hpcflow.app.SlurmPosix

class hpcflow.app.SlurmPosix(*args, **kwargs)

Bases: SlurmPosix

Notes

• runs in current working directory by default [2]

# TODO: consider getting memory usage like: https://stackoverflow.com/a/44143229/5042280

References

[1] https://manpages.org/sbatch [2] https://ri.itservices.manchester.ac.uk/csf4/batch/sge-to-slurm/

Methods

cancel_jobs
format_array_request
format_core_request_lines
format_options
format_std_stream_file_option_lines
format_switch
get_job_state_info	Query the scheduler to get the states of all of this user's jobs, optionally filtering by specified job IDs.
get_submit_command
get_version_info
is_jobscript_active	Query if a jobscript is running/pending.
parse_submission_output	Extract scheduler reference for a newly submitted jobscript
wait_for_jobscripts

Attributes

DEFAULT_ARRAY_ITEM_VAR
DEFAULT_ARRAY_SWITCH
DEFAULT_DEL_CMD
DEFAULT_JS_CMD
DEFAULT_SHEBANG_ARGS
DEFAULT_SHELL_ARGS
DEFAULT_SHELL_EXECUTABLE
DEFAULT_SHOW_CMD
DEFAULT_SUBMIT_CMD
app
state_lookup

DEFAULT_ARRAY_ITEM_VAR = 'SLURM_ARRAY_TASK_ID'

DEFAULT_ARRAY_SWITCH = '--array'

DEFAULT_DEL_CMD = 'scancel'

DEFAULT_JS_CMD = '#SBATCH'

DEFAULT_SHEBANG_ARGS = ''

DEFAULT_SHELL_ARGS = ''

DEFAULT_SHELL_EXECUTABLE = '/bin/bash'

DEFAULT_SHOW_CMD = ['squeue', '--me']

DEFAULT_SUBMIT_CMD = 'sbatch'

app = BaseApp(name='hpcFlow', version='0.2.0a78')

cancel_jobs(js_refs, jobscripts=None)

Parameters:

• js_refs (List[str]) –

• jobscripts (List) –

format_array_request(num_elements)

format_core_request_lines(num_cores, num_nodes)

format_options(resources, num_elements, is_array, sub_idx)

format_std_stream_file_option_lines(is_array, sub_idx)

format_switch(switch)

get_job_state_info(js_refs=None)

Query the scheduler to get the states of all of this user’s jobs, optionally filtering by specified job IDs.

Jobs that are not in the scheduler’s status output will not appear in the output of this method.

Parameters:

js_refs (List[str]) –

Return type:

Dict[str, Dict[int, JobscriptElementState]]

get_submit_command(shell, js_path, deps)

Parameters:

• shell (Shell) –

• js_path (str) –

• deps (List[Tuple]) –

Return type:

List[str]

get_version_info()

is_jobscript_active(job_ID)

Query if a jobscript is running/pending.

Parameters:

job_ID (str) –

parse_submission_output(stdout)

Extract scheduler reference for a newly submitted jobscript

Parameters:

stdout (str) –

Return type:

str

state_lookup = {'CANCELLED': JobscriptElementState.cancelled, 'COMPLETED': JobscriptElementState.finished, 'COMPLETING': JobscriptElementState.running, 'FAILED': JobscriptElementState.errored, 'OUT_OF_MEMORY': JobscriptElementState.errored, 'PENDING': JobscriptElementState.pending, 'RUNNING': JobscriptElementState.running, 'TIMEOUT': JobscriptElementState.errored}

wait_for_jobscripts(js_refs)

Parameters:

js_refs (List[Any]) –

Return type:

None