pyiron.base.master.generic module

class pyiron.base.master.generic.GenericMaster(project, job_name)[source]

Bases: pyiron.base.job.generic.GenericJob

The GenericMaster is the template class for all meta jobs - meaning all jobs which contain multiple other jobs. It defines the shared functionality of the different kind of job series.

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:: child_names

Dictionary matching the child ID to the child job name.

append(job)[source]

Append a job to the GenericMaster - just like you would append an element to a list.

Parameters

job (GenericJob) – job to append

property child_ids

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

Returns

list of child job ids

Return type

list

property child_names

Dictionary matching the child ID to the child job name

Returns

{child_id: child job name }

Return type

dict

collect_output()[source]

Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.

copy_to(project=None, new_job_name=None, input_only=False, new_database_entry=True)[source]

Copy the content of the job including the HDF5 file to a new location

Parameters
  • project (ProjectHDFio) – project to copy the job to

  • new_job_name (str) – to duplicate the job within the same porject it is necessary to modify the job name - optional

  • input_only (bool) – [True/False] to copy only the input - default False

  • new_database_entry (bool) – [True/False] to create a new database entry - default True

Returns

GenericJob object pointing to the new location.

Return type

GenericJob

first_child_name()[source]

Get the name of the first child job

Returns

name of the first child job

Return type

str

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

Restore the GenericMaster from an HDF5 file

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

  • group_name (str) – HDF5 subgroup name - optional

get_child_cores()[source]

Calculate the currently active number of cores, by summarizing all childs which are neither finished nor aborted.

Returns

number of cores used

Return type

(int)

interactive_close()[source]

interactive close is not implemtned for MetaJobs

interactive_fetch()[source]

interactive fetch is not implemtned for MetaJobs

interactive_flush(path='generic', include_last_step=True)[source]

interactive flush is not implemtned for MetaJobs

move_to(project)[source]

Move the content of the job including the HDF5 file to a new location

Parameters

project (ProjectHDFio) – project to move the job to

Returns

JobCore object pointing to the new location.

Return type

JobCore

pop(i=-1)[source]

Pop a job from the GenericMaster - just like you would pop an element from a list

Parameters

i (int) – position of the job. (Default is last element, -1.)

Returns

job

Return type

GenericJob

run_if_interactive()[source]

For jobs which executables are available as Python library, those can also be executed with a library call instead of calling an external executable. This is usually faster than a single core python job.

run_if_interactive_non_modal()[source]

Run if interactive non modal is not implemented for MetaJobs

run_if_refresh()[source]

Internal helper function the run if refresh function is called when the job status is ‘refresh’. If the job was suspended previously, the job is going to be started again, to be continued.

set_child_id_func(child_id_func)[source]

Add an external function to derive a list of child IDs - experimental feature

Parameters

child_id_func (Function) – Python function which returns the list of child IDs

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

Store the GenericMaster in an HDF5 file

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

  • group_name (str) – HDF5 subgroup name - optional

validate_ready_to_run()[source]

Validate that the calculation is ready to be executed. By default no generic checks are performed, but one could check that the input information is complete or validate the consistency of the input at this point.

write_input()[source]

Write the input files for the external executable. This method has to be implemented in the individual hamiltonians.

pyiron.base.master.generic.get_function_from_string(function_str)[source]

Convert a string of source code to a function

Parameters

function_str – function source code

Returns

Return type

function