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qflow

Workflow for qsub system, using DPDispatcher

thmd.qflow

Modules:

help_function

Define support functions for qflow package.

Functions:

read_nodes(file_name: str) -> list

Read node list from file. Support delimiter: '|', ',', ';', ':', ' ', ' '

Args:
    file_name (str): File name.

Returns:
    list: List of unique nodes.

format_ignore_string(nodes: list) -> str

Format qsub_string for ignore nodes.

format_select_string(nodes: list) -> str

Format qsub_string for selected nodes.

machine_unist

Functions:

  • Tachyon –

    Define Machine for running jobs on Tachyon cluster at UNIST.

  • Eagle –

    Define Machine for running jobs on Tachyon cluster at UNIST.

  • Lion –

    Define Machine for running jobs on Tachyon cluster at UNIST.

  • Leopard –

    Define Machine for running jobs on Tachyon cluster at UNIST.

  • CanCentosGpu –

    Define Machine for running jobs on CAN cluster at UNIST.

Attributes:

sge_template = {'context_type': 'SSHContext', 'batch_type': 'SGE', 'local_root': './', 'remote_root': '/home1/p001cao/work/w24_tmp', 'remote_profile': {'hostname': '10.0.7.53', 'username': 'p001cao', 'password': 'p001cao', 'port': 2022, 'timeout': 20}} module-attribute

Tachyon(remote_path: str = '/home1/p001cao/work/w24_alff')

Define Machine for running jobs on Tachyon cluster at UNIST.

Parameters:

  • remote_path (str, default: '/home1/p001cao/work/w24_alff' ) –

    Remote working folder.

Eagle(remote_path: str = '/uwork/p001cao/work/w24_alff')

Define Machine for running jobs on Tachyon cluster at UNIST.

Parameters:

  • remote_path (str, default: '/uwork/p001cao/work/w24_alff' ) –

    Remote working folder.

Lion(remote_path: str = '/uwork/p001cao/work/w24_alff')

Define Machine for running jobs on Tachyon cluster at UNIST.

Parameters:

  • remote_path (str, default: '/uwork/p001cao/work/w24_alff' ) –

    Remote working folder.

Leopard(remote_path: str = '/uwork/p001cao/work/w24_alff')

Define Machine for running jobs on Tachyon cluster at UNIST.

Parameters:

  • remote_path (str, default: '/uwork/p001cao/work/w24_alff' ) –

    Remote working folder.

CanCentosGpu(remote_path: str = '/home/tha/work/w24_alff')

Define Machine for running jobs on CAN cluster at UNIST.

Parameters:

  • remote_path (str, default: '/home/tha/work/w24_alff' ) –

    Remote working folder.

qsub_script

Define the template for qsub job submission.

Functions:

  • qsub_sge_job –

    Return the example script for submiting SGE job.

  • winBAT_submit_dispatcher –

    Return the windows batch script for submitting DP dispatcher.

  • winBAT_cmd –

    Return the example script for running command in cmd.

  • winBAT_wsl –

    Return the example script for running command in cmd.

  • python_dispatcher –

    Return the example script for using dpdispatcher.

qsub_sge_job() -> str

Return the example script for submiting SGE job.

winBAT_submit_dispatcher(conda_env: str = None) -> str

Return the windows batch script for submitting DP dispatcher.

winBAT_cmd(command: str, conda_env: str = 'py11') -> str

Return the example script for running command in cmd.

winBAT_wsl(command: str, conda_env: str = 'py11') -> str

Return the example script for running command in cmd.

python_dispatcher() -> str

Return the example script for using dpdispatcher.

resource_unist

Functions:

Attributes:

tachyon_template = {'group_size': 1, 'queue_name': 'ib.q', 'kwargs': {'pe_name': 'mpi_8', 'job_name': 'zDP'}, 'cpu_per_node': 8, 'custom_flags': ['#$ -l h_rt=168:00:00', '#$ -l mem_used=600M'], 'source_list': ['/etc/profile.d/modules.sh'], 'module_list': ['mpi/openmpi4.1.7-clang17-IB', 'lammps/llvmOMPI4-dev'], 'envs': {'OMP_NUM_THREADS': 1, 'OMPI_MCA_btl_openib_allow_ib': 1, 'OMPI_MCA_btl': '^tcp'}} module-attribute

Tachyon_lammps_ib(n_cpu: int = 16)

Define Resources for running LAMMPS on Tachyon cluster at UNIST, only InfiniBand nodes.

Parameters:

  • n_cpu (int, default: 16 ) –

    Number of CPU to run job.

Tachyon_lammps_tcp(n_cpu: int = 8)

Define Resources for running LAMMPS on Tachyon cluster at UNIST, only use TCP.

Parameters:

  • n_cpu (int, default: 8 ) –

    Number of CPU to run job.

Tachyon_gpaw_ib(n_cpu: int = 16)

Define Resources for running GPAW on Tachyon cluster at UNIST.

Parameters:

  • n_cpu (int, default: 16 ) –

    Number of CPU to run job.

Tachyon_gpaw_ucx(n_cpu: int = 16)

Define Resources for running GPAW on Tachyon cluster at UNIST.

Parameters:

  • n_cpu (int, default: 16 ) –

    Number of CPU to run job.

Tachyon_gpaw_tcp(n_cpu: int = 8)

Tachyon_lammps_ase(n_cpu: int = 16)

Tachyon_ase_ib(n_cpu: int = 16)

Tachyon_ase_tcp(n_cpu: int = 8)

Lion_lammps(n_cpu: int = 12, queue_name: str = 'lion-normal.q', pe_name: str = 'lion-normal', time: str = '168:00:00')

Define Resources for running LAMMPS on Eagle cluster at UNIST.

Parameters:

  • n_cpu (int, default: 12 ) –

    Number of CPU to run job. 12x for Lion, 8x for Leopard, 10x for Eagle.

  • queue_name (str, default: 'lion-normal.q' ) –

    SGE's queue name. Available queues: - Lion: lion-normal.q, lion-short.q, lion-long.q - Leopard: leopard-normal.q, leopard-short.q, leopard-long.q

  • pe_name (str, default: 'lion-normal' ) –

    SGE's Parallel environment name: mpi, mpi_1~mpi_20 - Lion: lion-normal, lion-short, lion-long - Leopard: leopard-normal, leopard-short, leopard-long

  • time (str, default: '168:00:00' ) –

    Time limit for the job. normal: '168:00:00', long: '540:00:00'

Leopard_lammps(n_cpu: int = 8, queue_name: str = 'leopard-normal.q', pe_name: str = 'leopard-normal', time: str = '168:00:00')

Eagle_lammps(n_cpu: int = 10, pe_name: str = 'mpi_10')

Define Resources for running LAMMPS on Eagle cluster at UNIST.

Parameters:

  • n_cpu (int, default: 10 ) –

    Number of CPU to run job. 12x for Lion, 8x for Leopard, 10x for Eagle.

  • pe_name (str, default: 'mpi_10' ) –

    SGE's Parallel environment name: mpi, mpi_1~mpi_20 - Eagle: mpi, mpi_1~mpi_20

CanCentosGpu_lammps(n_cpu: int = 12, pe_name: str = 'mpi_12')

Define Resources for running LAMMPS on Tachyon cluster at UNIST.

Parameters:

  • pe_name (str, default: 'mpi_12' ) –

    SGE's Parallel environment name.

  • n_cpu (int, default: 12 ) –

    Number of CPU to run job.

CanCentosGpu_gpaw(n_cpu: int = 12, pe_name: str = 'mpi_12')

Define Resources for running LAMMPS on Tachyon cluster at UNIST.

Parameters:

  • pe_name (str, default: 'mpi_12' ) –

    SGE's Parallel environment name.

  • n_cpu (int, default: 12 ) –

    Number of CPU to run job.

CanCentosGpu_ase(n_cpu: int = 12, pe_name: str = 'mpi_12')