pygromos.simulations.hpc_queuing.job_scheduling.schedulers package

Submodules

pygromos.simulations.hpc_queuing.job_scheduling.schedulers.scheduler_functions module

pygromos.simulations.hpc_queuing.job_scheduling.schedulers.scheduler_functions.chain_submission(simSystem: pygromos.files.gromos_system.gromos_system.Gromos_System, out_dir_path: str, out_prefix: str, chain_job_repetitions: int, worker_script: str, job_submission_system: pygromos.simulations.hpc_queuing.submission_systems._submission_system._SubmissionSystem, jobname: str, run_analysis_script_every_x_runs: int = 0, in_analysis_script_path: str = '', start_run_index: int = 1, prefix_command: str = '', previous_job_ID: Optional[int] = None, work_dir: Optional[str] = None, initialize_first_run: bool = True, reinitialize_every_run: bool = False, verbose: bool = False, verbose_lvl: int = 1) → Tuple[int, str, pygromos.files.gromos_system.gromos_system.Gromos_System][source]

this function submits a chain of simulation steps to the queuing system and does the file managment.

Parameters

  • simSystem (Gromos_System) – simulation system

  • out_dir_path (str) – out directory path

  • out_prefix (str) – out prefix for simulation files

  • chain_job_repetitions (int) – how often, should the simulation be repeated (in continuation)

  • worker_script (str) – worker, that should be submitted. This script will be executed at each scheduled job.

  • job_submission_system (_SubmissionSystem) – submission system, what type of submission?

  • jobname (str) – name of the simulation job

  • run_analysis_script_every_x_runs (int, optional) – run analysis in between - (careful will not be overwritten, make sure final analysis is correct.), by default 0

  • in_analysis_script_path (str, optional) – analysis script for simulation, that should be applied (will at least be applied after the full simulation chain.), by default “”

  • start_run_index (int, optional) – start index of the job chain., by default 1

  • prefix_command (str, optional) – any bash prefix commands, before submitting?, by default “”

  • previous_job_ID (int, optional) – ID of the prefious job, to be chained to. , by default None

  • work_dir (str, optional) – dir to wich the work in progress will be written. if None a tmp-srcatch dir will be used with LSF!, by default None

  • initialize_first_run (bool, optional) – should the velocities for the first run be initialized?, by default True

  • reinitialize_every_run (bool, optional) – should in every run, the velocities be reinitialized?, by default False

  • verbose (bool, optional) – more bla bla, by default False

  • verbose_lvl (int, optional) – nicely define ammount of bla bla, by default 1

Returns

Tuple[previous_job_ID, tmp_jobname, simSystem] will return the last job_ID, the last tmp_jobname and the final gromosSystem.

Return type

Tuple[int, str, Gromos_System]

Raises

ValueError – if submission fails. This can habe various reasons, always check also the present files! (*omd etc.)

pygromos.simulations.hpc_queuing.job_scheduling.schedulers.scheduler_functions.do_skip_job(tmp_out_cnf: str, simSystem: pygromos.files.gromos_system.gromos_system.Gromos_System, tmp_jobname: str, job_submission_system: pygromos.simulations.hpc_queuing.submission_systems._submission_system._SubmissionSystem, previous_job: int, verbose: bool = True, verbose_lvl: int = 1) → Tuple[bool, int][source]

This function returns true if the job was already submitted or already finished, as well as the job id.

Parameters

  • tmp_out_cnf (str) – the possible final out cnf

  • simSystem (Gromos_System) – the simulation system

  • tmp_jobname (str) – possible job-name

  • job_submission_system (_SubmissionSystem) – submission system

  • previous_job (int) – job, that was submitted before this one.

  • verbose (bool, optional) – more bla bla, by default True

  • verbose_lvl (int, optional) – nicely define ammount of bla bla, by default 1

Returns

the bool tells, if the job was already submitted, the id is the possibly found job id of the job, if it is in the queue.

Return type

Tuple[bool, int]

Raises

  • IOError – if a tmp_out_cnf is present, we assume the simulation run was successfull. If it can not be parsed in, something else is a problem, but we should not continue our chain!

  • ValueError – if multiple jobs with same name were found in the queue, we assume, the search regex did not work.

pygromos.simulations.hpc_queuing.job_scheduling.schedulers.simulation_scheduler module

Wrapper for Long simulations - similar to repex_EDS_long_production_run. This script schedules Simulations ons euler into the queue.

pygromos.simulations.hpc_queuing.job_scheduling.schedulers.simulation_scheduler.do(in_simSystem: pygromos.files.gromos_system.gromos_system.Gromos_System, out_dir_path: str, simulation_run_num: int, equilibration_run_num: int = 0, initialize_first_run=False, reinitialize_every_run=False, analysis_script_path: typing.Optional[str] = None, submission_system: pygromos.simulations.hpc_queuing.submission_systems._submission_system._SubmissionSystem = <pygromos.simulations.hpc_queuing.submission_systems.lsf.LSF object>, previous_job_ID: typing.Optional[int] = None, _no_double_submit_check: bool = False, _work_dir: typing.Optional[str] = None, verbose: bool = True, verbose_lvl: int = 1) → int[source]

This function schedules simulations starting from the gromos system.

Parameters

  • in_simSystem (Gromos_System) – system that should be submitted with the provided imd file

  • out_dir_path (str) – out directory path for the simulation

  • simulation_run_num (int) – number of simulations

  • equilibration_run_num (int, optional) – number of the equilibraitons, by default 0

  • initialize_first_run (bool, optional) – should the velocities be initialized in the first run?, by default False

  • reinitialize_every_run (bool, optional) – DEAPPRECIATED! should always the velocities be initialized, by default False

  • analysis_script_path (str, optional) – path to the analysis script, that should be used for this simulaiton approach, by default None

  • submission_system (_SubmissionSystem, optional) – system, to be used to submit the jobs, by default LSF()

  • previous_job_ID (int, optional) – previous job ID, by default None

  • _no_double_submit_check (bool, optional) – don’t check if job was already submit to queue (increases performance!), by default False

  • _work_dir (str, optional) – directory, to write out the tmp files, by default None

  • verbose (bool, optional) – Baeh Baeh, by default True

  • verbose_lvl (int, optional) – amount of Baehs, by default 1

Returns

the last job id, that was submitted.

Return type

int

Raises

IOError – If error happens in preperation of simulation or in the submission

Module contents