executor

FractalSlurmExecutor

Bases: SlurmExecutor

FractalSlurmExecutor (inherits from cfut.SlurmExecutor)

Attributes:

Name	Type	Description
slurm_user	str	Shell username that runs the sbatch command.
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

class FractalSlurmExecutor(SlurmExecutor):
    """
    FractalSlurmExecutor (inherits from cfut.SlurmExecutor)

    Attributes:
        slurm_user:
            Shell username that runs the `sbatch` command.
        common_script_lines:
            Arbitrary script lines that will always be included in the
            sbatch script
        workflow_dir_local:
            Directory for both the cfut/SLURM and fractal-server files and logs
        workflow_dir_remote:
            Directory for both the cfut/SLURM and fractal-server files and logs
        map_jobid_to_slurm_files:
            Dictionary with paths of slurm-related files for active jobs
    """

    wait_thread_cls = FractalSlurmWaitThread
    slurm_user: str
    shutdown_file: str
    common_script_lines: list[str]
    user_cache_dir: str
    workflow_dir_local: Path
    workflow_dir_remote: Path
    map_jobid_to_slurm_files: dict[str, tuple[str, str, str]]
    keep_pickle_files: bool
    slurm_account: Optional[str]
    jobs: dict[str, tuple[Future, SlurmJob]]

    def __init__(
        self,
        slurm_user: str,
        workflow_dir_local: Path,
        workflow_dir_remote: Path,
        shutdown_file: Optional[str] = None,
        user_cache_dir: Optional[str] = None,
        common_script_lines: Optional[list[str]] = None,
        slurm_poll_interval: Optional[int] = None,
        keep_pickle_files: bool = False,
        slurm_account: Optional[str] = None,
        *args,
        **kwargs,
    ):
        """
        Init method for FractalSlurmExecutor
        """

        if not slurm_user:
            raise RuntimeError(
                "Missing attribute FractalSlurmExecutor.slurm_user"
            )

        super().__init__(*args, **kwargs)

        # Assign `wait_thread.shutdown_callback` early, since it may be called
        # from within `_stop_and_join_wait_thread` (e.g. if an exception is
        # raised within `__init__`).
        self.wait_thread.shutdown_callback = self.shutdown

        self.keep_pickle_files = keep_pickle_files
        self.slurm_user = slurm_user
        self.slurm_account = slurm_account

        self.common_script_lines = common_script_lines or []

        # Check that SLURM account is not set here
        try:
            invalid_line = next(
                line
                for line in self.common_script_lines
                if line.startswith("#SBATCH --account=")
            )
            self._stop_and_join_wait_thread()
            raise RuntimeError(
                "Invalid line in `FractalSlurmExecutor.common_script_lines`: "
                f"'{invalid_line}'.\n"
                "SLURM account must be set via the request body of the "
                "apply-workflow endpoint, or by modifying the user properties."
            )
        except StopIteration:
            pass

        self.workflow_dir_local = workflow_dir_local
        if not _path_exists_as_user(
            path=str(workflow_dir_remote), user=self.slurm_user
        ):
            logger.info(f"Missing folder {workflow_dir_remote=}")
        self.user_cache_dir = user_cache_dir

        self.workflow_dir_remote = workflow_dir_remote
        self.map_jobid_to_slurm_files = {}

        # Set the attribute slurm_poll_interval for self.wait_thread (see
        # cfut.SlurmWaitThread)
        if not slurm_poll_interval:
            settings = Inject(get_settings)
            slurm_poll_interval = settings.FRACTAL_SLURM_POLL_INTERVAL
        self.wait_thread.slurm_poll_interval = slurm_poll_interval
        self.wait_thread.slurm_user = self.slurm_user

        self.wait_thread.shutdown_file = (
            shutdown_file
            or (self.workflow_dir_local / SHUTDOWN_FILENAME).as_posix()
        )

    def _cleanup(self, jobid: str) -> None:
        """
        Given a job ID as returned by _start, perform any necessary
        cleanup after the job has finished.
        """
        with self.jobs_lock:
            self.map_jobid_to_slurm_files.pop(jobid)

    def submit(
        self,
        fun: Callable[..., Any],
        *fun_args: Sequence[Any],
        slurm_config: SlurmConfig,
        task_files: TaskFiles,
        **fun_kwargs: dict,
    ) -> Future:
        """
        Submit a function for execution on `FractalSlurmExecutor`

        Arguments:
            fun: The function to be executed
            fun_args: Function positional arguments
            fun_kwargs: Function keyword arguments
            slurm_config:
                A `SlurmConfig` object.
            task_files:
                A `TaskFiles` object.

        Returns:
            Future representing the execution of the current SLURM job.
        """

        # Do not continue if auxiliary thread was shut down
        if self.wait_thread.shutdown:
            error_msg = "Cannot call `submit` method after executor shutdown"
            logger.warning(error_msg)
            raise JobExecutionError(info=error_msg)

        # Set slurm_file_prefix
        slurm_file_prefix = task_files.file_prefix

        # Include common_script_lines in extra_lines
        logger.debug(
            f"Adding {self.common_script_lines=} to "
            f"{slurm_config.extra_lines=}, from submit method."
        )
        current_extra_lines = slurm_config.extra_lines or []
        slurm_config.extra_lines = (
            current_extra_lines + self.common_script_lines
        )

        # Adapt slurm_config to the fact that this is a single-task SlurmJob
        # instance
        slurm_config.tasks_per_job = 1
        slurm_config.parallel_tasks_per_job = 1

        fut = self._submit_job(
            fun,
            slurm_config=slurm_config,
            slurm_file_prefix=slurm_file_prefix,
            task_files=task_files,
            single_task_submission=True,
            args=fun_args,
            kwargs=fun_kwargs,
        )
        return fut

    def map(
        self,
        fn: Callable[..., Any],
        iterable: list[Sequence[Any]],
        *,
        slurm_config: SlurmConfig,
        task_files: TaskFiles,
    ):
        """
        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:

        1. Only `fn` and `iterable` can be assigned as positional arguments;
        2. `*iterables` argument replaced with a single `iterable`;
        3. `timeout` and `chunksize` arguments are not supported.

        Arguments:
            fn:
                The function to be executed
            iterable:
                An iterable such that each element is the list of arguments to
                be passed to `fn`, as in `fn(*args)`.
            slurm_config:
                A `SlurmConfig` object.
            task_files:
                A `TaskFiles` object.

        """

        # Do not continue if auxiliary thread was shut down
        if self.wait_thread.shutdown:
            error_msg = "Cannot call `map` method after executor shutdown"
            logger.warning(error_msg)
            raise JobExecutionError(info=error_msg)

        def _result_or_cancel(fut):
            """
            This function is based on the Python Standard Library 3.11.
            Original Copyright 2009 Brian Quinlan. All Rights Reserved.
            Licensed to PSF under a Contributor Agreement.
            """
            try:
                try:
                    return fut.result()
                finally:
                    fut.cancel()
            finally:
                # Break a reference cycle with the exception in
                # self._exception
                del fut

        # Include common_script_lines in extra_lines
        logger.debug(
            f"Adding {self.common_script_lines=} to "
            f"{slurm_config.extra_lines=}, from map method."
        )
        current_extra_lines = slurm_config.extra_lines or []
        slurm_config.extra_lines = (
            current_extra_lines + self.common_script_lines
        )

        # Set file prefixes
        general_slurm_file_prefix = str(task_files.task_order)

        # Transform iterable into a list and count its elements
        list_args = list(iterable)
        tot_tasks = len(list_args)

        # Set/validate parameters for task batching
        tasks_per_job, parallel_tasks_per_job = heuristics(
            # Number of parallel components (always known)
            tot_tasks=len(list_args),
            # Optional WorkflowTask attributes:
            tasks_per_job=slurm_config.tasks_per_job,
            parallel_tasks_per_job=slurm_config.parallel_tasks_per_job,  # noqa
            # Task requirements (multiple possible sources):
            cpus_per_task=slurm_config.cpus_per_task,
            mem_per_task=slurm_config.mem_per_task_MB,
            # Fractal configuration variables (soft/hard limits):
            target_cpus_per_job=slurm_config.target_cpus_per_job,
            target_mem_per_job=slurm_config.target_mem_per_job,
            target_num_jobs=slurm_config.target_num_jobs,
            max_cpus_per_job=slurm_config.max_cpus_per_job,
            max_mem_per_job=slurm_config.max_mem_per_job,
            max_num_jobs=slurm_config.max_num_jobs,
        )
        slurm_config.parallel_tasks_per_job = parallel_tasks_per_job
        slurm_config.tasks_per_job = tasks_per_job

        # Divide arguments in batches of `n_tasks_per_script` tasks each
        args_batches = []
        batch_size = tasks_per_job
        for ind_chunk in range(0, tot_tasks, batch_size):
            args_batches.append(
                list_args[ind_chunk : ind_chunk + batch_size]  # noqa
            )
        if len(args_batches) != math.ceil(tot_tasks / tasks_per_job):
            raise RuntimeError("Something wrong here while batching tasks")

        # Fetch configuration variable
        settings = Inject(get_settings)
        FRACTAL_SLURM_SBATCH_SLEEP = settings.FRACTAL_SLURM_SBATCH_SLEEP

        # Construct list of futures (one per SLURM job, i.e. one per batch)
        fs = []
        current_component_index = 0
        for ind_batch, batch in enumerate(args_batches):
            batch_size = len(batch)
            this_slurm_file_prefix = (
                f"{general_slurm_file_prefix}_batch_{ind_batch:06d}"
            )
            fs.append(
                self._submit_job(
                    fn,
                    slurm_config=slurm_config,
                    slurm_file_prefix=this_slurm_file_prefix,
                    task_files=task_files,
                    single_task_submission=False,
                    components=batch,
                )
            )
            current_component_index += batch_size
            time.sleep(FRACTAL_SLURM_SBATCH_SLEEP)

        # Yield must be hidden in closure so that the futures are submitted
        # before the first iterator value is required.
        # NOTE: In this custom map() method, _result_or_cancel(fs.pop()) is an
        # iterable of results (if successful), and we should yield its elements
        # rather than the whole iterable.
        def result_iterator():
            """
            This function is based on the Python Standard Library 3.11.
            Original Copyright 2009 Brian Quinlan. All Rights Reserved.
            Licensed to PSF under a Contributor Agreement.
            """
            try:
                # reverse to keep finishing order
                fs.reverse()
                while fs:
                    # Careful not to keep a reference to the popped future
                    results = _result_or_cancel(fs.pop())
                    for res in results:
                        yield res
            finally:
                for future in fs:
                    future.cancel()

        return result_iterator()

    def _submit_job(
        self,
        fun: Callable[..., Any],
        slurm_file_prefix: str,
        task_files: TaskFiles,
        slurm_config: SlurmConfig,
        single_task_submission: bool = False,
        args: Optional[Sequence[Any]] = None,
        kwargs: Optional[dict] = None,
        components: Optional[list[Any]] = None,
    ) -> Future:
        """
        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 general `args` and
          `kwargs` arguments;
        * When called from `self.map`, there cannot be any `args` or `kwargs`
          argument, but there must be a `components` argument.

        Arguments:
            fun:
            slurm_file_prefix:
            task_files:
            slurm_config:
            single_task_submission:
            args:
            kwargs:
            components:

        Returns:
            Future representing the execution of the current SLURM job.
        """

        # Prevent calling sbatch if auxiliary thread was shut down
        if self.wait_thread.shutdown:
            error_msg = (
                "Cannot call `_submit_job` method after executor shutdown"
            )
            logger.warning(error_msg)
            raise JobExecutionError(info=error_msg)

        fut: Future = Future()

        # Inject SLURM account (if set) into slurm_config
        if self.slurm_account:
            slurm_config.account = self.slurm_account

        # Define slurm-job-related files
        if single_task_submission:
            if components is not None:
                raise ValueError(
                    f"{single_task_submission=} but components is not None"
                )
            job = SlurmJob(
                slurm_file_prefix=slurm_file_prefix,
                num_tasks_tot=1,
                slurm_config=slurm_config,
            )
            if job.num_tasks_tot > 1:
                raise ValueError(
                    "{single_task_submission=} but {job.num_tasks_tot=}"
                )
            job.single_task_submission = True
            job.wftask_file_prefixes = (task_files.file_prefix,)
            job.wftask_subfolder_name = task_files.subfolder_name

        else:
            if not components or len(components) < 1:
                raise ValueError(
                    "In FractalSlurmExecutor._submit_job, given "
                    f"{components=}."
                )
            num_tasks_tot = len(components)
            job = SlurmJob(
                slurm_file_prefix=slurm_file_prefix,
                num_tasks_tot=num_tasks_tot,
                slurm_config=slurm_config,
            )

            _prefixes = []
            _subfolder_names = []
            for component in components:
                if isinstance(component, dict):
                    # This is needed for V2
                    actual_component = component.get(_COMPONENT_KEY_, None)
                else:
                    actual_component = component
                _task_file_paths = get_task_file_paths(
                    workflow_dir_local=task_files.workflow_dir_local,
                    workflow_dir_remote=task_files.workflow_dir_remote,
                    task_name=task_files.task_name,
                    task_order=task_files.task_order,
                    component=actual_component,
                )
                _prefixes.append(_task_file_paths.file_prefix)
                _subfolder_names.append(_task_file_paths.subfolder_name)
            job.wftask_file_prefixes = tuple(_prefixes)

            num_subfolders = len(set(_subfolder_names))
            if num_subfolders != 1:
                error_msg_short = (
                    f"[_submit_job] Subfolder list has {num_subfolders} "
                    "different values, but it must have only one (since "
                    "workflow tasks are executed one by one)."
                )
                error_msg_detail = (
                    "[_submit_job] Current unique subfolder names: "
                    f"{set(_subfolder_names)}"
                )
                logger.error(error_msg_short)
                logger.error(error_msg_detail)
                raise ValueError(error_msg_short)
            job.wftask_subfolder_name = _subfolder_names[0]

        # Check that server-side subfolder exists
        subfolder_path = self.workflow_dir_local / job.wftask_subfolder_name
        if not subfolder_path.exists():
            raise FileNotFoundError(
                f"Missing folder {subfolder_path.as_posix()}."
            )

        job.input_pickle_files = tuple(
            get_pickle_file_path(
                arg=job.workerids[ind],
                workflow_dir=self.workflow_dir_local,
                subfolder_name=job.wftask_subfolder_name,
                in_or_out="in",
                prefix=job.wftask_file_prefixes[ind],
            )
            for ind in range(job.num_tasks_tot)
        )
        job.output_pickle_files = tuple(
            get_pickle_file_path(
                arg=job.workerids[ind],
                workflow_dir=self.workflow_dir_remote,
                subfolder_name=job.wftask_subfolder_name,
                in_or_out="out",
                prefix=job.wftask_file_prefixes[ind],
            )
            for ind in range(job.num_tasks_tot)
        )
        # Define SLURM-job file names/paths
        job.slurm_script = get_slurm_script_file_path(
            workflow_dir=self.workflow_dir_local,
            subfolder_name=job.wftask_subfolder_name,
            prefix=job.slurm_file_prefix,
        )
        job.slurm_stdout = get_slurm_file_path(
            workflow_dir=self.workflow_dir_remote,
            subfolder_name=job.wftask_subfolder_name,
            out_or_err="out",
            prefix=job.slurm_file_prefix,
        )
        job.slurm_stderr = get_slurm_file_path(
            workflow_dir=self.workflow_dir_remote,
            subfolder_name=job.wftask_subfolder_name,
            out_or_err="err",
            prefix=job.slurm_file_prefix,
        )

        # Dump serialized versions+function+args+kwargs to pickle
        versions = dict(
            python=sys.version_info[:3],
            cloudpickle=cloudpickle.__version__,
            fractal_server=__VERSION__,
        )
        if job.single_task_submission:
            _args = args or []
            _kwargs = kwargs or {}
            funcser = cloudpickle.dumps((versions, fun, _args, _kwargs))
            with open(job.input_pickle_files[0], "wb") as f:
                f.write(funcser)
        else:
            for ind_component, component in enumerate(components):
                _args = [component]
                _kwargs = {}
                funcser = cloudpickle.dumps((versions, fun, _args, _kwargs))
                with open(job.input_pickle_files[ind_component], "wb") as f:
                    f.write(funcser)

        # Submit job to SLURM, and get jobid
        jobid, job = self._start(job)

        # Add the SLURM script/out/err paths to map_jobid_to_slurm_files (this
        # must be after self._start(job), so that "%j" has already been
        # replaced with the job ID)
        with self.jobs_lock:
            self.map_jobid_to_slurm_files[jobid] = (
                job.slurm_script.as_posix(),
                job.slurm_stdout.as_posix(),
                job.slurm_stderr.as_posix(),
            )

        # Thread will wait for it to finish.
        self.wait_thread.wait(
            filenames=job.get_clean_output_pickle_files(),
            jobid=jobid,
        )

        with self.jobs_lock:
            self.jobs[jobid] = (fut, job)
        return fut

    def _prepare_JobExecutionError(
        self, jobid: str, info: str
    ) -> JobExecutionError:
        """
        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`.

        Arguments:
            jobid:
                ID of the SLURM job.
            info:
        """
        # Extract SLURM file paths
        with self.jobs_lock:
            (
                slurm_script_file,
                slurm_stdout_file,
                slurm_stderr_file,
            ) = self.map_jobid_to_slurm_files[jobid]
        # Construct JobExecutionError exception
        job_exc = JobExecutionError(
            cmd_file=slurm_script_file,
            stdout_file=slurm_stdout_file,
            stderr_file=slurm_stderr_file,
            info=info,
        )
        return job_exc

    def _completion(self, jobid: str) -> None:
        """
        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(...)`.

        Arguments:
            jobid: ID of the SLURM job
        """
        # Handle all uncaught exceptions in this broad try/except block
        try:
            # Retrieve job
            with self.jobs_lock:
                try:
                    fut, job = self.jobs.pop(jobid)
                except KeyError:
                    return
                if not self.jobs:
                    self.jobs_empty_cond.notify_all()

            # Copy all relevant files from self.workflow_dir_remote to
            # self.workflow_dir_local

            self._copy_files_from_remote_to_local(job)

            # Update the paths to use the files in self.workflow_dir_local
            # (rather than the user's ones in self.workflow_dir_remote)
            with self.jobs_lock:
                self.map_jobid_to_slurm_files[jobid]
                (
                    slurm_script_file,
                    slurm_stdout_file,
                    slurm_stderr_file,
                ) = self.map_jobid_to_slurm_files[jobid]
            new_slurm_stdout_file = str(
                self.workflow_dir_local
                / job.wftask_subfolder_name
                / Path(slurm_stdout_file).name
            )
            new_slurm_stderr_file = str(
                self.workflow_dir_local
                / job.wftask_subfolder_name
                / Path(slurm_stderr_file).name
            )
            with self.jobs_lock:
                self.map_jobid_to_slurm_files[jobid] = (
                    slurm_script_file,
                    new_slurm_stdout_file,
                    new_slurm_stderr_file,
                )

            in_paths = job.input_pickle_files
            out_paths = tuple(
                (self.workflow_dir_local / job.wftask_subfolder_name / f.name)
                for f in job.output_pickle_files
            )

            outputs = []
            for ind_out_path, out_path in enumerate(out_paths):
                in_path = in_paths[ind_out_path]

                # The output pickle file may be missing because of some slow
                # filesystem operation; wait some time before considering it as
                # missing
                if not out_path.exists():
                    settings = Inject(get_settings)
                    time.sleep(settings.FRACTAL_SLURM_ERROR_HANDLING_INTERVAL)
                if not out_path.exists():
                    # Output pickle file is missing
                    info = (
                        "Output pickle file of the FractalSlurmExecutor job "
                        "not found.\n"
                        f"Expected file path: {str(out_path)}.\n"
                        "Here are some possible reasons:\n"
                        "1. The SLURM job was scancel-ed, either by the user "
                        "or due to an error (e.g. an out-of-memory or timeout "
                        "error). Note that if the scancel took place before "
                        "the job started running, the SLURM out/err files "
                        "will be empty.\n"
                        "2. Some error occurred upon writing the file to disk "
                        "(e.g. because there is not enough space on disk, or "
                        "due to an overloaded NFS filesystem). "
                        "Note that the server configuration has "
                        "FRACTAL_SLURM_ERROR_HANDLING_INTERVAL="
                        f"{settings.FRACTAL_SLURM_ERROR_HANDLING_INTERVAL} "
                        "seconds.\n"
                    )
                    job_exc = self._prepare_JobExecutionError(jobid, info=info)
                    try:
                        fut.set_exception(job_exc)
                        return
                    except InvalidStateError:
                        logger.warning(
                            f"Future {fut} (SLURM job ID: {jobid}) was already"
                            " cancelled, exit from"
                            " FractalSlurmExecutor._completion."
                        )
                        if not self.keep_pickle_files:
                            in_path.unlink()
                        self._cleanup(jobid)
                        return

                # Read the task output (note: we now know that out_path exists)
                with out_path.open("rb") as f:
                    outdata = f.read()
                # Note: output can be either the task result (typically a
                # dictionary) or an ExceptionProxy object; in the latter
                # case, the ExceptionProxy definition is also part of the
                # pickle file (thanks to cloudpickle.dumps).
                success, output = cloudpickle.loads(outdata)
                try:
                    if success:
                        outputs.append(output)
                    else:
                        proxy = output
                        if proxy.exc_type_name == "JobExecutionError":
                            job_exc = self._prepare_JobExecutionError(
                                jobid, info=proxy.kwargs.get("info", None)
                            )
                            fut.set_exception(job_exc)
                            return
                        else:
                            # This branch catches both TaskExecutionError's
                            # (coming from the typical fractal-server
                            # execution of tasks, and with additional
                            # fractal-specific kwargs) or arbitrary
                            # exceptions (coming from a direct use of
                            # FractalSlurmExecutor, possibly outside
                            # fractal-server)
                            kwargs = {}
                            for key in [
                                "workflow_task_id",
                                "workflow_task_order",
                                "task_name",
                            ]:
                                if key in proxy.kwargs.keys():
                                    kwargs[key] = proxy.kwargs[key]
                            exc = TaskExecutionError(proxy.tb, **kwargs)
                            fut.set_exception(exc)
                            return
                    if not self.keep_pickle_files:
                        out_path.unlink()
                except InvalidStateError:
                    logger.warning(
                        f"Future {fut} (SLURM job ID: {jobid}) was already"
                        " cancelled, exit from"
                        " FractalSlurmExecutor._completion."
                    )
                    if not self.keep_pickle_files:
                        out_path.unlink()
                        in_path.unlink()
                    self._cleanup(jobid)
                    return

                # Clean up input pickle file
                if not self.keep_pickle_files:
                    in_path.unlink()
            self._cleanup(jobid)
            if job.single_task_submission:
                fut.set_result(outputs[0])
            else:
                fut.set_result(outputs)
            return

        except Exception as e:
            try:
                fut.set_exception(e)
                return
            except InvalidStateError:
                logger.warning(
                    f"Future {fut} (SLURM job ID: {jobid}) was already"
                    " cancelled, exit from"
                    " FractalSlurmExecutor._completion."
                )

    def _copy_files_from_remote_to_local(
        self,
        job: SlurmJob,
    ):
        """
        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`.

        Arguments:
            job:
                `SlurmJob` object (needed for its prefixes-related attributes).

        Raises:
            JobExecutionError: If a `cat` command fails.
        """
        logger.debug("[_copy_files_from_remote_to_local] Start")

        if self.workflow_dir_remote == self.workflow_dir_local:
            logger.debug(
                "[_copy_files_from_remote_to_local] "
                "workflow_dir_local corresponds to workflow_dir_remote, "
                "return."
            )
            return

        subfolder_name = job.wftask_subfolder_name
        prefixes = set(
            [job.slurm_file_prefix] + list(job.wftask_file_prefixes)
        )

        logger.debug(
            "[_copy_files_from_remote_to_local] "
            f"WorkflowTask subfolder_name: {subfolder_name}"
        )
        logger.debug(f"[_copy_files_from_remote_to_local] {prefixes=}")
        logger.debug(
            "[_copy_files_from_remote_to_local] "
            f"{str(self.workflow_dir_remote)=}"
        )

        for prefix in prefixes:
            if prefix == job.slurm_file_prefix:
                files_to_copy = _glob_as_user(
                    folder=str(self.workflow_dir_remote / subfolder_name),
                    user=self.slurm_user,
                    startswith=prefix,
                )
            else:
                files_to_copy = _glob_as_user_strict(
                    folder=str(self.workflow_dir_remote / subfolder_name),
                    user=self.slurm_user,
                    startswith=prefix,
                )

            logger.debug(
                "[_copy_files_from_remote_to_local] "
                f"{prefix=}, {len(files_to_copy)=}"
            )

            for source_file_name in files_to_copy:
                if " " in source_file_name:
                    raise ValueError(
                        f'source_file_name="{source_file_name}" '
                        "contains whitespaces"
                    )
                source_file_path = str(
                    self.workflow_dir_remote
                    / subfolder_name
                    / source_file_name
                )

                # Read source_file_path (requires sudo)
                # NOTE: By setting encoding=None, we read/write bytes instead
                # of strings; this is needed to also handle pickle files.
                cmd = f"cat {source_file_path}"
                res = _run_command_as_user(
                    cmd=cmd, user=self.slurm_user, encoding=None
                )
                if res.returncode != 0:
                    info = (
                        f'Running cmd="{cmd}" as {self.slurm_user=} failed\n\n'
                        f"{res.returncode=}\n\n"
                        f"{res.stdout=}\n\n{res.stderr=}\n"
                    )
                    logger.error(info)
                    raise JobExecutionError(info)
                # Write to dest_file_path (including empty files)
                dest_file_path = str(
                    self.workflow_dir_local / subfolder_name / source_file_name
                )
                with open(dest_file_path, "wb") as f:
                    f.write(res.stdout)
        logger.debug("[_copy_files_from_remote_to_local] End")

    def _start(
        self,
        job: SlurmJob,
    ) -> tuple[str, SlurmJob]:
        """
        Submit function for execution on a SLURM cluster
        """

        # Prepare commands to be included in SLURM submission script
        settings = Inject(get_settings)
        python_worker_interpreter = (
            settings.FRACTAL_SLURM_WORKER_PYTHON or sys.executable
        )

        cmdlines = []
        for ind_task in range(job.num_tasks_tot):
            input_pickle_file = job.input_pickle_files[ind_task]
            output_pickle_file = job.output_pickle_files[ind_task]
            cmdlines.append(
                (
                    f"{python_worker_interpreter}"
                    " -m fractal_server.app.runner.executors.slurm.remote "
                    f"--input-file {input_pickle_file} "
                    f"--output-file {output_pickle_file}"
                )
            )

        # ...
        sbatch_script = self._prepare_sbatch_script(
            slurm_config=job.slurm_config,
            list_commands=cmdlines,
            slurm_out_path=str(job.slurm_stdout),
            slurm_err_path=str(job.slurm_stderr),
        )

        # Print warning for ignored parameter
        if len(job.slurm_config.pre_submission_commands) > 0:
            logger.warning(
                f"Ignoring {job.slurm_config.pre_submission_commands=}."
            )

        # Submit job via sbatch, and retrieve jobid

        # Write script content to a job.slurm_script
        with job.slurm_script.open("w") as f:
            f.write(sbatch_script)

        # Prepare submission command
        pre_command = f"sudo --set-home --non-interactive -u {self.slurm_user}"
        submit_command = f"sbatch --parsable {job.slurm_script}"
        full_command = f"{pre_command} {submit_command}"

        # Submit SLURM job and retrieve job ID
        output = _subprocess_run_or_raise(full_command)
        try:
            jobid = int(output.stdout)
        except ValueError as e:
            error_msg = (
                f"Submit command `{full_command}` returned "
                f"`{output.stdout=}` which cannot be cast to an integer "
                f"SLURM-job ID. Original error:\n{str(e)}"
            )
            logger.error(error_msg)
            raise JobExecutionError(info=error_msg)
        jobid_str = str(jobid)

        # Plug SLURM job id in stdout/stderr file paths
        job.slurm_stdout = Path(
            job.slurm_stdout.as_posix().replace("%j", jobid_str)
        )
        job.slurm_stderr = Path(
            job.slurm_stderr.as_posix().replace("%j", jobid_str)
        )

        return jobid_str, job

    def _prepare_sbatch_script(
        self,
        *,
        list_commands: list[str],
        slurm_out_path: str,
        slurm_err_path: str,
        slurm_config: SlurmConfig,
    ):
        num_tasks_max_running = slurm_config.parallel_tasks_per_job
        mem_per_task_MB = slurm_config.mem_per_task_MB

        # Set ntasks
        ntasks = min(len(list_commands), num_tasks_max_running)
        if len(list_commands) < num_tasks_max_running:
            ntasks = len(list_commands)
            slurm_config.parallel_tasks_per_job = ntasks
            logger.debug(
                f"{len(list_commands)=} is smaller than "
                f"{num_tasks_max_running=}. Setting {ntasks=}."
            )

        # Prepare SLURM preamble based on SlurmConfig object
        script_lines = slurm_config.to_sbatch_preamble(
            remote_export_dir=self.user_cache_dir
        )

        # Extend SLURM preamble with variable which are not in SlurmConfig, and
        # fix their order
        script_lines.extend(
            [
                f"#SBATCH --err={slurm_err_path}",
                f"#SBATCH --out={slurm_out_path}",
                f"#SBATCH -D {self.workflow_dir_remote}",
            ]
        )
        script_lines = slurm_config.sort_script_lines(script_lines)
        logger.debug(script_lines)

        # Always print output of `pwd`
        script_lines.append('echo "Working directory (pwd): `pwd`"\n')

        # Complete script preamble
        script_lines.append("\n")

        # Include command lines
        tmp_list_commands = copy(list_commands)
        while tmp_list_commands:
            if tmp_list_commands:
                cmd = tmp_list_commands.pop(0)  # take first element
                script_lines.append(
                    "srun --ntasks=1 --cpus-per-task=$SLURM_CPUS_PER_TASK "
                    f"--mem={mem_per_task_MB}MB "
                    f"{cmd} &"
                )
        script_lines.append("wait\n")

        script = "\n".join(script_lines)
        return script

    def shutdown(self, wait=True, *, cancel_futures=False):
        """
        Clean up all executor variables. Note that this function is executed on
        the self.wait_thread thread, see _completion.
        """

        logger.debug("Executor shutdown: start")

        # Handle all job futures
        slurm_jobs_to_scancel = []
        with self.jobs_lock:
            while self.jobs:
                jobid, fut_and_job = self.jobs.popitem()
                slurm_jobs_to_scancel.append(jobid)
                fut = fut_and_job[0]
                self.map_jobid_to_slurm_files.pop(jobid)
                if not fut.cancelled():
                    fut.set_exception(
                        JobExecutionError(
                            "Job cancelled due to executor shutdown."
                        )
                    )
                    fut.cancel()

        # Cancel SLURM jobs
        if slurm_jobs_to_scancel:
            scancel_string = " ".join(slurm_jobs_to_scancel)
            logger.warning(f"Now scancel-ing SLURM jobs {scancel_string}")
            pre_command = f"sudo --non-interactive -u {self.slurm_user}"
            submit_command = f"scancel {scancel_string}"
            full_command = f"{pre_command} {submit_command}"
            validate_cmd(full_command)
            logger.debug(f"Now execute `{full_command}`")
            try:
                subprocess.run(  # nosec
                    shlex.split(full_command),
                    capture_output=True,
                    check=True,
                    encoding="utf-8",
                )
            except subprocess.CalledProcessError as e:
                error_msg = (
                    f"Cancel command `{full_command}` failed. "
                    f"Original error:\n{str(e)}"
                )
                logger.error(error_msg)
                raise JobExecutionError(info=error_msg)

        # Redudantly set thread shutdown attribute to True
        self.wait_thread.shutdown = True

        logger.debug("Executor shutdown: end")

    def _stop_and_join_wait_thread(self):
        self.wait_thread.stop()
        self.wait_thread.join()

    def __exit__(self, *args, **kwargs):
        """
        See
        https://github.com/fractal-analytics-platform/fractal-server/issues/1508
        """
        logger.debug(
            "[FractalSlurmExecutor.__exit__] Stop and join `wait_thread`"
        )
        self._stop_and_join_wait_thread()
        logger.debug("[FractalSlurmExecutor.__exit__] End")

__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

def __exit__(self, *args, **kwargs):
    """
    See
    https://github.com/fractal-analytics-platform/fractal-server/issues/1508
    """
    logger.debug(
        "[FractalSlurmExecutor.__exit__] Stop and join `wait_thread`"
    )
    self._stop_and_join_wait_thread()
    logger.debug("[FractalSlurmExecutor.__exit__] End")

__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

def __init__(
    self,
    slurm_user: str,
    workflow_dir_local: Path,
    workflow_dir_remote: Path,
    shutdown_file: Optional[str] = None,
    user_cache_dir: Optional[str] = None,
    common_script_lines: Optional[list[str]] = None,
    slurm_poll_interval: Optional[int] = None,
    keep_pickle_files: bool = False,
    slurm_account: Optional[str] = None,
    *args,
    **kwargs,
):
    """
    Init method for FractalSlurmExecutor
    """

    if not slurm_user:
        raise RuntimeError(
            "Missing attribute FractalSlurmExecutor.slurm_user"
        )

    super().__init__(*args, **kwargs)

    # Assign `wait_thread.shutdown_callback` early, since it may be called
    # from within `_stop_and_join_wait_thread` (e.g. if an exception is
    # raised within `__init__`).
    self.wait_thread.shutdown_callback = self.shutdown

    self.keep_pickle_files = keep_pickle_files
    self.slurm_user = slurm_user
    self.slurm_account = slurm_account

    self.common_script_lines = common_script_lines or []

    # Check that SLURM account is not set here
    try:
        invalid_line = next(
            line
            for line in self.common_script_lines
            if line.startswith("#SBATCH --account=")
        )
        self._stop_and_join_wait_thread()
        raise RuntimeError(
            "Invalid line in `FractalSlurmExecutor.common_script_lines`: "
            f"'{invalid_line}'.\n"
            "SLURM account must be set via the request body of the "
            "apply-workflow endpoint, or by modifying the user properties."
        )
    except StopIteration:
        pass

    self.workflow_dir_local = workflow_dir_local
    if not _path_exists_as_user(
        path=str(workflow_dir_remote), user=self.slurm_user
    ):
        logger.info(f"Missing folder {workflow_dir_remote=}")
    self.user_cache_dir = user_cache_dir

    self.workflow_dir_remote = workflow_dir_remote
    self.map_jobid_to_slurm_files = {}

    # Set the attribute slurm_poll_interval for self.wait_thread (see
    # cfut.SlurmWaitThread)
    if not slurm_poll_interval:
        settings = Inject(get_settings)
        slurm_poll_interval = settings.FRACTAL_SLURM_POLL_INTERVAL
    self.wait_thread.slurm_poll_interval = slurm_poll_interval
    self.wait_thread.slurm_user = self.slurm_user

    self.wait_thread.shutdown_file = (
        shutdown_file
        or (self.workflow_dir_local / SHUTDOWN_FILENAME).as_posix()
    )

_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

def _cleanup(self, jobid: str) -> None:
    """
    Given a job ID as returned by _start, perform any necessary
    cleanup after the job has finished.
    """
    with self.jobs_lock:
        self.map_jobid_to_slurm_files.pop(jobid)

_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

def _completion(self, jobid: str) -> None:
    """
    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(...)`.

    Arguments:
        jobid: ID of the SLURM job
    """
    # Handle all uncaught exceptions in this broad try/except block
    try:
        # Retrieve job
        with self.jobs_lock:
            try:
                fut, job = self.jobs.pop(jobid)
            except KeyError:
                return
            if not self.jobs:
                self.jobs_empty_cond.notify_all()

        # Copy all relevant files from self.workflow_dir_remote to
        # self.workflow_dir_local

        self._copy_files_from_remote_to_local(job)

        # Update the paths to use the files in self.workflow_dir_local
        # (rather than the user's ones in self.workflow_dir_remote)
        with self.jobs_lock:
            self.map_jobid_to_slurm_files[jobid]
            (
                slurm_script_file,
                slurm_stdout_file,
                slurm_stderr_file,
            ) = self.map_jobid_to_slurm_files[jobid]
        new_slurm_stdout_file = str(
            self.workflow_dir_local
            / job.wftask_subfolder_name
            / Path(slurm_stdout_file).name
        )
        new_slurm_stderr_file = str(
            self.workflow_dir_local
            / job.wftask_subfolder_name
            / Path(slurm_stderr_file).name
        )
        with self.jobs_lock:
            self.map_jobid_to_slurm_files[jobid] = (
                slurm_script_file,
                new_slurm_stdout_file,
                new_slurm_stderr_file,
            )

        in_paths = job.input_pickle_files
        out_paths = tuple(
            (self.workflow_dir_local / job.wftask_subfolder_name / f.name)
            for f in job.output_pickle_files
        )

        outputs = []
        for ind_out_path, out_path in enumerate(out_paths):
            in_path = in_paths[ind_out_path]

            # The output pickle file may be missing because of some slow
            # filesystem operation; wait some time before considering it as
            # missing
            if not out_path.exists():
                settings = Inject(get_settings)
                time.sleep(settings.FRACTAL_SLURM_ERROR_HANDLING_INTERVAL)
            if not out_path.exists():
                # Output pickle file is missing
                info = (
                    "Output pickle file of the FractalSlurmExecutor job "
                    "not found.\n"
                    f"Expected file path: {str(out_path)}.\n"
                    "Here are some possible reasons:\n"
                    "1. The SLURM job was scancel-ed, either by the user "
                    "or due to an error (e.g. an out-of-memory or timeout "
                    "error). Note that if the scancel took place before "
                    "the job started running, the SLURM out/err files "
                    "will be empty.\n"
                    "2. Some error occurred upon writing the file to disk "
                    "(e.g. because there is not enough space on disk, or "
                    "due to an overloaded NFS filesystem). "
                    "Note that the server configuration has "
                    "FRACTAL_SLURM_ERROR_HANDLING_INTERVAL="
                    f"{settings.FRACTAL_SLURM_ERROR_HANDLING_INTERVAL} "
                    "seconds.\n"
                )
                job_exc = self._prepare_JobExecutionError(jobid, info=info)
                try:
                    fut.set_exception(job_exc)
                    return
                except InvalidStateError:
                    logger.warning(
                        f"Future {fut} (SLURM job ID: {jobid}) was already"
                        " cancelled, exit from"
                        " FractalSlurmExecutor._completion."
                    )
                    if not self.keep_pickle_files:
                        in_path.unlink()
                    self._cleanup(jobid)
                    return

            # Read the task output (note: we now know that out_path exists)
            with out_path.open("rb") as f:
                outdata = f.read()
            # Note: output can be either the task result (typically a
            # dictionary) or an ExceptionProxy object; in the latter
            # case, the ExceptionProxy definition is also part of the
            # pickle file (thanks to cloudpickle.dumps).
            success, output = cloudpickle.loads(outdata)
            try:
                if success:
                    outputs.append(output)
                else:
                    proxy = output
                    if proxy.exc_type_name == "JobExecutionError":
                        job_exc = self._prepare_JobExecutionError(
                            jobid, info=proxy.kwargs.get("info", None)
                        )
                        fut.set_exception(job_exc)
                        return
                    else:
                        # This branch catches both TaskExecutionError's
                        # (coming from the typical fractal-server
                        # execution of tasks, and with additional
                        # fractal-specific kwargs) or arbitrary
                        # exceptions (coming from a direct use of
                        # FractalSlurmExecutor, possibly outside
                        # fractal-server)
                        kwargs = {}
                        for key in [
                            "workflow_task_id",
                            "workflow_task_order",
                            "task_name",
                        ]:
                            if key in proxy.kwargs.keys():
                                kwargs[key] = proxy.kwargs[key]
                        exc = TaskExecutionError(proxy.tb, **kwargs)
                        fut.set_exception(exc)
                        return
                if not self.keep_pickle_files:
                    out_path.unlink()
            except InvalidStateError:
                logger.warning(
                    f"Future {fut} (SLURM job ID: {jobid}) was already"
                    " cancelled, exit from"
                    " FractalSlurmExecutor._completion."
                )
                if not self.keep_pickle_files:
                    out_path.unlink()
                    in_path.unlink()
                self._cleanup(jobid)
                return

            # Clean up input pickle file
            if not self.keep_pickle_files:
                in_path.unlink()
        self._cleanup(jobid)
        if job.single_task_submission:
            fut.set_result(outputs[0])
        else:
            fut.set_result(outputs)
        return

    except Exception as e:
        try:
            fut.set_exception(e)
            return
        except InvalidStateError:
            logger.warning(
                f"Future {fut} (SLURM job ID: {jobid}) was already"
                " cancelled, exit from"
                " FractalSlurmExecutor._completion."
            )

_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	SlurmJob object (needed for its prefixes-related attributes).	required

Raises:

Type	Description
JobExecutionError	If a cat command fails.

Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py

def _copy_files_from_remote_to_local(
    self,
    job: SlurmJob,
):
    """
    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`.

    Arguments:
        job:
            `SlurmJob` object (needed for its prefixes-related attributes).

    Raises:
        JobExecutionError: If a `cat` command fails.
    """
    logger.debug("[_copy_files_from_remote_to_local] Start")

    if self.workflow_dir_remote == self.workflow_dir_local:
        logger.debug(
            "[_copy_files_from_remote_to_local] "
            "workflow_dir_local corresponds to workflow_dir_remote, "
            "return."
        )
        return

    subfolder_name = job.wftask_subfolder_name
    prefixes = set(
        [job.slurm_file_prefix] + list(job.wftask_file_prefixes)
    )

    logger.debug(
        "[_copy_files_from_remote_to_local] "
        f"WorkflowTask subfolder_name: {subfolder_name}"
    )
    logger.debug(f"[_copy_files_from_remote_to_local] {prefixes=}")
    logger.debug(
        "[_copy_files_from_remote_to_local] "
        f"{str(self.workflow_dir_remote)=}"
    )

    for prefix in prefixes:
        if prefix == job.slurm_file_prefix:
            files_to_copy = _glob_as_user(
                folder=str(self.workflow_dir_remote / subfolder_name),
                user=self.slurm_user,
                startswith=prefix,
            )
        else:
            files_to_copy = _glob_as_user_strict(
                folder=str(self.workflow_dir_remote / subfolder_name),
                user=self.slurm_user,
                startswith=prefix,
            )

        logger.debug(
            "[_copy_files_from_remote_to_local] "
            f"{prefix=}, {len(files_to_copy)=}"
        )

        for source_file_name in files_to_copy:
            if " " in source_file_name:
                raise ValueError(
                    f'source_file_name="{source_file_name}" '
                    "contains whitespaces"
                )
            source_file_path = str(
                self.workflow_dir_remote
                / subfolder_name
                / source_file_name
            )

            # Read source_file_path (requires sudo)
            # NOTE: By setting encoding=None, we read/write bytes instead
            # of strings; this is needed to also handle pickle files.
            cmd = f"cat {source_file_path}"
            res = _run_command_as_user(
                cmd=cmd, user=self.slurm_user, encoding=None
            )
            if res.returncode != 0:
                info = (
                    f'Running cmd="{cmd}" as {self.slurm_user=} failed\n\n'
                    f"{res.returncode=}\n\n"
                    f"{res.stdout=}\n\n{res.stderr=}\n"
                )
                logger.error(info)
                raise JobExecutionError(info)
            # Write to dest_file_path (including empty files)
            dest_file_path = str(
                self.workflow_dir_local / subfolder_name / source_file_name
            )
            with open(dest_file_path, "wb") as f:
                f.write(res.stdout)
    logger.debug("[_copy_files_from_remote_to_local] End")

_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

def _prepare_JobExecutionError(
    self, jobid: str, info: str
) -> JobExecutionError:
    """
    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`.

    Arguments:
        jobid:
            ID of the SLURM job.
        info:
    """
    # Extract SLURM file paths
    with self.jobs_lock:
        (
            slurm_script_file,
            slurm_stdout_file,
            slurm_stderr_file,
        ) = self.map_jobid_to_slurm_files[jobid]
    # Construct JobExecutionError exception
    job_exc = JobExecutionError(
        cmd_file=slurm_script_file,
        stdout_file=slurm_stdout_file,
        stderr_file=slurm_stderr_file,
        info=info,
    )
    return job_exc

_start(job)

Submit function for execution on a SLURM cluster

Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py

def _start(
    self,
    job: SlurmJob,
) -> tuple[str, SlurmJob]:
    """
    Submit function for execution on a SLURM cluster
    """

    # Prepare commands to be included in SLURM submission script
    settings = Inject(get_settings)
    python_worker_interpreter = (
        settings.FRACTAL_SLURM_WORKER_PYTHON or sys.executable
    )

    cmdlines = []
    for ind_task in range(job.num_tasks_tot):
        input_pickle_file = job.input_pickle_files[ind_task]
        output_pickle_file = job.output_pickle_files[ind_task]
        cmdlines.append(
            (
                f"{python_worker_interpreter}"
                " -m fractal_server.app.runner.executors.slurm.remote "
                f"--input-file {input_pickle_file} "
                f"--output-file {output_pickle_file}"
            )
        )

    # ...
    sbatch_script = self._prepare_sbatch_script(
        slurm_config=job.slurm_config,
        list_commands=cmdlines,
        slurm_out_path=str(job.slurm_stdout),
        slurm_err_path=str(job.slurm_stderr),
    )

    # Print warning for ignored parameter
    if len(job.slurm_config.pre_submission_commands) > 0:
        logger.warning(
            f"Ignoring {job.slurm_config.pre_submission_commands=}."
        )

    # Submit job via sbatch, and retrieve jobid

    # Write script content to a job.slurm_script
    with job.slurm_script.open("w") as f:
        f.write(sbatch_script)

    # Prepare submission command
    pre_command = f"sudo --set-home --non-interactive -u {self.slurm_user}"
    submit_command = f"sbatch --parsable {job.slurm_script}"
    full_command = f"{pre_command} {submit_command}"

    # Submit SLURM job and retrieve job ID
    output = _subprocess_run_or_raise(full_command)
    try:
        jobid = int(output.stdout)
    except ValueError as e:
        error_msg = (
            f"Submit command `{full_command}` returned "
            f"`{output.stdout=}` which cannot be cast to an integer "
            f"SLURM-job ID. Original error:\n{str(e)}"
        )
        logger.error(error_msg)
        raise JobExecutionError(info=error_msg)
    jobid_str = str(jobid)

    # Plug SLURM job id in stdout/stderr file paths
    job.slurm_stdout = Path(
        job.slurm_stdout.as_posix().replace("%j", jobid_str)
    )
    job.slurm_stderr = Path(
        job.slurm_stderr.as_posix().replace("%j", jobid_str)
    )

    return jobid_str, job

_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 general args and kwargs arguments;
• When called from self.map, there cannot be any args or kwargs argument, but there must be a components 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

def _submit_job(
    self,
    fun: Callable[..., Any],
    slurm_file_prefix: str,
    task_files: TaskFiles,
    slurm_config: SlurmConfig,
    single_task_submission: bool = False,
    args: Optional[Sequence[Any]] = None,
    kwargs: Optional[dict] = None,
    components: Optional[list[Any]] = None,
) -> Future:
    """
    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 general `args` and
      `kwargs` arguments;
    * When called from `self.map`, there cannot be any `args` or `kwargs`
      argument, but there must be a `components` argument.

    Arguments:
        fun:
        slurm_file_prefix:
        task_files:
        slurm_config:
        single_task_submission:
        args:
        kwargs:
        components:

    Returns:
        Future representing the execution of the current SLURM job.
    """

    # Prevent calling sbatch if auxiliary thread was shut down
    if self.wait_thread.shutdown:
        error_msg = (
            "Cannot call `_submit_job` method after executor shutdown"
        )
        logger.warning(error_msg)
        raise JobExecutionError(info=error_msg)

    fut: Future = Future()

    # Inject SLURM account (if set) into slurm_config
    if self.slurm_account:
        slurm_config.account = self.slurm_account

    # Define slurm-job-related files
    if single_task_submission:
        if components is not None:
            raise ValueError(
                f"{single_task_submission=} but components is not None"
            )
        job = SlurmJob(
            slurm_file_prefix=slurm_file_prefix,
            num_tasks_tot=1,
            slurm_config=slurm_config,
        )
        if job.num_tasks_tot > 1:
            raise ValueError(
                "{single_task_submission=} but {job.num_tasks_tot=}"
            )
        job.single_task_submission = True
        job.wftask_file_prefixes = (task_files.file_prefix,)
        job.wftask_subfolder_name = task_files.subfolder_name

    else:
        if not components or len(components) < 1:
            raise ValueError(
                "In FractalSlurmExecutor._submit_job, given "
                f"{components=}."
            )
        num_tasks_tot = len(components)
        job = SlurmJob(
            slurm_file_prefix=slurm_file_prefix,
            num_tasks_tot=num_tasks_tot,
            slurm_config=slurm_config,
        )

        _prefixes = []
        _subfolder_names = []
        for component in components:
            if isinstance(component, dict):
                # This is needed for V2
                actual_component = component.get(_COMPONENT_KEY_, None)
            else:
                actual_component = component
            _task_file_paths = get_task_file_paths(
                workflow_dir_local=task_files.workflow_dir_local,
                workflow_dir_remote=task_files.workflow_dir_remote,
                task_name=task_files.task_name,
                task_order=task_files.task_order,
                component=actual_component,
            )
            _prefixes.append(_task_file_paths.file_prefix)
            _subfolder_names.append(_task_file_paths.subfolder_name)
        job.wftask_file_prefixes = tuple(_prefixes)

        num_subfolders = len(set(_subfolder_names))
        if num_subfolders != 1:
            error_msg_short = (
                f"[_submit_job] Subfolder list has {num_subfolders} "
                "different values, but it must have only one (since "
                "workflow tasks are executed one by one)."
            )
            error_msg_detail = (
                "[_submit_job] Current unique subfolder names: "
                f"{set(_subfolder_names)}"
            )
            logger.error(error_msg_short)
            logger.error(error_msg_detail)
            raise ValueError(error_msg_short)
        job.wftask_subfolder_name = _subfolder_names[0]

    # Check that server-side subfolder exists
    subfolder_path = self.workflow_dir_local / job.wftask_subfolder_name
    if not subfolder_path.exists():
        raise FileNotFoundError(
            f"Missing folder {subfolder_path.as_posix()}."
        )

    job.input_pickle_files = tuple(
        get_pickle_file_path(
            arg=job.workerids[ind],
            workflow_dir=self.workflow_dir_local,
            subfolder_name=job.wftask_subfolder_name,
            in_or_out="in",
            prefix=job.wftask_file_prefixes[ind],
        )
        for ind in range(job.num_tasks_tot)
    )
    job.output_pickle_files = tuple(
        get_pickle_file_path(
            arg=job.workerids[ind],
            workflow_dir=self.workflow_dir_remote,
            subfolder_name=job.wftask_subfolder_name,
            in_or_out="out",
            prefix=job.wftask_file_prefixes[ind],
        )
        for ind in range(job.num_tasks_tot)
    )
    # Define SLURM-job file names/paths
    job.slurm_script = get_slurm_script_file_path(
        workflow_dir=self.workflow_dir_local,
        subfolder_name=job.wftask_subfolder_name,
        prefix=job.slurm_file_prefix,
    )
    job.slurm_stdout = get_slurm_file_path(
        workflow_dir=self.workflow_dir_remote,
        subfolder_name=job.wftask_subfolder_name,
        out_or_err="out",
        prefix=job.slurm_file_prefix,
    )
    job.slurm_stderr = get_slurm_file_path(
        workflow_dir=self.workflow_dir_remote,
        subfolder_name=job.wftask_subfolder_name,
        out_or_err="err",
        prefix=job.slurm_file_prefix,
    )

    # Dump serialized versions+function+args+kwargs to pickle
    versions = dict(
        python=sys.version_info[:3],
        cloudpickle=cloudpickle.__version__,
        fractal_server=__VERSION__,
    )
    if job.single_task_submission:
        _args = args or []
        _kwargs = kwargs or {}
        funcser = cloudpickle.dumps((versions, fun, _args, _kwargs))
        with open(job.input_pickle_files[0], "wb") as f:
            f.write(funcser)
    else:
        for ind_component, component in enumerate(components):
            _args = [component]
            _kwargs = {}
            funcser = cloudpickle.dumps((versions, fun, _args, _kwargs))
            with open(job.input_pickle_files[ind_component], "wb") as f:
                f.write(funcser)

    # Submit job to SLURM, and get jobid
    jobid, job = self._start(job)

    # Add the SLURM script/out/err paths to map_jobid_to_slurm_files (this
    # must be after self._start(job), so that "%j" has already been
    # replaced with the job ID)
    with self.jobs_lock:
        self.map_jobid_to_slurm_files[jobid] = (
            job.slurm_script.as_posix(),
            job.slurm_stdout.as_posix(),
            job.slurm_stderr.as_posix(),
        )

    # Thread will wait for it to finish.
    self.wait_thread.wait(
        filenames=job.get_clean_output_pickle_files(),
        jobid=jobid,
    )

    with self.jobs_lock:
        self.jobs[jobid] = (fut, job)
    return fut

map(fn, iterable, *, slurm_config, task_files)

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:

1. Only fn and iterable can be assigned as positional arguments;
2. *iterables argument replaced with a single iterable;
3. timeout and chunksize 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 fn, as in fn(*args).	required
slurm_config	SlurmConfig	A SlurmConfig object.	required
task_files	TaskFiles	A TaskFiles object.	required

Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py

def map(
    self,
    fn: Callable[..., Any],
    iterable: list[Sequence[Any]],
    *,
    slurm_config: SlurmConfig,
    task_files: TaskFiles,
):
    """
    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:

    1. Only `fn` and `iterable` can be assigned as positional arguments;
    2. `*iterables` argument replaced with a single `iterable`;
    3. `timeout` and `chunksize` arguments are not supported.

    Arguments:
        fn:
            The function to be executed
        iterable:
            An iterable such that each element is the list of arguments to
            be passed to `fn`, as in `fn(*args)`.
        slurm_config:
            A `SlurmConfig` object.
        task_files:
            A `TaskFiles` object.

    """

    # Do not continue if auxiliary thread was shut down
    if self.wait_thread.shutdown:
        error_msg = "Cannot call `map` method after executor shutdown"
        logger.warning(error_msg)
        raise JobExecutionError(info=error_msg)

    def _result_or_cancel(fut):
        """
        This function is based on the Python Standard Library 3.11.
        Original Copyright 2009 Brian Quinlan. All Rights Reserved.
        Licensed to PSF under a Contributor Agreement.
        """
        try:
            try:
                return fut.result()
            finally:
                fut.cancel()
        finally:
            # Break a reference cycle with the exception in
            # self._exception
            del fut

    # Include common_script_lines in extra_lines
    logger.debug(
        f"Adding {self.common_script_lines=} to "
        f"{slurm_config.extra_lines=}, from map method."
    )
    current_extra_lines = slurm_config.extra_lines or []
    slurm_config.extra_lines = (
        current_extra_lines + self.common_script_lines
    )

    # Set file prefixes
    general_slurm_file_prefix = str(task_files.task_order)

    # Transform iterable into a list and count its elements
    list_args = list(iterable)
    tot_tasks = len(list_args)

    # Set/validate parameters for task batching
    tasks_per_job, parallel_tasks_per_job = heuristics(
        # Number of parallel components (always known)
        tot_tasks=len(list_args),
        # Optional WorkflowTask attributes:
        tasks_per_job=slurm_config.tasks_per_job,
        parallel_tasks_per_job=slurm_config.parallel_tasks_per_job,  # noqa
        # Task requirements (multiple possible sources):
        cpus_per_task=slurm_config.cpus_per_task,
        mem_per_task=slurm_config.mem_per_task_MB,
        # Fractal configuration variables (soft/hard limits):
        target_cpus_per_job=slurm_config.target_cpus_per_job,
        target_mem_per_job=slurm_config.target_mem_per_job,
        target_num_jobs=slurm_config.target_num_jobs,
        max_cpus_per_job=slurm_config.max_cpus_per_job,
        max_mem_per_job=slurm_config.max_mem_per_job,
        max_num_jobs=slurm_config.max_num_jobs,
    )
    slurm_config.parallel_tasks_per_job = parallel_tasks_per_job
    slurm_config.tasks_per_job = tasks_per_job

    # Divide arguments in batches of `n_tasks_per_script` tasks each
    args_batches = []
    batch_size = tasks_per_job
    for ind_chunk in range(0, tot_tasks, batch_size):
        args_batches.append(
            list_args[ind_chunk : ind_chunk + batch_size]  # noqa
        )
    if len(args_batches) != math.ceil(tot_tasks / tasks_per_job):
        raise RuntimeError("Something wrong here while batching tasks")

    # Fetch configuration variable
    settings = Inject(get_settings)
    FRACTAL_SLURM_SBATCH_SLEEP = settings.FRACTAL_SLURM_SBATCH_SLEEP

    # Construct list of futures (one per SLURM job, i.e. one per batch)
    fs = []
    current_component_index = 0
    for ind_batch, batch in enumerate(args_batches):
        batch_size = len(batch)
        this_slurm_file_prefix = (
            f"{general_slurm_file_prefix}_batch_{ind_batch:06d}"
        )
        fs.append(
            self._submit_job(
                fn,
                slurm_config=slurm_config,
                slurm_file_prefix=this_slurm_file_prefix,
                task_files=task_files,
                single_task_submission=False,
                components=batch,
            )
        )
        current_component_index += batch_size
        time.sleep(FRACTAL_SLURM_SBATCH_SLEEP)

    # Yield must be hidden in closure so that the futures are submitted
    # before the first iterator value is required.
    # NOTE: In this custom map() method, _result_or_cancel(fs.pop()) is an
    # iterable of results (if successful), and we should yield its elements
    # rather than the whole iterable.
    def result_iterator():
        """
        This function is based on the Python Standard Library 3.11.
        Original Copyright 2009 Brian Quinlan. All Rights Reserved.
        Licensed to PSF under a Contributor Agreement.
        """
        try:
            # reverse to keep finishing order
            fs.reverse()
            while fs:
                # Careful not to keep a reference to the popped future
                results = _result_or_cancel(fs.pop())
                for res in results:
                    yield res
        finally:
            for future in fs:
                future.cancel()

    return result_iterator()

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

def shutdown(self, wait=True, *, cancel_futures=False):
    """
    Clean up all executor variables. Note that this function is executed on
    the self.wait_thread thread, see _completion.
    """

    logger.debug("Executor shutdown: start")

    # Handle all job futures
    slurm_jobs_to_scancel = []
    with self.jobs_lock:
        while self.jobs:
            jobid, fut_and_job = self.jobs.popitem()
            slurm_jobs_to_scancel.append(jobid)
            fut = fut_and_job[0]
            self.map_jobid_to_slurm_files.pop(jobid)
            if not fut.cancelled():
                fut.set_exception(
                    JobExecutionError(
                        "Job cancelled due to executor shutdown."
                    )
                )
                fut.cancel()

    # Cancel SLURM jobs
    if slurm_jobs_to_scancel:
        scancel_string = " ".join(slurm_jobs_to_scancel)
        logger.warning(f"Now scancel-ing SLURM jobs {scancel_string}")
        pre_command = f"sudo --non-interactive -u {self.slurm_user}"
        submit_command = f"scancel {scancel_string}"
        full_command = f"{pre_command} {submit_command}"
        validate_cmd(full_command)
        logger.debug(f"Now execute `{full_command}`")
        try:
            subprocess.run(  # nosec
                shlex.split(full_command),
                capture_output=True,
                check=True,
                encoding="utf-8",
            )
        except subprocess.CalledProcessError as e:
            error_msg = (
                f"Cancel command `{full_command}` failed. "
                f"Original error:\n{str(e)}"
            )
            logger.error(error_msg)
            raise JobExecutionError(info=error_msg)

    # Redudantly set thread shutdown attribute to True
    self.wait_thread.shutdown = True

    logger.debug("Executor shutdown: end")

submit(fun, *fun_args, slurm_config, task_files, **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	SlurmConfig	A SlurmConfig object.	required
task_files	TaskFiles	A TaskFiles object.	required

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

def submit(
    self,
    fun: Callable[..., Any],
    *fun_args: Sequence[Any],
    slurm_config: SlurmConfig,
    task_files: TaskFiles,
    **fun_kwargs: dict,
) -> Future:
    """
    Submit a function for execution on `FractalSlurmExecutor`

    Arguments:
        fun: The function to be executed
        fun_args: Function positional arguments
        fun_kwargs: Function keyword arguments
        slurm_config:
            A `SlurmConfig` object.
        task_files:
            A `TaskFiles` object.

    Returns:
        Future representing the execution of the current SLURM job.
    """

    # Do not continue if auxiliary thread was shut down
    if self.wait_thread.shutdown:
        error_msg = "Cannot call `submit` method after executor shutdown"
        logger.warning(error_msg)
        raise JobExecutionError(info=error_msg)

    # Set slurm_file_prefix
    slurm_file_prefix = task_files.file_prefix

    # Include common_script_lines in extra_lines
    logger.debug(
        f"Adding {self.common_script_lines=} to "
        f"{slurm_config.extra_lines=}, from submit method."
    )
    current_extra_lines = slurm_config.extra_lines or []
    slurm_config.extra_lines = (
        current_extra_lines + self.common_script_lines
    )

    # Adapt slurm_config to the fact that this is a single-task SlurmJob
    # instance
    slurm_config.tasks_per_job = 1
    slurm_config.parallel_tasks_per_job = 1

    fut = self._submit_job(
        fun,
        slurm_config=slurm_config,
        slurm_file_prefix=slurm_file_prefix,
        task_files=task_files,
        single_task_submission=True,
        args=fun_args,
        kwargs=fun_kwargs,
    )
    return fut

SlurmJob

Collect information related to a FractalSlurmExecutor job

This includes three groups of attributes:

1. Attributes related to the (possibly multi-task) SLURM job, e.g. submission-file path.
2. Attributes related to single tasks, e.g. the paths of their input/output pickle files.
3. 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 True for jobs submitted as part of the submit method, and False for jobs coming from the map method.
slurm_file_prefix	str	Prefix for SLURM-job related files (submission script and SLURM stdout/stderr); this is also needed in the _copy_files_from_remote_to_local method.
wftask_file_prefixes	tuple[str, ...]	Prefix for files that are created as part of the functions submitted for execution on the FractalSlurmExecutor; this is needed in the _copy_files_from_remote_to_local method, and also to construct the names of per-task input/output pickle files.
wftask_subfolder_name	str	Name of the per-task subfolder (e.g. 7_task_name).
slurm_script	Path	Path of SLURM submission script.
slurm_stdout	Path	Path of SLURM stdout file; if this includes "%j", then this string will be replaced by the SLURM job ID upon sbatch submission.
slurm_stderr	Path	Path of SLURM stderr file; see slurm_stdout concerning "%j".
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	SlurmConfig object.

Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py

class SlurmJob:
    """
    Collect information related to a FractalSlurmExecutor job

    This includes three groups of attributes:

    1. Attributes related to the (possibly multi-task) SLURM job, e.g.
       submission-file path.
    2. Attributes related to single tasks, e.g. the paths of their input/output
       pickle files.
    3. 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:
        num_tasks_tot:
            Total number of tasks to be executed as part of this SLURM job.
        single_task_submission:
            This must be `True` for jobs submitted as part of the `submit`
            method, and `False` for jobs coming from the `map` method.
        slurm_file_prefix:
            Prefix for SLURM-job related files (submission script and SLURM
            stdout/stderr); this is also needed in the
            `_copy_files_from_remote_to_local` method.
        wftask_file_prefixes:
            Prefix for files that are created as part of the functions
            submitted for execution on the `FractalSlurmExecutor`; this is
            needed in the `_copy_files_from_remote_to_local` method, and also
            to construct the names of per-task input/output pickle files.
        wftask_subfolder_name:
            Name of the per-task subfolder (e.g. `7_task_name`).
        slurm_script:
            Path of SLURM submission script.
        slurm_stdout:
            Path of SLURM stdout file; if this includes `"%j"`, then this
            string will be replaced by the SLURM job ID upon `sbatch`
            submission.
        slurm_stderr:
            Path of SLURM stderr file; see `slurm_stdout` concerning `"%j"`.
        workerids:
            IDs that enter in the per-task input/output pickle files (one per
            task).
        input_pickle_files:
            Input pickle files (one per task).
        output_pickle_files:
            Output pickle files (one per task).
        slurm_config:
            `SlurmConfig` object.
    """

    # Job-related attributes
    num_tasks_tot: int
    single_task_submission: bool
    slurm_file_prefix: str
    slurm_script: Path
    slurm_stdout: Path
    slurm_stderr: Path
    # Per-task attributes
    workerids: tuple[str, ...]
    wftask_file_prefixes: tuple[str, ...]
    wftask_subfolder_name: str
    input_pickle_files: tuple[Path, ...]
    output_pickle_files: tuple[Path, ...]
    # Slurm configuration
    slurm_config: SlurmConfig

    def __init__(
        self,
        num_tasks_tot: int,
        slurm_config: SlurmConfig,
        workflow_task_file_prefix: Optional[str] = None,
        slurm_file_prefix: Optional[str] = None,
        wftask_file_prefixes: Optional[tuple[str, ...]] = None,
        single_task_submission: bool = False,
    ):
        if single_task_submission and num_tasks_tot > 1:
            raise ValueError(
                "Trying to initialize SlurmJob with"
                f"{single_task_submission=} and {num_tasks_tot=}."
            )
        self.num_tasks_tot = num_tasks_tot
        self.single_task_submission = single_task_submission
        self.slurm_file_prefix = slurm_file_prefix or "default_slurm_prefix"
        if wftask_file_prefixes is None:
            self.wftask_file_prefixes = tuple(
                "default_wftask_prefix" for i in range(self.num_tasks_tot)
            )
        else:
            self.wftask_file_prefixes = wftask_file_prefixes
        self.workerids = tuple(
            random_string() for i in range(self.num_tasks_tot)
        )
        self.slurm_config = slurm_config

    def get_clean_output_pickle_files(self) -> tuple[str, ...]:
        """
        Transform all pathlib.Path objects in self.output_pickle_files to
        strings
        """
        return tuple(str(f.as_posix()) for f in self.output_pickle_files)

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

def get_clean_output_pickle_files(self) -> tuple[str, ...]:
    """
    Transform all pathlib.Path objects in self.output_pickle_files to
    strings
    """
    return tuple(str(f.as_posix()) for f in self.output_pickle_files)

_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 subprocess.run raises a CalledProcessError.

Returns:

Type	Description
Optional[CompletedProcess]	The actual CompletedProcess output of subprocess.run.

Source code in fractal_server/app/runner/executors/slurm/sudo/executor.py

def _subprocess_run_or_raise(full_command: str) -> Optional[CompletedProcess]:
    """
    Wrap `subprocess.run` and raise  appropriate `JobExecutionError` if needed.

    Args:
        full_command: Full string of the command to execute.

    Raises:
        JobExecutionError: If `subprocess.run` raises a `CalledProcessError`.

    Returns:
        The actual `CompletedProcess` output of `subprocess.run`.
    """
    validate_cmd(full_command)
    try:
        output = subprocess.run(  # nosec
            shlex.split(full_command),
            capture_output=True,
            check=True,
            encoding="utf-8",
        )
        return output
    except subprocess.CalledProcessError as e:
        error_msg = (
            f"Submit command `{full_command}` failed. "
            f"Original error:\n{str(e)}\n"
            f"Original stdout:\n{e.stdout}\n"
            f"Original stderr:\n{e.stderr}\n"
        )
        logger.error(error_msg)
        raise JobExecutionError(info=error_msg)