pyiron.base.master.parallel module¶
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class
pyiron.base.master.parallel.
GenericOutput
[source]¶ Bases:
collections.OrderedDict
Generic Output just a place holder to store the output of the last child directly in the ParallelMaster.
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class
pyiron.base.master.parallel.
JobGenerator
(job, no_job_checks=False)[source]¶ Bases:
object
JobGenerator - this class implements the functions to generate the parameter list, modify the individual jobs according to the parameter list and generate the new job names according to the parameter list.
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property
parameter_list
¶
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property
parameter_list_cached
¶
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property
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class
pyiron.base.master.parallel.
ParallelMaster
(project, job_name)[source]¶ Bases:
pyiron.base.master.generic.GenericMaster
MasterJob that handles the creation and analysis of several parallel jobs (including master and continuation jobs), Examples are Murnaghan or Phonon calculations
- 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
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.. attribute:: job_name
name of the job, which has to be unique within the project
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.. attribute:: status
- execution status of the job, can be one of the following [initialized, appended, created, submitted,
running, aborted, collect, suspended, refresh, busy, finished]
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.. attribute:: job_id
unique id to identify the job in the pyiron database
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.. attribute:: parent_id
job id of the predecessor job - the job which was executed before the current one in the current job series
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.. 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.
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.. attribute:: child_ids
list of child job ids - only meta jobs have child jobs - jobs which list the meta job as their master
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.. attribute:: project
Project instance the jobs is located in
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.. attribute:: project_hdf5
ProjectHDFio instance which points to the HDF5 file the job is stored in
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.. attribute:: job_info_str
short string to describe the job by it is job_name and job ID - mainly used for logging
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.. attribute:: working_directory
working directory of the job is executed in - outside the HDF5 file
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.. attribute:: path
path to the job as a combination of absolute file system path and path within the HDF5 file.
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.. attribute:: version
Version of the hamiltonian, which is also the version of the executable unless a custom executable is used.
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.. attribute:: executable
Executable used to run the job - usually the path to an external executable.
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.. attribute:: library_activated
For job types which offer a Python library pyiron can use the python library instead of an external executable.
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.. attribute:: server
Server object to handle the execution environment for the job.
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.. attribute:: queue_id
the ID returned from the queuing system - it is most likely not the same as the job ID.
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.. attribute:: logger
logger object to monitor the external execution and internal pyiron warnings.
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.. attribute:: restart_file_list
list of files which are used to restart the calculation from these files.
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.. attribute:: job_type
- Job type object with all the available job types: [‘ExampleJob’, ‘SerialMaster’, ‘ParallelMaster’,
‘ScriptJob’, ‘ListMaster’]
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.. attribute:: child_names
Dictionary matching the child ID to the child job name.
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.. attribute:: ref_job
Reference job template from which all jobs within the ParallelMaster are generated.
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.. attribute:: number_jobs_total
Total number of jobs
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collect_logfiles
()[source]¶ Collect the log files of the external executable and store the information in the HDF5 file. This method is currently not implemented for the ParallelMaster.
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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 meta jobs derived from the ParallelMaster.
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copy
()[source]¶ Copy the GenericJob object which links to the job and its HDF5 file
- Returns
New GenericJob object pointing to the same job
- Return type
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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
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create_child_job
(job_name)[source]¶ Internal helper function to create the next child job from the reference job template - usually this is called as part of the create_jobs() function.
- Parameters
job_name (str) – name of the next job
- Returns
next job
- Return type
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from_hdf
(hdf=None, group_name=None)[source]¶ Restore the ParallelMaster from an HDF5 file
- Parameters
hdf (ProjectHDFio) – HDF5 group object - optional
group_name (str) – HDF5 subgroup name - optional
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interactive_ref_job_initialize
()[source]¶ To execute the reference job in interactive mode it is necessary to initialize it.
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is_finished
()[source]¶ Check if the ParallelMaster job is finished - by checking the job status and the submission status.
- Returns
[True/False]
- Return type
bool
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iter_jobs
(convert_to_object=True)[source]¶ Iterate over the jobs within the ListMaster
- Parameters
convert_to_object (bool) – load the full GenericJob object (default) or just the HDF5 / JobCore object
- Returns
Yield of GenericJob or JobCore
- Return type
yield
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property
number_jobs_total
¶ Get number of total jobs
- Returns
number of total jobs
- Return type
int
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output_to_pandas
(sort_by=None, h5_path='output')[source]¶ Convert output of all child jobs to a pandas Dataframe object.
- Parameters
sort_by (str) – sort the output using pandas.DataFrame.sort_values(by=sort_by)
h5_path (str) – select child output to include - default=’output’
- Returns
output as dataframe
- Return type
pandas.Dataframe
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property
ref_job
¶ Get the reference job template from which all jobs within the ParallelMaster are generated.
- Returns
reference job
- Return type
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refresh_submission_status
()[source]¶ Refresh the submission status - if a job ID job_id is set then the submission status is loaded from the database.
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reset_job_id
(job_id=None)[source]¶ Reset the job id sets the job_id to None as well as all connected modules like JobStatus and SubmissionStatus.
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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.
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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.
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run_static
()[source]¶ The run_static function is executed within the GenericJob class and depending on the run_mode of the Parallelmaster and its child jobs a more specific run function is selected.
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save
()[source]¶ Save the object, by writing the content to the HDF5 file and storing an entry in the database.
- Returns
Job ID stored in the database
- Return type
(int)
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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.
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to_hdf
(hdf=None, group_name=None)[source]¶ Store the ParallelMaster in an HDF5 file
- Parameters
hdf (ProjectHDFio) – HDF5 group object - optional
group_name (str) – HDF5 subgroup name - optional