podspec¶

The parts of a pod which every backend shares: image, shapes, command, environment.

simrun.argo and simrun.cwl run the same commands with the same environment; they differ in where the run store and the scratch directory are (a mount, a path) and in how a worker is named.

number ¶

number(value)

A number of GiB for the environment, e.g. 0.5.

task_dir ¶

task_dir(record, task_id, store)

The directory of a task below the store root store.

output ¶

output(record, ref)

The output a reference <task>.<port> names, relative to the store.

env_values ¶

env_values(record, task, task_type, shape, store, scratch)

The environment of the worker harness, see simrun.worker.

Parameters:

Name	Type	Description	Default
`record`	`RunRecord`	The run.	required
`task`	`TaskSpec`	The task.	required
`task_type`	`TaskType`	Its type.	required
`shape`	`PodShape`	The pod shape.	required
`store`	`str`	The root of the store as the pod sees it.	required
`scratch`	`str`	The scratch directory of the pod.	required

Returns:

Type	Description
`dict[str, str]`	The variables by name, `PYTHONPATH` the root of the model
`dict[str, str]`	(`import_root`); the caller adds the ones of its backend.

Raises:

Type	Description
`ValueError`	The task stages a port which is no input.

import_root ¶

import_root(record, store)

The root of the model, which a task imports from first.

As python -m in a checkout puts the checkout first on the path, a task of a model imports from the root of the model, e.g. examples at the root of a checkout of sbmlsim, which no installed package has.

Parameters:

Name	Type	Description	Default
`record`	`RunRecord`	The run, its first source the model.	required
`store`	`str`	The root of the store as the pod sees it.	required

Returns:

Type	Description
`str \| None`	The snapshot of the model, else its recorded working tree, None for a run
`str \| None`	without sources.

image ¶

image(record, task, task_type)

The image of a task: the one of its type, else the one of the run.

Raises:

Type	Description
`ValueError`	The type has no image and the run has none.

merge_shape ¶

merge_shape(shape, base_gb)

The merge: one core and the memory of one worker process besides the base.

unsplit_command ¶

unsplit_command(record, task, task_type, store, scratch)

The image and argv of an unsplit task.

The image of a command task is the one of its settings, the image of a plugin type the one of image; the argv is unsplit_argv.

Parameters:

Name	Type	Description	Default
`record`	`RunRecord`	The run.	required
`task`	`TaskSpec`	The task.	required
`task_type`	`TaskType`	Its type.	required
`store`	`str`	The root of the store as the pod sees it.	required
`scratch`	`str`	The scratch directory of the pod, as in `env_values`.	required

Returns:

Type	Description
`tuple[str, list[str]]`	The image and the argv.

Raises:

Type	Description
`ValueError`	The type is neither splittable nor has a command, or it has no image and the run has none.

unsplit_argv ¶

unsplit_argv(record, task, task_type, store, scratch)

The argv of an unsplit task, without its image.

The command of a plugin type runs through simrun-exec, which installs the snapshots, sets the thread variables and writes a report; a command task runs its args. In the command template of a type and in the args of a command task, {settings} is the path of the settings file and {out} the output directory of the task, and a part with {input} is repeated once per input port of the task, sorted by port, with {input} replaced by <port>=<path>, the output the port reads as the pod sees it, or <scratch>/<port> for a staged port of a plugin type, the copy simrun-exec stages; without inputs the part is dropped. The local backend runs it without an image, which a run there does not have.

Parameters:

Name	Type	Description	Default
`record`	`RunRecord`	The run.	required
`task`	`TaskSpec`	The task.	required
`task_type`	`TaskType`	Its type.	required
`store`	`str`	The root of the store as the pod sees it.	required
`scratch`	`str`	The scratch directory of the pod, as in `env_values`.	required

Returns:

Type	Description
`list[str]`	The argv.

Raises:

Type	Description
`ValueError`	The type is neither splittable nor has a command.