nipype.pipeline.plugins.dagman module

Parallel workflow execution via Condor DAGMan

class nipype.pipeline.plugins.dagman.CondorDAGManPlugin(**kwargs)

Bases: nipype.pipeline.plugins.base.GraphPluginBase

Execute using Condor DAGMan

The plugin_args input to run can be used to control the DAGMan execution. The value of most arguments can be a literal string or a filename, where in the latter case the content of the file will be used as the argument value.

Currently supported options are:

• submit_template : submit spec template for individual jobs in a DAG (see

  CondorDAGManPlugin.default_submit_template for the default.

• initial_specs : additional submit specs that are prepended to any job’s

  submit file

• override_specs : additional submit specs that are appended to any job’s

  submit file

• wrapper_cmd : path to an executable that will be started instead of a node

  script. This is useful for wrapper script that execute certain functionality prior or after a node runs. If this option is given the wrapper command is called with the respective Python executable and the path to the node script as final arguments

• wrapper_args : optional additional arguments to a wrapper command

• dagman_args : arguments to be prepended to the arguments of the

  condor_submit_dag call

• block : if True the plugin call will block until Condor has finished

  processing the entire workflow (default: False)

default_submit_template = '\nuniverse = vanilla\nnotification = Never\nexecutable = %(executable)s\narguments = %(nodescript)s\noutput = %(basename)s.out\nerror = %(basename)s.err\nlog = %(basename)s.log\ngetenv = True\n'