pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers package

Submodules

pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.clean_up_simulation_files module

After simulation cleanup This module is thought to be used as a clean up script after each run, reducing the need of storage for RE-EDS simulations on Euler or any other cluster :) it mainly removes not needed temporary files and compresses long trajectory files. It should be hanged in after each simulation step.

pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.clean_up_simulation_files.do(in_simulation_dir: str, n_processes: int = 1, verbose: bool = True) → None[source]

do clean_up_simulation_files

Parameters

  • in_simulation_dir (str) – path to folder, which contains the raw gromos output

  • n_processes (int, optional) – how many processes should be used?

  • verbose (bool, optional) – loud and noisy?

Return type

None

pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.simulation_run_worker module

pygromos.simulations.hpc_queuing.job_scheduling.workers.simulation_workers.simulation_run_worker.work(out_dir: str, in_cnf_path: str, in_imd_path: str, in_top_path: str, runID: int = 1, in_perttopo_path: Optional[str] = None, in_disres_path: Optional[str] = None, in_posres_path: Optional[str] = None, in_refpos_path: Optional[str] = None, in_qmmm_path: Optional[str] = None, out_trc: bool = False, out_tre: bool = False, out_trg: bool = False, out_trv: bool = False, out_trf: bool = False, out_trs: bool = False, nmpi: int = 1, nomp: int = 1, reinitialize_every_run: bool = False, initialize_first_run: bool = True, gromosXX_bin_dir: Optional[str] = None, gromosXX_check_binary_paths: bool = True, work_dir: Optional[str] = None, zip_trajectories: bool = True, **kwargs)[source]

Executed by repex_EDS_long_production_run as workers

Parameters

  • out_dir (str) – final output dir

  • in_cnf_path (str) – input coordinates

  • in_imd_path (str) – input imd-parameter file

  • in_top_path (str) – input topology

  • in_perttopo_path (str) – input pertubation

  • in_disres_path (str) – input disres

  • in_qmmm_path (str) – input qmmm

  • nmpi (int, optional) – number of mpi cores (def.=1)

  • nomp (int, optional) – number of omp cores (def.= 1)

  • out_trg (bool, optional) – True if trg shall be written out.

  • out_trv (bool, optional) – True if trv shall be written out.

  • out_trf (bool, optional) – True if trf shall be written out.

  • out_trs (bool, optional) – True if trs shall be written out.

  • gromosXX_bin_dir (str, optional) – path to gromos binary directory

  • work_dir (str, optional) – work directory

  • zip_trajectories (bool) – determines whether trajectories are zipped

Returns

return number

Return type

int

Module contents