.job_info/qstat and drmaa.wait/qacct using the above functions qacct/wait is only called if waitqacct is True. the function returns the state (one of the drmaa states) and extended information in the extinfo dict """ if extinfo is None: extinfo = {} # log.debug("UnivaJobRunner._get_drmaa_state ({jobid}) {qw}".format(jobid=job_id, qw=waitqacct)) state = self.drmaa.JobState.UNDETERMINED # try to get the state with drmaa.job_status (does not work for jobs # started as real user) or qstat (works only for jobs that are running) try: # log.debug("UnivaJobRunner trying job_status ({jobid})".format(jobid=job_id)) state = ds.job_status(job_id) except self.drmaa.errors.DrmaaException: # log.debug("UnivaJobRunner trying qstat ({jobid})".format(jobid=job_id)) state = self._get_drmaa_state_qstat(job_id, extinfo) # if the job is finished (in whatever state) get (additional) infos # drmaa.wait or qacct (oposed to job_status/qstat these methods work # only for finished jobs) if waitqacct and state in [self.drmaa.JobState.UNDETERMINED, self.drmaa.JobState.DONE, self.drmaa.JobState.FAILED]: try: # log.debug("UnivaJobRunner trying wait ({jobid})".format(jobid=job_id)) wstate = self._get_drmaa_state_wait(job_id, ds, extinfo) except DRMAAWaitUnusable: # log.debug("UnivaJobRunner trying qacct ({jobid})".format(jobid=job_id)) wstate = self._get_drmaa_state_qacct(job_id, extinfo) if self._drmaa_state_is_refined(state, wstate): # log.debug("DRMAAUniva: job {job_id} wait/qacct {qacct} refines qacct {qstat}".format(job_id=job_id, qacct=self.drmaa_job_state_strings[wstate], qstat=self.drmaa_job_state_strings[state])) state = wstate return state def _map_qstat_drmaa_states(self, job_id, state, extinfo): """ helper function that tries to map the states that are in the output of `qstat` and `qstat -j ID` to the states that are returned by the jobStatus function of the drmaa python library. useful information that can not be mapped to a drmaa state is stored in the extinfo dict. this is extinfo["deleted"] = True for jobs that are deleted. note 1: DONE is not found here, since qstat contains not output for jobs that are 'done' (i.e. left the queueing system sucessfully of unsuccessfully) note 2: the *suspend and *hold are mapped 'sloppily', but this should be OK since galaxy does not evaluate them at all (it only checks for QUEUED_ACTIVE, RUNNING, DONE, and FAILED) the drmaa states are: UNDETERMINED: 'process status cannot be determined', QUEUED_ACTIVE: 'job is queued and active', SYSTEM_ON_HOLD: 'job is queued and in system hold', USER_ON_HOLD: 'job is queued and in user hold', USER_SYSTEM_ON_HOLD:'job is queued and in user and system hold', RUNNING: 'job is running', SYSTEM_SUSPENDED: 'job is system suspended', USER_SUSPENDED: 'job is user suspended', DONE: 'job finished normally', FAILED: 'job finished, but failed', the qstat states are Pending qw pending, pending (user hold) hqw pending (system hold), pending (user and system hold) hRqw pending (user and/or system hold, re-queue) Running r running t transferring, i.e. the job is transferred to the node(s) and about to be started Rr running (re-submit) Rt transferring (re-submit) Suspended s, ts job suspended S, tS queue suspended iT, tT queue suspended by alarm, e.g. the grid engine suspended the queue (and the job), because the queue is overloaded Rs, Rts, RS, RtS, RT, RtT all suspended states with re-submit Error Eqw, Ehqw, EhRqw all pending states with error == GE tried to execute a job in a queue, but it failed for a reason that is specific to the job Deleted dr, dt, dRr, ds, dS, dT, dRs, dRS, dRT all running and suspended states with deletion, i.e. these jobs have been deleted, but have not yet been purged from the system the qstat -j ID states are d(eletion), qdel has been used E(rror), pending jobs hat couldn't be started due to job properties h(old), job currently is not eligible for execution due to a hold state assigned to it r(unning), job is about to be executed or is already executing R(estarted), the job was restarted. This can be caused by a job migration or because of one of the reasons described in the -r section s(uspended), caused by suspending the job via qmod -s S(uspended), either that the queue containing the job is suspended ... or that a pending job got suspended due to a preemptive action that was either triggered automatically by the system or by a manual preemption request triggered via qmod(1) -p ... S e(N)hanced suspended, preemptive states shown for pending jobs triggered either automatically or via qmod(1) -p ... N or -p ... P (P)reempted, -"- t(ransfering), job is about to be executed or is already executing T(hreshold) or shows that at least one suspend threshold of the corresponding queue was exceeded (see queue_conf(5)) and that the job has been suspended as a consequence w(aiting). or that the job is waiting for completion of the jobs to which job dependencies have been assigned to the job job_id: the jobid (for logging) state: a state from the qstat output return: one of the drmaa states """ if "d" in state: extinfo["deleted"] = True return self.drmaa.JobState.FAILED if "E" in state: return self.drmaa.JobState.FAILED elif "s" in state: return self.drmaa.JobState.USER_SUSPENDED elif "S" in state or "T" in state or 'N' in state or 'P' in state: return self.drmaa.JobState.SYSTEM_SUSPENDED elif "h" in state: return self.drmaa.JobState.USER_SYSTEM_ON_HOLD elif "r" in state.lower() or "t" in state: return self.drmaa.JobState.RUNNING elif "w" in state: return self.drmaa.JobState.QUEUED_ACTIVE else: log.error("DRMAAUniva: job {job_id} unknown state from qstat: {state}".format(job_id=job_id, state=state)) return self.drmaa.JobState.UNDETERMINED
def _parse_time(tstring): tme = None m = re.search("([0-9:.]+)", tstring) if m is not None: timespl = m.group(1).split(':') tme = float(timespl[-1]) # sec if len(timespl) > 1: # min tme += float(timespl[-2]) * 60 if len(timespl) > 2: # hour tme += float(timespl[-3]) * 3600 if len(timespl) > 3: # day tme += float(timespl[-4]) * 86400 return tme def _parse_native_specs(job_id, native_spec): """ determine requested run time and memory from native specs native_spec (e.g. h_rt=01:00:02 -l h_vmem=1G) the native job_id the job ID (only used for logging) specification string passed to GE return time,mem (or None,None if nothing found) """ tme = None mem = None # parse time m = re.search(r"rt=([0-9:]+)[\s,]*", native_spec) if m is not None: tme = _parse_time(m.group(1)) if tme is None: log.error("DRMAAUniva: job {job_id} has unparsable time native spec {spec}".format(job_id=job_id, spec=native_spec)) # parse memory m = re.search(r"mem=([\d.]+[KGMT]?)[\s,]*", native_spec) if m is not None: mem = size_to_bytes(m.group(1)) # mem = _parse_mem(m.group(1)) if mem is None: log.error("DRMAAUniva: job {job_id} has unparsable memory native spec {spec}".format(job_id=job_id, spec=native_spec)) return tme, mem