executor
FractalSlurmExecutor
¶
Bases: SlurmExecutor
FractalSlurmExecutor (inherits from cfut.SlurmExecutor)
Attributes:
Name | Type | Description |
---|---|---|
slurm_user |
str
|
Shell username that runs the |
common_script_lines |
list[str]
|
Arbitrary script lines that will always be included in the sbatch script |
workflow_dir_local |
Path
|
Directory for both the cfut/SLURM and fractal-server files and logs |
workflow_dir_remote |
Path
|
Directory for both the cfut/SLURM and fractal-server files and logs |
map_jobid_to_slurm_files |
dict[str, tuple[str, str, str]]
|
Dictionary with paths of slurm-related files for active jobs |
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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|
__exit__(*args, **kwargs)
¶
See https://github.com/fractal-analytics-platform/fractal-server/issues/1508
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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__init__(slurm_user, workflow_dir_local, workflow_dir_remote, shutdown_file=None, user_cache_dir=None, common_script_lines=None, slurm_poll_interval=None, keep_pickle_files=False, slurm_account=None, *args, **kwargs)
¶
Init method for FractalSlurmExecutor
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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|
_cleanup(jobid)
¶
Given a job ID as returned by _start, perform any necessary cleanup after the job has finished.
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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|
_completion(jobid)
¶
Callback function to be executed whenever a job finishes.
This function is executed by self.wait_thread (triggered by either
finding an existing output pickle file out_path
or finding that the
SLURM job is over). Since this takes place on a different thread,
failures may not be captured by the main thread; we use a broad
try/except block, so that those exceptions are reported to the main
thread via fut.set_exception(...)
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
jobid |
str
|
ID of the SLURM job |
required |
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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_copy_files_from_remote_to_local(job)
¶
Impersonate the user and copy task-related files
For all files in self.workflow_dir_remote
that start with
job.file_prefix
, read them (with sudo -u
impersonation) and write
them to self.workflow_dir_local
.
Files to copy:
* Job-related files (SLURM stderr/stdout files); with prefix
job.slurm_file_prefix
;
* Task-related files (stderr/stdout, args.json, metadiff.json, output
pickle), with prefixes job.wftask_file_prefixes
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
job |
SlurmJob
|
|
required |
Raises:
Type | Description |
---|---|
JobExecutionError
|
If a |
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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_prepare_JobExecutionError(jobid, info)
¶
Prepare the JobExecutionError
for a given job
This method creates a JobExecutionError
object and sets its attribute
to the appropriate SLURM-related file names. Note that the method
should always be called after values in self.map_jobid_to_slurm_files
have been updated, so that they point to self.workflow_dir_local
files which are readable from fractal-server
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
jobid |
str
|
ID of the SLURM job. |
required |
info |
str
|
|
required |
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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|
_start(job)
¶
Submit function for execution on a SLURM cluster
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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_submit_job(fun, slurm_file_prefix, task_files, slurm_config, single_task_submission=False, args=None, kwargs=None, components=None)
¶
Submit a multi-task job to the pool, where each task is handled via the pickle/remote logic
NOTE: this method has different behaviors when it is called from the
self.submit
or self.map
methods (which is also encoded in
single_task_submission
):
- When called from
self.submit
, it supports generalargs
andkwargs
arguments; - When called from
self.map
, there cannot be anyargs
orkwargs
argument, but there must be acomponents
argument.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
fun |
Callable[..., Any]
|
|
required |
slurm_file_prefix |
str
|
|
required |
task_files |
TaskFiles
|
|
required |
slurm_config |
SlurmConfig
|
|
required |
single_task_submission |
bool
|
|
False
|
args |
Optional[Sequence[Any]]
|
|
None
|
kwargs |
Optional[dict]
|
|
None
|
components |
Optional[list[Any]]
|
|
None
|
Returns:
Type | Description |
---|---|
Future
|
Future representing the execution of the current SLURM job. |
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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|
get_default_task_files()
¶
This will be called when self.submit or self.map are called from outside fractal-server, and then lack some optional arguments.
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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map(fn, iterable, *, slurm_config=None, task_files=None)
¶
Return an iterator with the results of several execution of a function
This function is based on concurrent.futures.Executor.map
from Python
Standard Library 3.11.
Original Copyright 2009 Brian Quinlan. All Rights Reserved. Licensed to
PSF under a Contributor Agreement.
Main modifications from the PSF function:
- Only
fn
anditerable
can be assigned as positional arguments; *iterables
argument replaced with a singleiterable
;timeout
andchunksize
arguments are not supported.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
fn |
Callable[..., Any]
|
The function to be executed |
required |
iterable |
list[Sequence[Any]]
|
An iterable such that each element is the list of arguments to
be passed to |
required |
slurm_config |
Optional[SlurmConfig]
|
A |
None
|
task_files |
Optional[TaskFiles]
|
A |
None
|
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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|
shutdown(wait=True, *, cancel_futures=False)
¶
Clean up all executor variables. Note that this function is executed on the self.wait_thread thread, see _completion.
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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submit(fun, *fun_args, slurm_config=None, task_files=None, **fun_kwargs)
¶
Submit a function for execution on FractalSlurmExecutor
Parameters:
Name | Type | Description | Default |
---|---|---|---|
fun |
Callable[..., Any]
|
The function to be executed |
required |
fun_args |
Sequence[Any]
|
Function positional arguments |
()
|
fun_kwargs |
dict
|
Function keyword arguments |
{}
|
slurm_config |
Optional[SlurmConfig]
|
A |
None
|
task_files |
Optional[TaskFiles]
|
A |
None
|
Returns:
Type | Description |
---|---|
Future
|
Future representing the execution of the current SLURM job. |
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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SlurmJob
¶
Collect information related to a FractalSlurmExecutor job
This includes three groups of attributes:
- Attributes related to the (possibly multi-task) SLURM job, e.g. submission-file path.
- Attributes related to single tasks, e.g. the paths of their input/output pickle files.
- SLURM configuration options, encoded in a SlurmConfig object.
Note: A SlurmJob object is generally defined as a multi-task job. Jobs
coming from the map
method must have single_task_submission=False
(even
if num_tasks_tot=1
), while jobs coming from submit
must have it set to
True
.
Attributes:
Name | Type | Description |
---|---|---|
num_tasks_tot |
int
|
Total number of tasks to be executed as part of this SLURM job. |
single_task_submission |
bool
|
This must be |
slurm_file_prefix |
str
|
Prefix for SLURM-job related files (submission script and SLURM
stdout/stderr); this is also needed in the
|
wftask_file_prefixes |
tuple[str, ...]
|
Prefix for files that are created as part of the functions
submitted for execution on the |
wftask_subfolder_name |
str
|
Name of the per-task subfolder (e.g. |
slurm_script |
Path
|
Path of SLURM submission script. |
slurm_stdout |
Path
|
Path of SLURM stdout file; if this includes |
slurm_stderr |
Path
|
Path of SLURM stderr file; see |
workerids |
tuple[str, ...]
|
IDs that enter in the per-task input/output pickle files (one per task). |
input_pickle_files |
tuple[Path, ...]
|
Input pickle files (one per task). |
output_pickle_files |
tuple[Path, ...]
|
Output pickle files (one per task). |
slurm_config |
SlurmConfig
|
|
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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get_clean_output_pickle_files()
¶
Transform all pathlib.Path objects in self.output_pickle_files to strings
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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_subprocess_run_or_raise(full_command)
¶
Wrap subprocess.run
and raise appropriate JobExecutionError
if needed.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
full_command |
str
|
Full string of the command to execute. |
required |
Raises:
Type | Description |
---|---|
JobExecutionError
|
If |
Returns:
Type | Description |
---|---|
Optional[CompletedProcess]
|
The actual |
Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py
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|