def jobStatus(jobId): """ returns the program status of the job identified by jobId. The possible values returned from this method are: * `JobState.UNDETERMINED`: process status cannot be determined, * `JobState.QUEUED_ACTIVE`: job is queued and active, * `JobState.SYSTEM_ON_HOLD`: job is queued and in system hold, * `JobState.USER_ON_HOLD`: job is queued and in user hold, * `JobState.USER_SYSTEM_ON_HOLD`: job is queued and in user and system hold, * `JobState.RUNNING`: job is running, * `JobState.SYSTEM_SUSPENDED`: job is system suspended, * `JobState.USER_SUSPENDED`: job is user suspended, * `JobState.DONE`: job finished normally, and * `JobState.FAILED`: job finished, but failed. The DRMAA implementation should always get the status of the job from the DRM system unless the status has already been determined to be FAILED or DONE and the status has been successfully cached. Terminated jobs return a FAILED status. """ status = c_int() if isinstance(jobId, str): jobId = jobId.encode(ENCODING) c(drmaa_job_ps, jobId, byref(status)) return status_to_string(status.value)
def runJob(jobTemplate): """ Submit a job with attributes defined in the job template. :Parameters: jobTemplate : JobTemplate the template representing the job to be run The returned job identifier is a String identical to that returned from the underlying DRM system. """ jid = create_string_buffer(128) c(drmaa_run_job, jid, sizeof(jid), jobTemplate) return jid.value.decode()
def __init__(self, **kwargs): """\ Builds a JobTemplate instance. Attributes can be passed as keyword arguments.""" jt = _ct.pointer(_ct.POINTER(_w.drmaa_job_template_t)()) _h.c(_w.drmaa_allocate_job_template, jt) self._jt = self._as_parameter_ = jt.contents try: for aname in kwargs: setattr(self, aname, kwargs.get(aname)) except: self.delete() raise
def __init__(self, **kwargs): """ Builds a JobTemplate instance. Attributes can be passed as keyword arguments. """ jt = pointer(POINTER(drmaa_job_template_t)()) c(drmaa_allocate_job_template, jt) self._jt = self._as_parameter_ = jt.contents try: for aname in kwargs: setattr(self, aname, kwargs.get(aname)) except: self.delete() raise
def synchronize(jobIds, timeout=-1, dispose=False): """ Waits until all jobs specified by jobList have finished execution. :Parameters: jobIds If jobIds contains `Session.JOB_IDS_SESSION_ALL`, then this method waits for all jobs submitted during this DRMAA session up to the moment synchronize() is called timeout : int maximum time (in seconds) to be waited for the completion of a job. The value `Session.TIMEOUT_WAIT_FOREVER` may be specified to wait indefinitely for a result. The value `Session.TIMEOUT_NO_WAIT` may be specified to return immediately if no result is available. dispose : bool specifies how to treat the reaping of the remote job's internal data record, which includes a record of the job's consumption of system resources during its execution and other statistical information. If set to True, the DRM will dispose of the job's data record at the end of the synchronize() call. If set to False, the data record will be left for future access via the wait() method. It is the responsibility of the application to make sure that either `synchronize()` or `wait()`is called for every job. Not doing so creates a memory leak. Note that calling synchronize() with dispose set to true flushes all accounting information for all jobs in the list. To avoid thread race conditions in multithreaded applications, the DRMAA implementation user should explicitly synchronize this call with any other job submission calls or control calls that may change the number of remote jobs. If the call exits before the timeout has elapsed, all the jobs have been waited on or there was an interrupt. If the invocation exits on timeout, an ExitTimeoutException is thrown. The caller should check system time before and after this call in order to be sure of how much time has passed. """ if dispose: d = 1 else: d = 0 c(drmaa_synchronize, string_vector(jobIds), timeout, d)
def control(jobId, operation): """ Used to hold, release, suspend, resume, or kill the job identified by jobId. :Parameters: jobId : string if jobId is `Session.JOB_IDS_SESSION_ALL` then this routine acts on all jobs submitted during this DRMAA session up to the moment control() is called. The legal values for action and their meanings are operation : string possible values are: `JobControlAction.SUSPEND` stop the job `JobControlAction.RESUME` (re)start the job `JobControlAction.HOLD` put the job on-hold `JobControlAction.RELEASE` release the hold on the job `JobControlAction.TERMINATE` kill the job To avoid thread races in multithreaded applications, the DRMAA implementation user should explicitly synchronize this call with any other job submission calls or control calls that may change the number of remote jobs. This method returns once the action has been acknowledged by the DRM system, but does not necessarily wait until the action has been completed. Some DRMAA implementations may allow this method to be used to control jobs submitted external to the DRMAA session, such as jobs submitted by other DRMAA session in other DRMAA implementations or jobs submitted via native utilities. """ if isinstance(jobId, str): jobId = jobId.encode(ENCODING) c(drmaa_control, jobId, string_to_control_action(operation))
def wait(jobId, timeout=-1): """ Wait for a job with jobId to finish execution or fail. :Parameters: `jobId` : str The job id to wait completion for. If the special string, `Session.JOB_IDS_SESSION_ANY`, is provided as the jobId, this routine will wait for any job from the session `timeout` : float The timeout value is used to specify the desired behavior when a result is not immediately available. The value `Session.TIMEOUT_WAIT_FOREVER` may be specified to wait indefinitely for a result. The value `Session.TIMEOUT_NO_WAIT` may be specified to return immediately if no result is available. Alternatively, a number of seconds may be specified to indicate how long to wait for a result to become available This routine is modeled on the wait3 POSIX routine. If the call exits before timeout, either the job has been waited on successfully or there was an interrupt. If the invocation exits on timeout, an `ExitTimeoutException` is thrown. The caller should check system time before and after this call in order to be sure how much time has passed. The routine reaps job data records on a successful call, so any subsequent calls to wait() will fail, throwing an `InvalidJobException`, meaning that the job's data record has been already reaped. This exception is the same as if the job were unknown. (The only case where wait() can be successfully called on a single job more than once is when the previous call to wait() timed out before the job finished.) """ stat = c_int() jid_out = create_string_buffer(128) rusage = pointer(POINTER(drmaa_attr_values_t)()) if isinstance(jobId, str): jobId = jobId.encode(ENCODING) c(drmaa_wait, jobId, jid_out, sizeof(jid_out), byref(stat), timeout, rusage) res_usage = adapt_rusage(rusage) exited = c_int() c(drmaa_wifexited, byref(exited), stat) aborted = c_int() c(drmaa_wifaborted, byref(aborted), stat) signaled = c_int() c(drmaa_wifsignaled, byref(signaled), stat) coredumped = c_int() if exited.value == 0: c(drmaa_wcoredump, byref(coredumped), stat) exit_status = c_int() c(drmaa_wexitstatus, byref(exit_status), stat) term_signal = create_string_buffer(SIGNAL_BUFFER) if signaled.value == 1: c(drmaa_wtermsig, term_signal, sizeof(term_signal), stat) return JobInfo(jid_out.value.decode(), bool(exited), bool(signaled), term_signal.value.decode(), bool(coredumped), bool(aborted), int(exit_status.value), res_usage)
def delete(self): """Deallocate the underlying DRMAA job template.""" c(drmaa_delete_job_template, self)
def wait(jobId, timeout=-1): """ Wait for a job with jobId to finish execution or fail. :Parameters: `jobId` : str The job id to wait completion for. If the special string, `Session.JOB_IDS_SESSION_ANY`, is provided as the jobId, this routine will wait for any job from the session `timeout` : float The timeout value is used to specify the desired behavior when a result is not immediately available. The value `Session.TIMEOUT_WAIT_FOREVER` may be specified to wait indefinitely for a result. The value `Session.TIMEOUT_NO_WAIT` may be specified to return immediately if no result is available. Alternatively, a number of seconds may be specified to indicate how long to wait for a result to become available This routine is modeled on the wait3 POSIX routine. If the call exits before timeout, either the job has been waited on successfully or there was an interrupt. If the invocation exits on timeout, an `ExitTimeoutException` is thrown. The caller should check system time before and after this call in order to be sure how much time has passed. The routine reaps job data records on a successful call, so any subsequent calls to wait() will fail, throwing an `InvalidJobException`, meaning that the job's data record has been already reaped. This exception is the same as if the job were unknown. (The only case where wait() can be successfully called on a single job more than once is when the previous call to wait() timed out before the job finished.) """ stat = c_int() jid_out = create_string_buffer(128) rusage = pointer(POINTER(drmaa_attr_values_t)()) if isinstance(jobId, str): jobId = jobId.encode(ENCODING) c(drmaa_wait, jobId, jid_out, sizeof(jid_out), byref(stat), timeout, rusage) res_usage = adapt_rusage(rusage) exited = c_int() c(drmaa_wifexited, byref(exited), stat) aborted = c_int() c(drmaa_wifaborted, byref(aborted), stat) signaled = c_int() c(drmaa_wifsignaled, byref(signaled), stat) coredumped = c_int() c(drmaa_wcoredump, byref(coredumped), stat) exit_status = c_int() c(drmaa_wexitstatus, byref(exit_status), stat) term_signal = create_string_buffer(SIGNAL_BUFFER) c(drmaa_wtermsig, term_signal, sizeof(term_signal), stat) return JobInfo(jid_out.value.decode(), bool(exited), bool(signaled), term_signal.value.decode(), bool(coredumped), bool(aborted), int(exit_status.value), res_usage)