seisflows.system.lsf
====================

.. py:module:: seisflows.system.lsf

.. autoapi-nested-parse::

   This is the subclass seisflows.system.lsf.Lsf

   This class provides the core utilities interaction with HPC systems which run
   using the Platform Load Sharing Facility (LSF) workload management platform.



Classes
-------

.. autoapisummary::

   seisflows.system.lsf.Lsf


Functions
---------

.. autoapisummary::

   seisflows.system.lsf._modify_run_call_single_proc


Module Contents
---------------

.. py:class:: Lsf

   Bases: :py:obj:`seisflows.system.cluster.Cluster`


   An interface through which to submit workflows, run tasks in serial or
   parallel, and perform other system functions.

   By hiding environment details behind a python interface layer, these
   classes provide a consistent command set across different computing
   environments.

   Intermediate files are written to a global scratch path self.path.SCRATCH,
   which must be accessible to all compute nodes.

   Optionally, users can provide a local scratch path self.path.LOCAL if each
   compute node has its own local filesystem.

   For important additional information, please see
   http://seisflows.readthedocs.org/en/latest/manual/
                                               manual.html#system-configuration


   .. py:method:: submit(submit_call=None)

      Submits workflow using 'bsub' arguments



   .. py:method:: run(classname, method, single=False, run_call=None, **kwargs)

      Runs task multiple times in embarrassingly parallel fasion on the
      maui cluster

      Executes classname.method(*args, **kwargs) NTASK times,
      each time on NPROC CPU cores

      :type classname: str
      :param classname: the class to run
      :type method: str
      :param method: the method from the given `classname` to run



   .. py:method:: taskid()

      Provides a unique identifier for each running task



   .. py:method:: checkpoint(path, classname, method, kwargs)

      Inherits from workflow.system.workstation.Workstation



   .. py:method:: _check_job_status(job_ids)

      Queries completion status of a single job

      TODO this function is mangled, needs to be rewritten

      :type job: str
      :param job: job id to query



   .. py:method:: _job_id_list(stdout, single)

      Parses job id list from LSF standard output

      :type stdout: str
      :param stdout: the output of subprocess.check_output()
      :type single: bool
      :param single: if running a single process job, returns a list of length
          1 with a single job id, else returns a list of length self.par.NTASK
          for all arrayed jobs
      :rtype: list
      :return: a list of array jobs that should be currently running



   .. py:method:: _query(jobid)

      Retrives job state from LSF database

      :type jobid: str
      :param jobid: job id to query LSF system about



.. py:function:: _modify_run_call_single_proc(run_call)