gc3libs.backends.batch

This module provides a generic BatchSystem class from which all batch-like backends should inherit.

class gc3libs.backends.batch.BatchSystem(name, architecture, max_cores, max_cores_per_job, max_memory_per_core, max_walltime, auth, frontend, transport, accounting_delay=15, ssh_config=None, keyfile=None, ignore_ssh_host_keys=False, ssh_timeout=None, large_file_threshold=None, large_file_chunk_size=None, **extra_args)

Base class for backends dealing with a batch-queue system (e.g., PBS/TORQUE, Grid Engine, etc.)

This is an abstract class, that you should subclass in order to interface with a given batch queuing system. (Remember to call this class’ constructor in the derived class __init__ method.)

cancel_job(*args, **kwargs)

Cancel a running job. If app is associated to a queued or running remote job, tell the execution middleware to cancel it.

close(*args, **kwargs)

Return True if the list of files is expressed in one of the file transfer protocols the LRMS supports.

Return False otherwise.

free(*args, **kwargs)

Free up any remote resources used for the execution of app. In particular, this should delete any remote directories and files.

Call this method when app.execution.state is anything other than TERMINATED results in undefined behavior and will likely be the cause of errors later on. Be cautious.

get_epilogue_script(app)

This method will get the epilogue script(s) for the app application and will return a string which contains the contents of the script(s) merged together.

get_jobid_from_submit_output(output, regexp)

Parse the output of the submission command. Regexp is provided by the caller.

get_prologue_script(app)

This method will get the prologue script(s) for the app application and will return a string which contains the contents of the script(s) merged together.

get_results(*args, **kwargs)

Retrieve job output files into local directory download_dir.

Directory download_dir must already exists.

If optional 3rd argument overwrite is False (default), then existing files within download_dir (or subdirectories thereof) will not be altered in any way.

If overwrite is instead True, then the (optional) 4th argument changed_only determines what files are overwritten:

  • if changed_only is True (default), then only files for which the source has a different size or has been modified more recently than the destination are copied;
  • if changed_only is False, then all files in source will be copied into destination, unconditionally.

Output files that do not exist in download_dir will be copied, independently of the overwrite and changed_only settings.

Parameters:
  • job (Task) – the Task instance whose output should be retrieved
  • download_dir (str) – path to download files into
  • overwrite (bool) – if False, do not download files that already exist
  • changed_only (bool) – if both this and overwrite are True, only overwrite those files such that the source is newer or different in size than the destination.
peek(*args, **kwargs)

Download size bytes (at offset offset from the start) from remote file remote_filename and write them into local_file. If size is None (default), then snarf contents of remote file from offset unto the end.

First argument remote_filename is the path to a file relative to the remote job “sandbox”.

Argument local_file is either a local path name (string), or a file-like object supporting a .write() method. If local_file is a path name, it is created if not existent, otherwise overwritten. In any case, upon exit from this procedure, the stream will be positioned just after the written bytes.

Fourth optional argument offset is the offset from the start of the file. If offset is negative, it is interpreted as an offset from the end of the remote file.

Any exception raised by operations will be re-raised to the caller.

submit_job(*args, **kwargs)

This method will create a remote directory to store job’s sandbox, and will copy the sandbox in there.

update_job_state(*args, **kwargs)

Query the state of the remote job associated with app and update app.execution.state accordingly. Return the corresponding Run.State; see Run.State for more details.

validate_data(data_file_list)

Return True if the list of files is expressed in one of the file transfer protocols the LRMS supports.

Return False otherwise.

gc3libs.backends.batch.generic_filename_mapping(jobname, jobid, file_name)

Map STDOUT/STDERR filenames (as recorded in Application.outputs) to commonly used default STDOUT/STDERR file names (e.g., <jobname>.o<jobid>).