clustercontroldrmaa.py

#!/usr/bin/env python3
 
 
 
# std
import sys
 
# ours
from clustercontrolbase import ClusterBase
from validationscript import Script
 
 
class Cluster(ClusterBase):
    """
    A class that provides the controls for running jobs on a (remote)
    Sun Grid Engine cluster. It provides two methods:
    - is_job_finished(job): Returns True or False, depending on whether the job
        has finished execution
    - execute(job): Takes a job and executes it by sending it to the cluster
    """
 
    @staticmethod
    def is_supported():
        """
        Check if qsub is available
        """
        try:
            import drmaa  # noqa
 
            return True
        except ImportError:
            print(
                "drmaa library is not installed, please use 'pip3 install "
                "drmaa'"
            )
            return False
        except RuntimeError as re:
            print("drmaa library not properly configured")
            print(str(re))
            return False
 
    @staticmethod
    def name():
        """
        Returns name of this job control
        """
        return "cluster-drmaa"
 
    @staticmethod
    def description():
        """
        Returns description of this job control
        """
        return "Batch submission via the drmaa interface to Grid Engine"
 
    def __init__(self):
        """!
        The default constructor.
        - Holds the current working directory, which is also the location of
          the shellscripts that are being sent to the cluster.
        - Initializes a logger which writes to validate_basf2.py's log.
        - Finds the revision of basf2 that will be set up on the cluster.
        """
 
        
        self.native_spec = (
            "-l h_vmem={requirement_vmem}G,h_fsize={"
            "requirement_storage}G "
            "-q {queuename} -V"
        )
 
        
        self.requirement_vmem = 4
 
        
        self.requirement_storage = 50
 
        
        self.queuename = "short.q"
 
        # call the base constructor, which will setup the batch cluster
        # common stuff
        super().__init__()
 
    # noinspection PyMethodMayBeStatic
    def adjust_path(self, path: str):
        """!
        This method can be used if path names are different on submission
        and execution hosts.
        @param path: The past that needs to be adjusted
        @return: The adjusted path
        """
 
        return path
 
    # noinspection PyMethodMayBeStatic
    def available(self):
        """!
        The cluster should always be available to accept new jobs.
        @return: Will always return True if the function can be called
        """
 
        return True
 
    def execute(self, job: Script, options="", dry=False, tag="current"):
        """!
        Takes a Script object and a string with options and runs it on the
        cluster, either with ROOT or with basf2, depending on the file type.
 
        @param job: The steering file object that should be executed
        @param options: Options that will be given to the basf2 command
        @param dry: Whether to perform a dry run or not
        @param tag: The folder within the results directory
        @return: None
        """
 
        # import here first so the whole module can also be imported on python
        # installations which have no drmaa at all
        import drmaa
 
        print(str(drmaa.Session()))
 
        with drmaa.Session() as session:
            print("got session ")
            print(str(session))
 
            shell_script_name = self.prepareSubmission(job, options, tag)
 
            # native specification with all the good settings for the batch
            # server
            native_spec_string = self.native_spec.format(
                requirement_storage=self.requirement_storage,
                requirement_vmem=self.requirement_vmem,
                queuename=self.queuename,
            )
            print(
                f"Creating job template for wrapper script {shell_script_name}"
            )
            jt = session.createJobTemplate()
            jt.remoteCommand = shell_script_name
            jt.joinFiles = True
            jt.nativeSpecification = native_spec_string
 
            if not dry:
                jobid = session.runJob(jt)
                self.logger.debug(
                    f"Script {job.name} started with job id {jobid}"
                )
                job.job_id = jobid
 
            session.deleteJobTemplate(jt)
        return
 
    def is_job_finished(self, job: Script):
        """!
        Checks whether the '.done'-file has been created for a job. If so, it
        returns True, else it returns False.
        Also deletes the .done-File once it has returned True.
 
        @param job: The job of which we want to know if it finished
        @return: (True if the job has finished, exit code). If we can't find the
            exit code in the '.done'-file, the returncode will be -654.
            If the job is not finished, the exit code is returned as 0.
        """
 
        # import here first so the whole module can also be imported on python
        # installations which have no drmaa at all
        import drmaa
 
        if job.job_id is None:
            print(
                "Job has not been started with cluster drmaaa because "
                "job id is missing"
            )
            sys.exit(0)
 
        with drmaa.Session() as session:
 
            # some batch server will forget completed jobs right away
            try:
                status = session.jobStatus(job.job_id)
            except drmaa.errors.InvalidJobException:
                print(
                    f"Job info for jobid {job.job_id} cannot be retrieved, assuming job has terminated"
                )
 
                (donefile_exists, donefile_returncode) = self.checkDoneFile(job)
 
                # always return the job es complete even if there is no done
                #  file at this point tho job is also not longer
                # running/queued on the cluster
                return [True, donefile_returncode]
 
            # Return that the job is finished + the return code for it
            # depending when we look for the job this might never be used,
            # because the jobs disappear from qstat before we can query them
            #  ..
            if status == drmaa.JobState.DONE:
                # todo: return code
                return [True, 0]
            if status == drmaa.JobState.FAILED:
                return [True, 1]
 
            return [False, 0]