fractal-server 1.4.10__py3-none-any.whl → 2.0.0a0__py3-none-any.whl

fractal_server/app/runner/v1/_slurm/__init__.py

@@ -0,0 +1,310 @@
+# Copyright 2022 (C) Friedrich Miescher Institute for Biomedical Research and
+# University of Zurich
+#
+# Original authors:
+# Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
+# Tommaso Comparin <tommaso.comparin@exact-lab.it>
+# Marco Franzon <marco.franzon@exact-lab.it>
+#
+# This file is part of Fractal and was originally developed by eXact lab S.r.l.
+# <exact-lab.it> under contract with Liberali Lab from the Friedrich Miescher
+# Institute for Biomedical Research and Pelkmans Lab from the University of
+# Zurich.
+"""
+Slurm Bakend
+
+This backend runs fractal workflows in a SLURM cluster using Clusterfutures
+Executor objects.
+"""
+from pathlib import Path
+from typing import Any
+from typing import Optional
+from typing import Union
+
+from ...async_wrap import async_wrap
+from ...executors.slurm.executor import FractalSlurmExecutor
+from ...set_start_and_last_task_index import set_start_and_last_task_index
+from .._common import execute_tasks
+from ..common import TaskParameters
+from ._submit_setup import _slurm_submit_setup
+from fractal_server.app.models.v1 import Workflow
+from fractal_server.app.models.v1 import WorkflowTask
+from fractal_server.app.runner.executors.slurm._slurm_config import (
+    _parse_mem_value,
+)
+from fractal_server.app.runner.executors.slurm._slurm_config import (
+    load_slurm_config_file,
+)
+from fractal_server.app.runner.executors.slurm._slurm_config import logger
+from fractal_server.app.runner.executors.slurm._slurm_config import SlurmConfig
+from fractal_server.app.runner.executors.slurm._slurm_config import (
+    SlurmConfigError,
+)
+
+
+def _process_workflow(
+    *,
+    workflow: Workflow,
+    input_paths: list[Path],
+    output_path: Path,
+    input_metadata: dict[str, Any],
+    input_history: list[dict[str, Any]],
+    logger_name: str,
+    workflow_dir: Path,
+    workflow_dir_user: Path,
+    first_task_index: int,
+    last_task_index: int,
+    slurm_user: Optional[str] = None,
+    slurm_account: Optional[str] = None,
+    user_cache_dir: str,
+    worker_init: Optional[Union[str, list[str]]] = None,
+) -> dict[str, Any]:
+    """
+    Internal processing routine for the SLURM backend
+
+    This function initialises the a FractalSlurmExecutor, setting logging,
+    workflow working dir and user to impersonate. It then schedules the
+    workflow tasks and returns the output dataset metadata.
+
+    Cf. [process_workflow][fractal_server.app.runner._local.process_workflow]
+
+    Returns:
+        output_dataset_metadata: Metadata of the output dataset
+    """
+
+    if not slurm_user:
+        raise RuntimeError(
+            "slurm_user argument is required, for slurm backend"
+        )
+
+    if isinstance(worker_init, str):
+        worker_init = worker_init.split("\n")
+
+    with FractalSlurmExecutor(
+        debug=True,
+        keep_logs=True,
+        slurm_user=slurm_user,
+        user_cache_dir=user_cache_dir,
+        working_dir=workflow_dir,
+        working_dir_user=workflow_dir_user,
+        common_script_lines=worker_init,
+        slurm_account=slurm_account,
+    ) as executor:
+        output_task_pars = execute_tasks(
+            executor=executor,
+            task_list=workflow.task_list[
+                first_task_index : (last_task_index + 1)  # noqa
+            ],  # noqa
+            task_pars=TaskParameters(
+                input_paths=input_paths,
+                output_path=output_path,
+                metadata=input_metadata,
+                history=input_history,
+            ),
+            workflow_dir=workflow_dir,
+            workflow_dir_user=workflow_dir_user,
+            submit_setup_call=_slurm_submit_setup,
+            logger_name=logger_name,
+        )
+    output_dataset_metadata_history = dict(
+        metadata=output_task_pars.metadata, history=output_task_pars.history
+    )
+    return output_dataset_metadata_history
+
+
+async def process_workflow(
+    *,
+    workflow: Workflow,
+    input_paths: list[Path],
+    output_path: Path,
+    input_metadata: dict[str, Any],
+    input_history: list[dict[str, Any]],
+    logger_name: str,
+    workflow_dir: Path,
+    workflow_dir_user: Optional[Path] = None,
+    user_cache_dir: Optional[str] = None,
+    slurm_user: Optional[str] = None,
+    slurm_account: Optional[str] = None,
+    worker_init: Optional[str] = None,
+    first_task_index: Optional[int] = None,
+    last_task_index: Optional[int] = None,
+) -> dict[str, Any]:
+    """
+    Process workflow (SLURM backend public interface)
+
+    Cf. [process_workflow][fractal_server.app.runner._local.process_workflow]
+    """
+
+    # Set values of first_task_index and last_task_index
+    num_tasks = len(workflow.task_list)
+    first_task_index, last_task_index = set_start_and_last_task_index(
+        num_tasks,
+        first_task_index=first_task_index,
+        last_task_index=last_task_index,
+    )
+
+    output_dataset_metadata_history = await async_wrap(_process_workflow)(
+        workflow=workflow,
+        input_paths=input_paths,
+        output_path=output_path,
+        input_metadata=input_metadata,
+        input_history=input_history,
+        logger_name=logger_name,
+        workflow_dir=workflow_dir,
+        workflow_dir_user=workflow_dir_user,
+        slurm_user=slurm_user,
+        slurm_account=slurm_account,
+        user_cache_dir=user_cache_dir,
+        worker_init=worker_init,
+        first_task_index=first_task_index,
+        last_task_index=last_task_index,
+    )
+    return output_dataset_metadata_history
+
+
+def get_slurm_config(
+    wftask: WorkflowTask,
+    workflow_dir: Path,
+    workflow_dir_user: Path,
+    config_path: Optional[Path] = None,
+) -> SlurmConfig:
+    """
+    Prepare a `SlurmConfig` configuration object
+
+    The sources for `SlurmConfig` attributes, in increasing priority order, are
+
+    1. The general content of the Fractal SLURM configuration file.
+    2. The GPU-specific content of the Fractal SLURM configuration file, if
+        appropriate.
+    3. Properties in `wftask.meta` (which, for `WorkflowTask`s added through
+       `Workflow.insert_task`, also includes `wftask.task.meta`);
+
+    Note: `wftask.meta` may be `None`.
+
+    Arguments:
+        wftask:
+            WorkflowTask for which the SLURM configuration is is to be
+            prepared.
+        workflow_dir:
+            Server-owned directory to store all task-execution-related relevant
+            files (inputs, outputs, errors, and all meta files related to the
+            job execution). Note: users cannot write directly to this folder.
+        workflow_dir_user:
+            User-side directory with the same scope as `workflow_dir`, and
+            where a user can write.
+        config_path:
+            Path of aFractal  SLURM configuration file; if `None`, use
+            `FRACTAL_SLURM_CONFIG_FILE` variable from settings.
+
+    Returns:
+        slurm_config:
+            The SlurmConfig object
+    """
+
+    logger.debug(
+        "[get_slurm_config] WorkflowTask meta attribute: {wftask.meta=}"
+    )
+
+    # Incorporate slurm_env.default_slurm_config
+    slurm_env = load_slurm_config_file(config_path=config_path)
+    slurm_dict = slurm_env.default_slurm_config.dict(
+        exclude_unset=True, exclude={"mem"}
+    )
+    if slurm_env.default_slurm_config.mem:
+        slurm_dict["mem_per_task_MB"] = slurm_env.default_slurm_config.mem
+
+    # Incorporate slurm_env.batching_config
+    for key, value in slurm_env.batching_config.dict().items():
+        slurm_dict[key] = value
+
+    # Incorporate slurm_env.user_local_exports
+    slurm_dict["user_local_exports"] = slurm_env.user_local_exports
+
+    logger.debug(
+        "[get_slurm_config] Fractal SLURM configuration file: "
+        f"{slurm_env.dict()=}"
+    )
+
+    # GPU-related options
+    # Notes about priority:
+    # 1. This block of definitions takes priority over other definitions from
+    #    slurm_env which are not under the `needs_gpu` subgroup
+    # 2. This block of definitions has lower priority than whatever comes next
+    #    (i.e. from WorkflowTask.meta).
+    if wftask.meta is not None:
+        needs_gpu = wftask.meta.get("needs_gpu", False)
+    else:
+        needs_gpu = False
+    logger.debug(f"[get_slurm_config] {needs_gpu=}")
+    if needs_gpu:
+        for key, value in slurm_env.gpu_slurm_config.dict(
+            exclude_unset=True, exclude={"mem"}
+        ).items():
+            slurm_dict[key] = value
+        if slurm_env.gpu_slurm_config.mem:
+            slurm_dict["mem_per_task_MB"] = slurm_env.gpu_slurm_config.mem
+
+    # Number of CPUs per task, for multithreading
+    if wftask.meta is not None and "cpus_per_task" in wftask.meta:
+        cpus_per_task = int(wftask.meta["cpus_per_task"])
+        slurm_dict["cpus_per_task"] = cpus_per_task
+
+    # Required memory per task, in MB
+    if wftask.meta is not None and "mem" in wftask.meta:
+        raw_mem = wftask.meta["mem"]
+        mem_per_task_MB = _parse_mem_value(raw_mem)
+        slurm_dict["mem_per_task_MB"] = mem_per_task_MB
+
+    # Job name
+    job_name = wftask.task.name.replace(" ", "_")
+    slurm_dict["job_name"] = job_name
+
+    # Optional SLURM arguments and extra lines
+    if wftask.meta is not None:
+        account = wftask.meta.get("account", None)
+        if account is not None:
+            error_msg = (
+                f"Invalid {account=} property in WorkflowTask `meta` "
+                "attribute.\n"
+                "SLURM account must be set in the request body of the "
+                "apply-workflow endpoint, or by modifying the user properties."
+            )
+            logger.error(error_msg)
+            raise SlurmConfigError(error_msg)
+        for key in ["time", "gres", "constraint"]:
+            value = wftask.meta.get(key, None)
+            if value:
+                slurm_dict[key] = value
+    if wftask.meta is not None:
+        extra_lines = wftask.meta.get("extra_lines", [])
+    else:
+        extra_lines = []
+    extra_lines = slurm_dict.get("extra_lines", []) + extra_lines
+    if len(set(extra_lines)) != len(extra_lines):
+        logger.debug(
+            "[get_slurm_config] Removing repeated elements "
+            f"from {extra_lines=}."
+        )
+        extra_lines = list(set(extra_lines))
+    slurm_dict["extra_lines"] = extra_lines
+
+    # Job-batching parameters (if None, they will be determined heuristically)
+    if wftask.meta is not None:
+        tasks_per_job = wftask.meta.get("tasks_per_job", None)
+        parallel_tasks_per_job = wftask.meta.get(
+            "parallel_tasks_per_job", None
+        )
+    else:
+        tasks_per_job = None
+        parallel_tasks_per_job = None
+    slurm_dict["tasks_per_job"] = tasks_per_job
+    slurm_dict["parallel_tasks_per_job"] = parallel_tasks_per_job
+
+    # Put everything together
+    logger.debug(
+        "[get_slurm_config] Now create a SlurmConfig object based "
+        f"on {slurm_dict=}"
+    )
+    slurm_config = SlurmConfig(**slurm_dict)
+
+    return slurm_config

fractal_server/app/runner/{_slurm → v1/_slurm}/_submit_setup.py

@@ -15,12 +15,10 @@ implementation of `submit_setup_call` in
 [fractal_server.app.runner._common][]).
 """
 from pathlib import Path
-from typing import Optional
 
-from ...models import WorkflowTask
-from .._common import get_task_file_paths
-from ..common import TaskParameters
-from ._slurm_config import get_slurm_config
+from ...task_files import get_task_file_paths
+from .get_slurm_config import get_slurm_config
+from fractal_server.app.models.v1 import WorkflowTask
 
 
 def _slurm_submit_setup(
@@ -28,7 +26,6 @@ def _slurm_submit_setup(
     wftask: WorkflowTask,
     workflow_dir: Path,
     workflow_dir_user: Path,
-    task_pars: Optional[TaskParameters] = None,
 ) -> dict[str, object]:
     """
     Collect WorfklowTask-specific configuration parameters from different
@@ -46,9 +43,6 @@ def _slurm_submit_setup(
     Arguments:
         wftask:
             WorkflowTask for which the configuration is to be assembled
-        task_pars:
-            Task parameters to be passed to the task
-            (not used in this function)
         workflow_dir:
             Server-owned directory to store all task-execution-related relevant
             files (inputs, outputs, errors, and all meta files related to the

fractal_server/app/runner/v1/_slurm/get_slurm_config.py

@@ -0,0 +1,163 @@
+from pathlib import Path
+from typing import Optional
+
+from fractal_server.app.models.v1 import WorkflowTask
+from fractal_server.app.runner.executors.slurm._slurm_config import (
+    _parse_mem_value,
+)
+from fractal_server.app.runner.executors.slurm._slurm_config import (
+    load_slurm_config_file,
+)
+from fractal_server.app.runner.executors.slurm._slurm_config import logger
+from fractal_server.app.runner.executors.slurm._slurm_config import SlurmConfig
+from fractal_server.app.runner.executors.slurm._slurm_config import (
+    SlurmConfigError,
+)
+
+
+def get_slurm_config(
+    wftask: WorkflowTask,
+    workflow_dir: Path,
+    workflow_dir_user: Path,
+    config_path: Optional[Path] = None,
+) -> SlurmConfig:
+    """
+    Prepare a `SlurmConfig` configuration object
+
+    The sources for `SlurmConfig` attributes, in increasing priority order, are
+
+    1. The general content of the Fractal SLURM configuration file.
+    2. The GPU-specific content of the Fractal SLURM configuration file, if
+        appropriate.
+    3. Properties in `wftask.meta` (which, for `WorkflowTask`s added through
+       `Workflow.insert_task`, also includes `wftask.task.meta`);
+
+    Note: `wftask.meta` may be `None`.
+
+    Arguments:
+        wftask:
+            WorkflowTask for which the SLURM configuration is is to be
+            prepared.
+        workflow_dir:
+            Server-owned directory to store all task-execution-related relevant
+            files (inputs, outputs, errors, and all meta files related to the
+            job execution). Note: users cannot write directly to this folder.
+        workflow_dir_user:
+            User-side directory with the same scope as `workflow_dir`, and
+            where a user can write.
+        config_path:
+            Path of aFractal  SLURM configuration file; if `None`, use
+            `FRACTAL_SLURM_CONFIG_FILE` variable from settings.
+
+    Returns:
+        slurm_config:
+            The SlurmConfig object
+    """
+
+    logger.debug(
+        "[get_slurm_config] WorkflowTask meta attribute: {wftask.meta=}"
+    )
+
+    # Incorporate slurm_env.default_slurm_config
+    slurm_env = load_slurm_config_file(config_path=config_path)
+    slurm_dict = slurm_env.default_slurm_config.dict(
+        exclude_unset=True, exclude={"mem"}
+    )
+    if slurm_env.default_slurm_config.mem:
+        slurm_dict["mem_per_task_MB"] = slurm_env.default_slurm_config.mem
+
+    # Incorporate slurm_env.batching_config
+    for key, value in slurm_env.batching_config.dict().items():
+        slurm_dict[key] = value
+
+    # Incorporate slurm_env.user_local_exports
+    slurm_dict["user_local_exports"] = slurm_env.user_local_exports
+
+    logger.debug(
+        "[get_slurm_config] Fractal SLURM configuration file: "
+        f"{slurm_env.dict()=}"
+    )
+
+    # GPU-related options
+    # Notes about priority:
+    # 1. This block of definitions takes priority over other definitions from
+    #    slurm_env which are not under the `needs_gpu` subgroup
+    # 2. This block of definitions has lower priority than whatever comes next
+    #    (i.e. from WorkflowTask.meta).
+    if wftask.meta is not None:
+        needs_gpu = wftask.meta.get("needs_gpu", False)
+    else:
+        needs_gpu = False
+    logger.debug(f"[get_slurm_config] {needs_gpu=}")
+    if needs_gpu:
+        for key, value in slurm_env.gpu_slurm_config.dict(
+            exclude_unset=True, exclude={"mem"}
+        ).items():
+            slurm_dict[key] = value
+        if slurm_env.gpu_slurm_config.mem:
+            slurm_dict["mem_per_task_MB"] = slurm_env.gpu_slurm_config.mem
+
+    # Number of CPUs per task, for multithreading
+    if wftask.meta is not None and "cpus_per_task" in wftask.meta:
+        cpus_per_task = int(wftask.meta["cpus_per_task"])
+        slurm_dict["cpus_per_task"] = cpus_per_task
+
+    # Required memory per task, in MB
+    if wftask.meta is not None and "mem" in wftask.meta:
+        raw_mem = wftask.meta["mem"]
+        mem_per_task_MB = _parse_mem_value(raw_mem)
+        slurm_dict["mem_per_task_MB"] = mem_per_task_MB
+
+    # Job name
+    job_name = wftask.task.name.replace(" ", "_")
+    slurm_dict["job_name"] = job_name
+
+    # Optional SLURM arguments and extra lines
+    if wftask.meta is not None:
+        account = wftask.meta.get("account", None)
+        if account is not None:
+            error_msg = (
+                f"Invalid {account=} property in WorkflowTask `meta` "
+                "attribute.\n"
+                "SLURM account must be set in the request body of the "
+                "apply-workflow endpoint, or by modifying the user properties."
+            )
+            logger.error(error_msg)
+            raise SlurmConfigError(error_msg)
+        for key in ["time", "gres", "constraint"]:
+            value = wftask.meta.get(key, None)
+            if value:
+                slurm_dict[key] = value
+    if wftask.meta is not None:
+        extra_lines = wftask.meta.get("extra_lines", [])
+    else:
+        extra_lines = []
+    extra_lines = slurm_dict.get("extra_lines", []) + extra_lines
+    if len(set(extra_lines)) != len(extra_lines):
+        logger.debug(
+            "[get_slurm_config] Removing repeated elements "
+            f"from {extra_lines=}."
+        )
+        extra_lines = list(set(extra_lines))
+    slurm_dict["extra_lines"] = extra_lines
+
+    # Job-batching parameters (if None, they will be determined heuristically)
+    if wftask.meta is not None:
+        tasks_per_job = wftask.meta.get("tasks_per_job", None)
+        parallel_tasks_per_job = wftask.meta.get(
+            "parallel_tasks_per_job", None
+        )
+    else:
+        tasks_per_job = None
+        parallel_tasks_per_job = None
+    slurm_dict["tasks_per_job"] = tasks_per_job
+    slurm_dict["parallel_tasks_per_job"] = parallel_tasks_per_job
+
+    # Put everything together
+    logger.debug(
+        "[get_slurm_config] Now create a SlurmConfig object based "
+        f"on {slurm_dict=}"
+    )
+    slurm_config = SlurmConfig(**slurm_dict)
+
+    return slurm_config

fractal_server/app/runner/v1/common.py

@@ -0,0 +1,117 @@
+"""
+Common utilities and routines for runner backends (public API)
+
+This module includes utilities and routines that are of use to implement
+runner backends but that should also be exposed to the other components of
+`Fractal Server`.
+"""
+import json
+from json import JSONEncoder
+from pathlib import Path
+from typing import Any
+
+from pydantic import BaseModel
+
+from ....logger import close_logger as close_job_logger  # noqa F401
+from ...models.v1 import Dataset
+from ...models.v1 import Workflow
+
+
+class TaskParameterEncoder(JSONEncoder):
+    """
+    Convenience JSONEncoder that serialises `Path`s as strings
+    """
+
+    def default(self, value):
+        if isinstance(value, Path):
+            return value.as_posix()
+        return JSONEncoder.default(self, value)
+
+
+class TaskParameters(BaseModel):
+    """
+    Wrapper for task input parameters
+
+    Instances of this class are used to pass parameters from the output of a
+    task to the input of the next one.
+
+    Attributes:
+        input_paths:
+            Input paths as derived by the input dataset.
+        output_paths:
+            Output path as derived from the output dataset.
+        metadata:
+            Dataset metadata, as found in the input dataset or as updated by
+            the previous task.
+        history:
+            Dataset history, as found in the input dataset or as updated by
+            the previous task.
+    """
+
+    input_paths: list[Path]
+    output_path: Path
+    metadata: dict[str, Any]
+    history: list[dict[str, Any]]
+
+    class Config:
+        arbitrary_types_allowed = True
+        extra = "forbid"
+
+
+def validate_workflow_compatibility(
+    *,
+    input_dataset: Dataset,
+    workflow: Workflow,
+    output_dataset: Dataset,
+    first_task_index: int,
+    last_task_index: int,
+) -> None:
+    """
+    Check compatibility of workflow and input / ouptut dataset
+    """
+    # Check input_dataset type
+    workflow_input_type = workflow.task_list[first_task_index].task.input_type
+    if (
+        workflow_input_type != "Any"
+        and workflow_input_type != input_dataset.type
+    ):
+        raise TypeError(
+            f"Incompatible types `{workflow_input_type}` of workflow "
+            f"`{workflow.name}` and `{input_dataset.type}` of dataset "
+            f"`{input_dataset.name}`"
+        )
+
+    # Check output_dataset type
+    workflow_output_type = workflow.task_list[last_task_index].task.output_type
+    if (
+        workflow_output_type != "Any"
+        and workflow_output_type != output_dataset.type
+    ):
+        raise TypeError(
+            f"Incompatible types `{workflow_output_type}` of workflow "
+            f"`{workflow.name}` and `{output_dataset.type}` of dataset "
+            f"`{output_dataset.name}`"
+        )
+
+
+def write_args_file(
+    *args: dict[str, Any],
+    path: Path,
+):
+    """
+    Merge arbitrary dictionaries and write to file
+
+    Args:
+        *args:
+            One or more dictionaries that will be merged into one respecting
+            the order with which they are passed in, i.e., last in overrides
+            previous ones.
+        path:
+            Destination for serialised file.
+    """
+    out = {}
+    for d in args:
+        out.update(d)
+
+    with open(path, "w") as f:
+        json.dump(out, f, cls=TaskParameterEncoder, indent=4)

fractal_server/app/runner/{handle_failed_job.py → v1/handle_failed_job.py}

@@ -19,13 +19,13 @@ from pathlib import Path
 from typing import Any
 from typing import Optional
 
-from ..models import ApplyWorkflow
-from ..models import Dataset
-from ..models import Workflow
-from ..models import WorkflowTask
-from ..models import WorkflowTaskStatusType
-from ._common import HISTORY_FILENAME
-from ._common import METADATA_FILENAME
+from ...models.v1 import ApplyWorkflow
+from ...models.v1 import Dataset
+from ...models.v1 import Workflow
+from ...models.v1 import WorkflowTask
+from ...schemas.v1 import WorkflowTaskStatusTypeV1
+from ..filenames import HISTORY_FILENAME
+from ..filenames import METADATA_FILENAME
 
 
 def assemble_history_failed_job(
@@ -98,7 +98,7 @@ def assemble_history_failed_job(
         failed_wftask_dump["task"] = failed_wftask.task.model_dump()
         new_history_item = dict(
             workflowtask=failed_wftask_dump,
-            status=WorkflowTaskStatusType.FAILED,
+            status=WorkflowTaskStatusTypeV1.FAILED,
             parallelization=dict(
                 parallelization_level=failed_wftask.parallelization_level,
             ),