fractal-server 2.14.0a13__py3-none-any.whl → 2.14.0a15__py3-none-any.whl

fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py

@@ -0,0 +1,677 @@
+import json
+import math
+import sys
+import time
+from pathlib import Path
+from typing import Any
+from typing import Literal
+from typing import Optional
+
+import cloudpickle
+
+from ..slurm_common._slurm_config import SlurmConfig
+from ..slurm_common.slurm_job_task_models import SlurmJob
+from ..slurm_common.slurm_job_task_models import SlurmTask
+from ._batching import heuristics
+from ._handle_exception_proxy import _handle_exception_proxy
+from ._job_states import STATES_FINISHED
+from fractal_server import __VERSION__
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.runner.exceptions import JobExecutionError
+from fractal_server.app.runner.executors.base_runner import BaseRunner
+from fractal_server.app.runner.filenames import SHUTDOWN_FILENAME
+from fractal_server.app.runner.task_files import MULTISUBMIT_PREFIX
+from fractal_server.app.runner.task_files import SUBMIT_PREFIX
+from fractal_server.app.runner.task_files import TaskFiles
+from fractal_server.app.runner.v2.db_tools import update_status_of_history_unit
+from fractal_server.app.schemas.v2 import HistoryUnitStatus
+from fractal_server.config import get_settings
+from fractal_server.logger import set_logger
+from fractal_server.syringe import Inject
+
+logger = set_logger(__name__)
+
+# FIXME: Transform several logger.info into logger.debug.
+
+
+class BaseSlurmRunner(BaseRunner):
+    shutdown_file: Path
+    common_script_lines: list[str]
+    user_cache_dir: str
+    root_dir_local: Path
+    root_dir_remote: Path
+    poll_interval: int
+    jobs: dict[str, SlurmJob]
+    python_worker_interpreter: str
+    slurm_runner_type: Literal["ssh", "sudo"]
+
+    def __init__(
+        self,
+        root_dir_local: Path,
+        root_dir_remote: Path,
+        slurm_runner_type: Literal["ssh", "sudo"],
+        common_script_lines: Optional[list[str]] = None,
+        user_cache_dir: Optional[str] = None,
+        poll_interval: Optional[int] = None,
+    ):
+        self.slurm_runner_type = slurm_runner_type
+        self.root_dir_local = root_dir_local
+        self.root_dir_remote = root_dir_remote
+        self.common_script_lines = common_script_lines or []
+        self._check_slurm_account()
+        self.user_cache_dir = user_cache_dir
+
+        settings = Inject(get_settings)
+
+        self.poll_interval = (
+            poll_interval or settings.FRACTAL_SLURM_POLL_INTERVAL
+        )
+        self.check_fractal_server_versions()
+
+        # Create job folders. Note that the local one may or may not exist
+        # depending on whether it is a test or an actual run
+        if not self.root_dir_local.is_dir():
+            self._mkdir_local_folder(self.root_dir_local.as_posix())
+        self._mkdir_remote_folder(self.root_dir_remote.as_posix())
+
+        self.shutdown_file = self.root_dir_local / SHUTDOWN_FILENAME
+        self.jobs = {}
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        return False
+
+    def _run_local_cmd(self, cmd: str) -> str:
+        raise NotImplementedError("Implement in child class.")
+
+    def _run_remote_cmd(self, cmd: str) -> str:
+        raise NotImplementedError("Implement in child class.")
+
+    def run_squeue(self, job_ids: list[str]) -> tuple[bool, str]:
+        # FIXME: review different cases (exception vs no job found)
+        job_id_single_str = ",".join([str(j) for j in job_ids])
+        cmd = (
+            f"squeue --noheader --format='%i %T' --jobs {job_id_single_str}"
+            " --states=all"
+        )
+
+        try:
+            if self.slurm_runner_type == "sudo":
+                stdout = self._run_local_cmd(cmd)
+            else:
+                stdout = self._run_remote_cmd(cmd)
+            return True, stdout
+        except Exception as e:
+            logger.info(f"{cmd=} failed with {str(e)}")
+            return False, ""
+
+    def _get_finished_jobs(self, job_ids: list[str]) -> set[str]:
+        #  If there is no Slurm job to check, return right away
+
+        if not job_ids:
+            return set()
+        id_to_state = dict()
+
+        success, stdout = self.run_squeue(job_ids)
+        if success:
+            id_to_state = {
+                out.split()[0]: out.split()[1] for out in stdout.splitlines()
+            }
+        else:
+            id_to_state = dict()
+            for j in job_ids:
+                success, res = self.run_squeue([j])
+                if not success:
+                    logger.info(f"Job {j} not found. Marked it as completed")
+                    id_to_state.update({str(j): "COMPLETED"})
+                else:
+                    id_to_state.update(
+                        {res.stdout.split()[0]: res.stdout.split()[1]}
+                    )
+
+        # Finished jobs only stay in squeue for a few mins (configurable). If
+        # a job ID isn't there, we'll assume it's finished.
+        return {
+            j
+            for j in job_ids
+            if id_to_state.get(j, "COMPLETED") in STATES_FINISHED
+        }
+
+    def _mkdir_local_folder(self, folder: str) -> None:
+        raise NotImplementedError("Implement in child class.")
+
+    def _mkdir_remote_folder(self, folder: str) -> None:
+        raise NotImplementedError("Implement in child class.")
+
+    def _submit_single_sbatch(
+        self,
+        func,
+        slurm_job: SlurmJob,
+        slurm_config: SlurmConfig,
+    ) -> str:
+        logger.info("[_submit_single_sbatch] START")
+        # Prepare input pickle(s)
+        versions = dict(
+            python=sys.version_info[:3],
+            cloudpickle=cloudpickle.__version__,
+            fractal_server=__VERSION__,
+        )
+        for task in slurm_job.tasks:
+            # Wrinte input pickle
+            _args = []
+            _kwargs = dict(
+                parameters=task.parameters,
+                remote_files=task.task_files.remote_files_dict,
+            )
+            funcser = cloudpickle.dumps((versions, func, _args, _kwargs))
+            with open(task.input_pickle_file_local, "wb") as f:
+                f.write(funcser)
+            logger.info(
+                "[_submit_single_sbatch] Written "
+                f"{task.input_pickle_file_local=}"
+            )
+
+            if self.slurm_runner_type == "ssh":
+                # Send input pickle (only relevant for SSH)
+                self.fractal_ssh.send_file(
+                    local=task.input_pickle_file_local,
+                    remote=task.input_pickle_file_remote,
+                )
+                logger.info(
+                    "[_submit_single_sbatch] Transferred "
+                    f"{task.input_pickle_file_local=}"
+                )
+
+        # Prepare commands to be included in SLURM submission script
+        cmdlines = []
+        for task in slurm_job.tasks:
+            if self.slurm_runner_type == "ssh":
+                input_pickle_file = task.input_pickle_file_remote
+            else:
+                input_pickle_file = task.input_pickle_file_local
+            output_pickle_file = task.output_pickle_file_remote
+            cmdlines.append(
+                (
+                    f"{self.python_worker_interpreter}"
+                    " -m fractal_server.app.runner."
+                    "executors.slurm_common.remote "
+                    f"--input-file {input_pickle_file} "
+                    f"--output-file {output_pickle_file}"
+                )
+            )
+
+        # Set ntasks
+        num_tasks_max_running = slurm_config.parallel_tasks_per_job
+        ntasks = min(len(cmdlines), num_tasks_max_running)
+        slurm_config.parallel_tasks_per_job = 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_job.slurm_stderr_remote}",
+                f"#SBATCH --out={slurm_job.slurm_stdout_remote}",
+                f"#SBATCH -D {slurm_job.workdir_remote}",
+            ]
+        )
+        script_lines = slurm_config.sort_script_lines(script_lines)
+        logger.info(script_lines)
+
+        # Always print output of `uname -n` and `pwd`
+        script_lines.append("Hostname: $(uname -n)\n")
+        script_lines.append("Current directory : $(pwd)\n")
+        script_lines.append('Start time: $(date + "%Y-%m-%dT%H:%M:%S%z")\n')
+
+        # Complete script preamble
+        script_lines.append("\n")
+
+        # Include command lines
+        mem_per_task_MB = slurm_config.mem_per_task_MB
+        for cmd in cmdlines:
+            script_lines.append(
+                "srun --ntasks=1 --cpus-per-task=$SLURM_CPUS_PER_TASK "
+                f"--mem={mem_per_task_MB}MB "
+                f"{cmd} &"
+            )
+        script_lines.append("wait\n")
+        script = "\n".join(script_lines)
+        script_lines.append('End time:   $(date + "%Y-%m-%dT%H:%M:%S%z")\n')
+
+        # Write submission script
+        with open(slurm_job.slurm_submission_script_local, "w") as f:
+            f.write(script)
+        logger.info(
+            "[_submit_single_sbatch] Written "
+            f"{slurm_job.slurm_submission_script_local=}"
+        )
+
+        if self.slurm_runner_type == "ssh":
+            self.fractal_ssh.send_file(
+                local=slurm_job.slurm_submission_script_local,
+                remote=slurm_job.slurm_submission_script_remote,
+            )
+            submit_command = (
+                "sbatch --parsable "
+                f"{slurm_job.slurm_submission_script_remote}"
+            )
+        else:
+            submit_command = (
+                "sbatch --parsable "
+                f"{slurm_job.slurm_submission_script_local}"
+            )
+        # Run sbatch
+        pre_submission_cmds = slurm_config.pre_submission_commands
+        if len(pre_submission_cmds) == 0:
+            logger.info(f"Now run {submit_command=}")
+            sbatch_stdout = self._run_remote_cmd(submit_command)
+        else:
+            logger.info(f"Now using {pre_submission_cmds=}")
+            script_lines = pre_submission_cmds + [submit_command]
+            wrapper_script_contents = "\n".join(script_lines)
+            wrapper_script_contents = f"{wrapper_script_contents}\n"
+            if self.slurm_runner_type == "ssh":
+                wrapper_script = (
+                    f"{slurm_job.slurm_submission_script_remote}_wrapper.sh"
+                )
+                self.fractal_ssh.write_remote_file(
+                    path=wrapper_script, content=wrapper_script_contents
+                )
+            else:
+                wrapper_script = (
+                    f"{slurm_job.slurm_submission_script_local}_wrapper.sh"
+                )
+                with open(wrapper_script, "w") as f:
+                    f.write(wrapper_script_contents)
+            logger.info(f"Now run {wrapper_script=}")
+            sbatch_stdout = self._run_remote_cmd(f"bash {wrapper_script}")
+
+        # Submit SLURM job and retrieve job ID
+        logger.info(f"[_submit_single_sbatc] {sbatch_stdout=}")
+        stdout = sbatch_stdout.strip("\n")
+        submitted_job_id = int(stdout)
+        slurm_job.slurm_job_id = str(submitted_job_id)
+
+        # Add job to self.jobs
+        self.jobs[slurm_job.slurm_job_id] = slurm_job
+        logger.info(
+            "[_submit_single_sbatch] Added "
+            f"{slurm_job.slurm_job_id} to self.jobs."
+        )
+        logger.info("[_submit_single_sbatch] END")
+
+    def _copy_files_from_remote_to_local(
+        self,
+        slurm_job: SlurmJob,
+    ) -> None:
+        raise NotImplementedError("Implement in child class.")
+
+    def _check_slurm_account(self) -> None:
+        """
+        Check that SLURM account is not set here in `common_script_lines`.
+        """
+        try:
+            invalid_line = next(
+                line
+                for line in self.common_script_lines
+                if line.startswith("#SBATCH --account=")
+            )
+            raise RuntimeError(
+                "Invalid line in `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
+
+    def _postprocess_single_task(
+        self, *, task: SlurmTask
+    ) -> tuple[Any, Exception]:
+        try:
+            with open(task.output_pickle_file_local, "rb") as f:
+                outdata = f.read()
+            success, output = cloudpickle.loads(outdata)
+            if success:
+                result = output
+                return result, None
+            else:
+                exception = _handle_exception_proxy(output)
+                return None, exception
+        except Exception as e:
+            exception = JobExecutionError(f"ERROR, {str(e)}")
+            return None, exception
+        finally:
+            pass
+            # FIXME: Re-include unlinks of pickle files
+            # Path(task.input_pickle_file_local).unlink(missing_ok=True)
+            # Path(task.output_pickle_file_local).unlink(missing_ok=True)
+
+    def is_shutdown(self) -> bool:
+        # FIXME: shutdown is not implemented
+        return self.shutdown_file.exists()
+
+    @property
+    def job_ids(self) -> list[str]:
+        return list(self.jobs.keys())
+
+    def submit(
+        self,
+        func: callable,
+        parameters: dict[str, Any],
+        history_unit_id: int,
+        task_files: TaskFiles,
+        config: SlurmConfig,
+        task_type: Literal[
+            "non_parallel",
+            "converter_non_parallel",
+            "compound",
+            "converter_compound",
+        ],
+    ) -> tuple[Any, Exception]:
+
+        logger.info("[submit] START")
+
+        workdir_local = task_files.wftask_subfolder_local
+        workdir_remote = task_files.wftask_subfolder_remote
+
+        if self.jobs != {}:
+            raise JobExecutionError("Unexpected branch: jobs should be empty.")
+
+        if self.is_shutdown():
+            raise JobExecutionError("Cannot continue after shutdown.")
+
+        # Validation phase
+        self.validate_submit_parameters(
+            parameters=parameters,
+            task_type=task_type,
+        )
+
+        # Create task subfolder
+        logger.info("[submit] Create local/remote folders - START")
+        self._mkdir_local_folder(folder=workdir_local.as_posix())
+        self._mkdir_remote_folder(folder=workdir_remote.as_posix())
+        logger.info("[submit] Create local/remote folders - END")
+
+        # Add prefix to task_files object
+        task_files.prefix = SUBMIT_PREFIX
+
+        # Submission phase
+        slurm_job = SlurmJob(
+            prefix=SUBMIT_PREFIX,
+            workdir_local=workdir_local,
+            workdir_remote=workdir_remote,
+            tasks=[
+                SlurmTask(
+                    prefix=SUBMIT_PREFIX,
+                    index=0,
+                    component=task_files.component,
+                    parameters=parameters,
+                    workdir_remote=workdir_remote,
+                    workdir_local=workdir_local,
+                    task_files=task_files,
+                )
+            ],
+        )
+
+        config.parallel_tasks_per_job = 1
+        self._submit_single_sbatch(
+            func,
+            slurm_job=slurm_job,
+            slurm_config=config,
+        )
+        logger.info(f"[submit] END submission phase, {self.job_ids=}")
+
+        # FIXME: replace this sleep a more precise check
+        settings = Inject(get_settings)
+        sleep_time = settings.FRACTAL_SLURM_INTERVAL_BEFORE_RETRIEVAL
+        logger.warning(f"[submit] Now sleep {sleep_time} (FIXME)")
+        time.sleep(sleep_time)
+
+        # Retrieval phase
+        logger.info("[submit] START retrieval phase")
+        while len(self.jobs) > 0:
+            if self.is_shutdown():
+                self.scancel_jobs()
+            finished_job_ids = self._get_finished_jobs(job_ids=self.job_ids)
+            logger.info(f"{finished_job_ids=}")
+            with next(get_sync_db()) as db:
+                for slurm_job_id in finished_job_ids:
+                    logger.info(f"Now process {slurm_job_id=}")
+                    slurm_job = self.jobs.pop(slurm_job_id)
+
+                    self._copy_files_from_remote_to_local(slurm_job)
+                    result, exception = self._postprocess_single_task(
+                        task=slurm_job.tasks[0]
+                    )
+                    if exception is not None:
+                        update_status_of_history_unit(
+                            history_unit_id=history_unit_id,
+                            status=HistoryUnitStatus.FAILED,
+                            db_sync=db,
+                        )
+                    else:
+                        if task_type not in ["compound", "converter_compound"]:
+                            update_status_of_history_unit(
+                                history_unit_id=history_unit_id,
+                                status=HistoryUnitStatus.DONE,
+                                db_sync=db,
+                            )
+
+            time.sleep(self.poll_interval)
+
+        logger.info("[submit] END")
+        return result, exception
+
+    def multisubmit(
+        self,
+        func: callable,
+        list_parameters: list[dict],
+        history_unit_ids: list[int],
+        list_task_files: list[TaskFiles],
+        task_type: Literal["parallel", "compound", "converter_compound"],
+        config: SlurmConfig,
+    ):
+
+        if len(self.jobs) > 0:
+            raise RuntimeError(
+                f"Cannot run .multisubmit when {len(self.jobs)=}"
+            )
+
+        self.validate_multisubmit_parameters(
+            list_parameters=list_parameters,
+            task_type=task_type,
+            list_task_files=list_task_files,
+        )
+        self.validate_multisubmit_history_unit_ids(
+            history_unit_ids=history_unit_ids,
+            task_type=task_type,
+            list_parameters=list_parameters,
+        )
+
+        logger.info(f"[multisubmit] START, {len(list_parameters)=}")
+
+        workdir_local = list_task_files[0].wftask_subfolder_local
+        workdir_remote = list_task_files[0].wftask_subfolder_remote
+
+        # Create local&remote task subfolders
+        if task_type == "parallel":
+            self._mkdir_local_folder(workdir_local.as_posix())
+            self._mkdir_remote_folder(folder=workdir_remote.as_posix())
+
+        # Execute tasks, in chunks of size `parallel_tasks_per_job`
+        # TODO Pick a data structure for results and exceptions, or review the
+        # interface
+        results: dict[int, Any] = {}
+        exceptions: dict[int, BaseException] = {}
+
+        tot_tasks = len(list_parameters)
+
+        # Set/validate parameters for task batching
+        tasks_per_job, parallel_tasks_per_job = heuristics(
+            # Number of parallel components (always known)
+            tot_tasks=tot_tasks,
+            # Optional WorkflowTask attributes:
+            tasks_per_job=config.tasks_per_job,
+            parallel_tasks_per_job=config.parallel_tasks_per_job,  # noqa
+            # Task requirements (multiple possible sources):
+            cpus_per_task=config.cpus_per_task,
+            mem_per_task=config.mem_per_task_MB,
+            # Fractal configuration variables (soft/hard limits):
+            target_cpus_per_job=config.target_cpus_per_job,
+            target_mem_per_job=config.target_mem_per_job,
+            target_num_jobs=config.target_num_jobs,
+            max_cpus_per_job=config.max_cpus_per_job,
+            max_mem_per_job=config.max_mem_per_job,
+            max_num_jobs=config.max_num_jobs,
+        )
+        config.parallel_tasks_per_job = parallel_tasks_per_job
+        config.tasks_per_job = tasks_per_job
+
+        # Divide arguments in batches of `tasks_per_job` tasks each
+        args_batches = []
+        batch_size = tasks_per_job
+        for ind_chunk in range(0, tot_tasks, batch_size):
+            args_batches.append(
+                list_parameters[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")
+
+        logger.info(f"START submission phase, {list(self.jobs.keys())=}")
+        for ind_batch, chunk in enumerate(args_batches):
+            prefix = f"{MULTISUBMIT_PREFIX}-{ind_batch:06d}"
+            tasks = []
+            for ind_chunk, parameters in enumerate(chunk):
+                index = (ind_batch * batch_size) + ind_chunk
+                current_task_files = list_task_files[index]
+                current_task_files.prefix = prefix
+                tasks.append(
+                    SlurmTask(
+                        prefix=prefix,
+                        index=index,
+                        component=current_task_files.component,
+                        workdir_local=workdir_local,
+                        workdir_remote=workdir_remote,
+                        parameters=parameters,
+                        zarr_url=parameters["zarr_url"],
+                        task_files=current_task_files,
+                    ),
+                )
+
+            slurm_job = SlurmJob(
+                prefix=prefix,
+                workdir_local=workdir_local,
+                workdir_remote=workdir_remote,
+                tasks=tasks,
+            )
+            self._submit_single_sbatch(
+                func,
+                slurm_job=slurm_job,
+                slurm_config=config,
+            )
+        logger.info(f"END submission phase, {self.job_ids=}")
+
+        # FIXME: replace this sleep a more precise check
+        settings = Inject(get_settings)
+        sleep_time = settings.FRACTAL_SLURM_INTERVAL_BEFORE_RETRIEVAL
+        logger.warning(f"[submit] Now sleep {sleep_time} (FIXME)")
+        time.sleep(sleep_time)
+
+        # Retrieval phase
+        logger.info("START retrieval phase")
+        while len(self.jobs) > 0:
+            if self.is_shutdown():
+                self.scancel_jobs()
+            finished_job_ids = self._get_finished_jobs(job_ids=self.job_ids)
+            logger.info(f"{finished_job_ids=}")
+            with next(get_sync_db()) as db:
+                for slurm_job_id in finished_job_ids:
+                    logger.info(f"Now processing {slurm_job_id=}")
+                    slurm_job = self.jobs.pop(slurm_job_id)
+                    self._copy_files_from_remote_to_local(slurm_job)
+                    for task in slurm_job.tasks:
+                        logger.info(f"Now processing {task.index=}")
+                        result, exception = self._postprocess_single_task(
+                            task=task
+                        )
+
+                        # Note: the relevant done/failed check is based on
+                        # whether `exception is None`. The fact that
+                        # `result is None` is not relevant for this purpose.
+                        if exception is not None:
+                            exceptions[task.index] = exception
+                            if task_type == "parallel":
+                                update_status_of_history_unit(
+                                    history_unit_id=history_unit_ids[
+                                        task.index
+                                    ],
+                                    status=HistoryUnitStatus.FAILED,
+                                    db_sync=db,
+                                )
+                        else:
+                            results[task.index] = result
+                            if task_type == "parallel":
+                                update_status_of_history_unit(
+                                    history_unit_id=history_unit_ids[
+                                        task.index
+                                    ],
+                                    status=HistoryUnitStatus.DONE,
+                                    db_sync=db,
+                                )
+
+            time.sleep(self.poll_interval)
+        return results, exceptions
+
+    def check_fractal_server_versions(self):
+        """
+        Compare fractal-server versions of local/remote Python interpreters.
+        """
+
+        # Skip check when the local and remote interpreters are the same
+        # (notably for some sudo-slurm deployments)
+        if self.python_worker_interpreter == sys.executable:
+            return
+
+        # Fetch remote fractal-server version
+        cmd = (
+            f"{self.python_worker_interpreter} "
+            "-m fractal_server.app.runner.versions"
+        )
+        stdout = self._run_remote_cmd(cmd)
+        remote_version = json.loads(stdout.strip("\n"))["fractal_server"]
+
+        # Verify local/remote version match
+        if remote_version != __VERSION__:
+            error_msg = (
+                "Fractal-server version mismatch.\n"
+                "Local interpreter: "
+                f"({sys.executable}): {__VERSION__}.\n"
+                "Remote interpreter: "
+                f"({self.python_worker_interpreter}): {remote_version}."
+            )
+            logger.error(error_msg)
+            raise RuntimeError(error_msg)
+
+    def scancel_jobs(self) -> None:
+        logger.info("[scancel_jobs] START")
+
+        if self.jobs:
+            scancel_string = " ".join(self.job_ids)
+            scancel_cmd = f"scancel {scancel_string}"
+            logger.warning(f"Now scancel-ing SLURM jobs {scancel_string}")
+            try:
+                self._run_remote_cmd(scancel_cmd)
+            except Exception as e:
+                logger.warning(
+                    "[scancel_jobs] `scancel` command failed. "
+                    f"Original error:\n{str(e)}"
+                )
+
+        logger.info("[scancel_jobs] END")