matflow.ResourceSpec#

class matflow.ResourceSpec(scope=None, scratch=None, parallel_mode=None, num_cores=None, num_cores_per_node=None, num_threads=None, num_nodes=None, scheduler=None, shell=None, use_job_array=None, max_array_items=None, time_limit=None, scheduler_args=None, shell_args=None, os_name=None, environments=None, SGE_parallel_env=None, SLURM_partition=None, SLURM_num_tasks=None, SLURM_num_tasks_per_node=None, SLURM_num_nodes=None, SLURM_num_cpus_per_task=None)#

Bases: ResourceSpec

Class to represent specification of resource requirements for a (set of) actions.

Notes

os_name is used for retrieving a default shell name and for retrieving the correct Shell class; when using WSL, it should still be nt (i.e. Windows).

Parameters:

scope (app.ActionScope) – Which scope does this apply to.
scratch (str) – Which scratch space to use.
parallel_mode (ParallelMode) – Which parallel mode to use.
num_cores (int) – How many cores to request.
num_cores_per_node (int) – How many cores per compute node to request.
num_threads (int) – How many threads to request.
num_nodes (int) – How many compute nodes to request.
scheduler (str) – Which scheduler to use.
shell (str) – Which system shell to use.
use_job_array (bool) – Whether to use array jobs.
max_array_items (int) – If using array jobs, up to how many items should be in the job array.
time_limit (str) – How long to run for.
scheduler_args (dict[str, Any]) – Additional arguments to pass to the scheduler.
shell_args (dict[str, Any]) – Additional arguments to pass to the shell.
os_name (str) – Which OS to use.
environments (dict) – Which execution environments to use.
SGE_parallel_env (str) – Which SGE parallel environment to request.
SLURM_partition (str) – Which SLURM partition to request.
SLURM_num_tasks (str) – How many SLURM tasks to request.
SLURM_num_tasks_per_node (str) – How many SLURM tasks per compute node to request.
SLURM_num_nodes (str) – How many compute nodes to request.
SLURM_num_cpus_per_task (str) – How many CPU cores to ask for per SLURM task.

Methods

`copy_non_persistent`	Make a non-persistent copy.
`from_json_like`	Make an instance of this class from JSON (or YAML) data.
`make_persistent`	Save to a persistent workflow.
`to_dict`	Serialize this object as a dictionary.
`to_json_like`	Serialize this object as an object structure that can be trivially converted to JSON.

Attributes

`ALLOWED_PARAMETERS`	The names of parameters that may be used when making an instance of this class.
`SGE_parallel_env`	Which SGE parallel environment to request.
`SLURM_num_cpus_per_task`	How many CPU cores to ask for per SLURM task.
`SLURM_num_nodes`	How many compute nodes to request.
`SLURM_num_tasks`	How many SLURM tasks to request.
`SLURM_num_tasks_per_node`	How many SLURM tasks per compute node to request.
`SLURM_partition`	Which SLURM partition to request.
`app`
`element_set`	The element set that will use this resource spec.
`environments`	Which execution environments to use.
`max_array_items`	If using array jobs, up to how many items should be in the job array.
`normalised_path`	Full name of this resource spec.
`normalised_resources_path`	Standard name of this resource spec.
`num_cores`	How many cores to request.
`num_cores_per_node`	How many cores per compute node to request.
`num_nodes`	How many compute nodes to request.
`num_threads`	How many threads to request.
`os_name`	Which OS to use.
`parallel_mode`	Which parallel mode to use.
`scheduler`	Which scheduler to use.
`scheduler_args`	Additional arguments to pass to the scheduler.
`scratch`	Which scratch space to use.
`shell`	Which system shell to use.
`shell_args`	Additional arguments to pass to the shell.
`time_limit`	How long to run for.
`use_job_array`	Whether to use array jobs.
`workflow`	The workflow owning this resource spec.
`workflow_template`	The workflow template that will use this resource spec.
`scope`	Which scope does this apply to.

ALLOWED_PARAMETERS = {'SGE_parallel_env', 'SLURM_num_cpus_per_task', 'SLURM_num_nodes', 'SLURM_num_tasks', 'SLURM_num_tasks_per_node', 'SLURM_partition', 'environments', 'max_array_items', 'num_cores', 'num_cores_per_node', 'num_nodes', 'num_threads', 'os_name', 'parallel_mode', 'scheduler', 'scheduler_args', 'scratch', 'shell', 'shell_args', 'time_limit', 'use_job_array'}#: The names of parameters that may be used when making an instance of this class.

property SGE_parallel_env#: Which SGE parallel environment to request.

property SLURM_num_cpus_per_task#: How many CPU cores to ask for per SLURM task.

property SLURM_num_nodes#: How many compute nodes to request.

property SLURM_num_tasks#: How many SLURM tasks to request.

property SLURM_num_tasks_per_node#: How many SLURM tasks per compute node to request.

property SLURM_partition#: Which SLURM partition to request.

app = App(name='MatFlow', version='0.3.0a132')#

copy_non_persistent()#: Make a non-persistent copy.

property element_set#: The element set that will use this resource spec.

property environments#: Which execution environments to use.

classmethod from_json_like(json_like, shared_data=None)#

Make an instance of this class from JSON (or YAML) data.

Parameters:

json_like (Union[Dict, List]) – The data to deserialise.
shared_data (Optional[Dict[str, ObjectList]]) – Shared context data.

Return type:

The deserialised object.

make_persistent(workflow, source)#

Save to a persistent workflow.

Returns:

String is the data path for this task input and integer list
contains the indices of the parameter data Zarr groups where the data is
stored.

Parameters:

workflow (Workflow) –
source (Dict) –

Return type:

Tuple[str, List[int], bool]

property max_array_items#: If using array jobs, up to how many items should be in the job array.

property normalised_path#: Full name of this resource spec.

property normalised_resources_path#: Standard name of this resource spec.

property num_cores#: How many cores to request.

property num_cores_per_node#: How many cores per compute node to request.

property num_nodes#: How many compute nodes to request.

property num_threads#: How many threads to request.

property os_name#: Which OS to use.

property parallel_mode#: Which parallel mode to use.

property scheduler#: Which scheduler to use.

property scheduler_args#: Additional arguments to pass to the scheduler.

scope#: Which scope does this apply to.

property scratch#: Which scratch space to use.

property shell#: Which system shell to use.

property shell_args#: Additional arguments to pass to the shell.

property time_limit#: How long to run for.

to_dict()#: Serialize this object as a dictionary.

to_json_like(dct=None, shared_data=None, exclude=None, path=None)#: Serialize this object as an object structure that can be trivially converted to JSON. Note that YAML can also be produced from the result of this method; it just requires a different final serialization step.

property use_job_array#: Whether to use array jobs.

property workflow#: The workflow owning this resource spec.

property workflow_template#: The workflow template that will use this resource spec.