YamboCalculator

This module manages calculations performed with Yambo. The run of the computation is performed by the python subprocess package (direct scheduler) or by the slurm scheduler.

class mppi.Calculators.YamboCalculator.YamboCalculator(runRules, executable='yambo', skip=True, clean_restart=True, dry_run=False, wait_end_run=True, activate_BeeOND=False, verbose=True, fatlog=False, **kwargs)

Bases: Runner

Perform a Yambo calculation. The parameters used to define the parellelization strategy are provided in the runRules object.

Parameters:

• runRulues (RunRules) – instance of the RunRules class

• executable (string) – set the executable (yambo, ypp, yambo_rt, …) of the Yambo package

• skip (bool) – if True evaluate if the computation can be skipped. This is done by checking that the report file built by yambo exists and contains the string game_over, defined as a data member of this class

• clean_restart (bool) – if True delete the folder with the output files and the database before running the computation

• dry_run (bool) – with this option enabled the calculator setup the calculations and write the script for submitting the job, but the computations are not run

• wait_end_run (bool) – with this option disabled the run method does not wait the end of the run. This option may be useful for interacting with the code in particular in _asincronous_ computation managed by the slurm scheduler

• activate_BeeOND (bool) – if True set I/O of the run in the BeeOND_dir created by the slurm scheduler. The value of the BeeOND_dir is written as a data member of the class and can be modified if needed

• verbose (bool) – set the amount of information provided on terminal

• fatlog (bool) – if True set the -fatlog key to provide more information in the report file

• kwargs –

  other parameters that are stored in the _global_options dictionary

  Computations are performed in the folder specified by the run_dir parameter. The name parameter is used as name of the yambo input and as the name of the folder where yambo writes the o- output files. The jobname parameter is the name of the folder where yambo writes the .ndb databases. If this parameter is not provided in the run method the assumption jobname=name is made by the calculator.

  Example:

  >>> rr = RunRules(scheduler='slurm',ntasks_per_node=4,memory='124GB')
  >>> code = YamboCalculator(rr,executable='yambo',skip=True,verbose=True)
  >>> code.run(input = ..., run_dir = ...,name = ...,jobname = ..., **kwargs)
  

  When the run method is called the class runs the command:

  cd run_dir ; mpirun command executable_name -F name.in -J jobname -C name - O out_dir

  where the arguments of the run method are:

• run_dir (string) – the folder in which the simulation is performed

• input (string) – instance of the YamboInput class that define the input objects

• name (string) – string with the names associated to the input file (without extension). This string is used also as the name of the folder in which results are written (argument of the -C option of yambo) as well as a part of the name of the output files

• jobname (list or string) – string (or list of strings) with the value(s) of the jobname folders (argument of the -J option of yambo). The first element is the folder name, where yambo writes the database. The other values (if provided) are the folders where yambo seeks for pre existing databases. All the elements of the list are assumed to be located in the run_dir of the calculator. If this variable is not specified the value of name is attributed to jobname

• out_dir (string) – position of the folder in which the $jobname folder is located. This parameter is automatically set by the calculator the value of BeeOND_dir if the option activate_BeeOND is enabled. Otherwise all the folders are written in the run_dir

• kwargs – other parameters that are stored in the run_options dictionary

BeeOND_dir = '/mnt/${SLURM_JOB_USER}-jobid_${SLURM_JOB_ID}'

build_slurm_script()

Create the slurm script associated to the run.

Returns:

string with the name of the slurm script

Return type:

string

clean_run()

Delete existing results before performing the computation. Delete the out_dir folder and the folder with the databases. If several folders are provided in the jobname field, only the first one is deleted, since the others are assumed to contain databases obtained from other computations.

clean_slurm_out()

Delete the job_$name.out file.

game_over = 'Game Over & Game summary'

is_to_run()

The method evaluates if the computation has to be performed. If skip is False the run is always performed, instead if skip is True the method checks if the report file exists and contains the string game_over defined as a member of the class. The method adds the key is_to_run to the run_options of the class.

Note that the first element of the report list is used, so caution is needed if there is more than one report file in the report key of the results dictionary.

post_processing()

Return a dictionary with the names of the o- file(s), the report ‘r-’ file, the ns.db1 in the SAVE folder and the names of the ndb databases written by yambo in the jobname folder. The method performs a sanity check of the computation by checking that the game_over string is found in the report and shows the time needed to perform the simulation (if the time_profile string is found in the report).

Returns:

the dictionary

{‘output’ : [o-1,o-2,…],’report’:…,’dft’:…,’dipoles’:…, ….}

Return type:

dict

pre_processing()

Process local run dictionary. Check that the run_dir exists and that it contains the SAVE folder. If clean_restart = True the results associated to previous computations are deleted before the run. The slurm out script is always deleted before the run, otherwise the calculator can erroneously assume that the run is completed.

Note

If the run_dir and/or the SAVE folder do not exist an alert is written but the execution of the run method proceedes.

process_run()

Method associated to the running of the executable. The method runs the computation and wait the end of the computation before passing to the post_processing() method.

run_command()

Define the run command used to run the computation.

Returns:

command that runs the computation

Return type:

string

run_ended(job)

Check the status of the running job.

Parameters:

job – reference to the actual job. job is an istance of Popen for direct scheduler or a string for slurm scheduler

Returns:

return True if the computation is ended and False if it is running

Return type:

bool

run_job()

Run the computation. The operations performed depend on the scheduler adopted. If the dry_run option is enabled the run is not performed but the slurm script is written on disk.

Returns:

The type of the object depends on the chosen scheduler. For scheduler direct job is an instance of Popen, while for slurm scheduler job is the name of the slurm script.

time_profile = 'Time-Profile'

wait(job)

Wait the end of the job. If the dry_run option is enabled or wait_end_run is False the check is not performed.

Parameters:

jobs – The reference to the job to be executed. If the scheduler is direct jobs is an instance of Popen of the :py:class:subprocess package. If the scheduler is slurm jobs is a string with the name of the slurm script

mppi.Calculators.YamboCalculator.build_results_dict(run_dir, outputPath, dbsPath, verbose=True)

Return a dictionary with the names of the o- file(s), the report ‘r-’ file, the ns.db1 in the SAVE folder and the names of the ndb database written by yambo in the jobname folder. Databases are sought in the dbsPath.

Parameters:

• run_dir (string) – run_dir folder of the calculation

• outputPath (string) – folder with the ‘o-’ files

• dbsPath (list) – list of folders with the ndb databases

• verbose (bool) – set the amount of information provided on terminal

Returns:

the dictionary

{‘output’ : [o-1,o-2,…],’dft’:…,’dipoles’:…, ….}

Return type:

dict

mppi.Calculators.YamboCalculator.get_db_files(dbsPath)

Look for the files of tht type ndb.* in the dbsPath. Note that the first element of dbsPath is the folder where Yambo writes the ndb database. If a ndb is found in this folder its (eventual) replica in the other folders of dbsPath are not considered (this behavior protects under erroneuos identification of the correct databas that can happen, for instance, if a ndb given as input is not compliant with the actual computation so that Yambo has to compute it).

Parameters:

dbstPath (list) – list of folders in which the ndb databases created by Yambo are sought

Returns:

A dictionary in which the keys are the extension of the

databases found and the values are their names, including the path

Return type:

dict

mppi.Calculators.YamboCalculator.get_output_files(path)

Scan the path with the output files and build a dictionary in which the keys are type of output (hf,qp,carriers,…) and the values are the names of the file for each type. If the path contains several replica of the output files (due to the fact the Yambo has been exectuted many times without cleaning the output folder) the function identifies the files associated to the last run.

Parameters:

path (string) – folder where the o-* files are stored

Returns:

Dictionary with the types (keys) and names values,

including the path, of the files o-* produced by the run

Return type:

dict

mppi.Calculators.YamboCalculator.get_report(path)

Look for the name of the r-* file(s) produced by the execution of the code. If multiple istances of the report are found, the function selects the one assciated to the last computation.

Parameters:

path (string) – folder with the r-* and the o-* files

Returns:

String with the name, including the path, of the file r-* produced by the run. If no report files is found an empty string is provided as output

Return type:

string

mppi.Calculators.YamboCalculator.type_identifier(file)

Found the type of the o-file according to its name. Different extension like ‘hf’ or ‘hf_01’ are recognized with the same type, that is ‘hf’ in this example.

Parameters:

file (string) – file name

Returns:

string with the type of the file

Return type:

string