pyiron.base.job.script module

class pyiron.base.job.script.Notebook[source]

Bases: object

class for pyiron notebook objects

static get_custom_dict()[source]
static store_custom_output_dict(output_dict)[source]
class pyiron.base.job.script.ScriptJob(project, job_name)[source]

Bases: pyiron.base.job.generic.GenericJob

The ScriptJob class allows to submit Python scripts and Jupyter notebooks to the pyiron job management system.

Parameters
  • project (ProjectHDFio) – ProjectHDFio instance which points to the HDF5 file the job is stored in

  • job_name (str) – name of the job, which has to be unique within the project

attribute

job_name

name of the job, which has to be unique within the project

.. attribute:: status
execution status of the job, can be one of the following [initialized, appended, created, submitted, running,

aborted, collect, suspended, refresh, busy, finished]

.. attribute:: job_id

unique id to identify the job in the pyiron database

.. attribute:: parent_id

job id of the predecessor job - the job which was executed before the current one in the current job series

.. attribute:: master_id

job id of the master job - a meta job which groups a series of jobs, which are executed either in parallel or in serial.

.. attribute:: child_ids

list of child job ids - only meta jobs have child jobs - jobs which list the meta job as their master

.. attribute:: project

Project instance the jobs is located in

.. attribute:: project_hdf5

ProjectHDFio instance which points to the HDF5 file the job is stored in

.. attribute:: job_info_str

short string to describe the job by it is job_name and job ID - mainly used for logging

.. attribute:: working_directory

working directory of the job is executed in - outside the HDF5 file

.. attribute:: path

path to the job as a combination of absolute file system path and path within the HDF5 file.

.. attribute:: version

Version of the hamiltonian, which is also the version of the executable unless a custom executable is used.

.. attribute:: executable

Executable used to run the job - usually the path to an external executable.

.. attribute:: library_activated

For job types which offer a Python library pyiron can use the python library instead of an external executable.

.. attribute:: server

Server object to handle the execution environment for the job.

.. attribute:: queue_id

the ID returned from the queuing system - it is most likely not the same as the job ID.

.. attribute:: logger

logger object to monitor the external execution and internal pyiron warnings.

.. attribute:: restart_file_list

list of files which are used to restart the calculation from these files.

.. attribute:: job_type
Job type object with all the available job types: [‘ExampleJob’, ‘SerialMaster’, ‘ParallelMaster’, ‘ScriptJob’,

‘ListMaster’]

.. attribute:: script_path

the absolute path to the python script

collect_logfiles()[source]

Compatibility function - but no log files are being collected

collect_output()[source]

Collect output function updates the master ID entries for all the child jobs created by this script job, if the child job is already assigned to an master job nothing happens - master IDs are not overwritten.

from_hdf(hdf=None, group_name=None)[source]

Restore the ScriptJob from an HDF5 file

Parameters
  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

run_if_lib()[source]

Compatibility function - but library run mode is not available

property script_path

Python script path

Returns

absolute path to the python script

Return type

str

set_input_to_read_only()[source]

This function enforces read-only mode for the input classes, but it has to be implement in the individual classes.

to_hdf(hdf=None, group_name=None)[source]

Store the ScriptJob in an HDF5 file

Parameters
  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

write_input()[source]

Copy the script to the working directory - only python scripts and jupyter notebooks are supported