fractal-server 2.14.0a8__py3-none-any.whl → 2.14.0a10__py3-none-any.whl

fractal_server/app/runner/executors/slurm_ssh/runner.py

@@ -0,0 +1,711 @@
+import json
+import math
+import sys
+import time
+from copy import copy
+from pathlib import Path
+from typing import Any
+from typing import Optional
+
+import cloudpickle
+from pydantic import BaseModel
+from pydantic import ConfigDict
+
+from ._check_job_status_ssh import get_finished_jobs_ssh
+from fractal_server import __VERSION__
+from fractal_server.app.runner.components import _COMPONENT_KEY_
+from fractal_server.app.runner.exceptions import JobExecutionError
+from fractal_server.app.runner.exceptions import TaskExecutionError
+from fractal_server.app.runner.executors.base_runner import BaseRunner
+from fractal_server.app.runner.executors.slurm_common._batching import (
+    heuristics,
+)
+from fractal_server.app.runner.executors.slurm_common._slurm_config import (
+    SlurmConfig,
+)
+from fractal_server.app.runner.filenames import SHUTDOWN_FILENAME
+from fractal_server.app.runner.task_files import TaskFiles
+from fractal_server.app.schemas.v2.task import TaskTypeType
+from fractal_server.config import get_settings
+from fractal_server.logger import set_logger
+from fractal_server.ssh._fabric import FractalSSH
+from fractal_server.syringe import Inject
+
+# from fractal_server.app.history import ImageStatus
+# from fractal_server.app.history import update_all_images
+# from fractal_server.app.history import update_single_image
+# from fractal_server.app.history import update_single_image_logfile
+
+
+logger = set_logger(__name__)
+
+
+def _handle_exception_proxy(proxy):  # FIXME
+    if proxy.exc_type_name == "JobExecutionError":
+        return JobExecutionError(str(proxy))
+    else:
+        kwargs = {}
+        for key in [
+            "workflow_task_id",
+            "workflow_task_order",
+            "task_name",
+        ]:
+            if key in proxy.kwargs.keys():
+                kwargs[key] = proxy.kwargs[key]
+        return TaskExecutionError(proxy.tb, **kwargs)
+
+
+class SlurmTask(BaseModel):
+    model_config = ConfigDict(arbitrary_types_allowed=True)
+    component: str
+    workdir_local: Path
+    workdir_remote: Path
+    parameters: dict[str, Any]
+    zarr_url: Optional[str] = None
+    task_files: TaskFiles
+    index: int
+
+    @property
+    def input_pickle_file_local(self) -> str:
+        return (
+            self.workdir_local / f"{self.component}-input.pickle"
+        ).as_posix()
+
+    @property
+    def output_pickle_file_local(self) -> str:
+        return (
+            self.workdir_local / f"{self.component}-output.pickle"
+        ).as_posix()
+
+    @property
+    def input_pickle_file_remote(self) -> str:
+        return (
+            self.workdir_remote / f"{self.component}-input.pickle"
+        ).as_posix()
+
+    @property
+    def output_pickle_file_remote(self) -> str:
+        return (
+            self.workdir_remote / f"{self.component}-output.pickle"
+        ).as_posix()
+
+
+class SlurmJob(BaseModel):
+    slurm_job_id: Optional[str] = None
+    label: str
+    workdir_local: Path
+    workdir_remote: Path
+    tasks: list[SlurmTask]
+
+    @property
+    def slurm_log_file_local(self) -> str:
+        if self.slurm_job_id:
+            return (
+                self.workdir_local
+                / f"slurm-{self.label}-{self.slurm_job_id}.log"
+            ).as_posix()
+        else:
+            return (
+                self.workdir_local / f"slurm-{self.label}-%j.log"
+            ).as_posix()
+
+    @property
+    def slurm_log_file_remote(self) -> str:
+        if self.slurm_job_id:
+            return (
+                self.workdir_remote
+                / f"slurm-{self.label}-{self.slurm_job_id}.log"
+            ).as_posix()
+        else:
+            return (
+                self.workdir_remote / f"slurm-{self.label}-%j.log"
+            ).as_posix()
+
+    @property
+    def slurm_submission_script_local(self) -> str:
+        return (
+            self.workdir_local / f"slurm-{self.label}-submit.sh"
+        ).as_posix()
+
+    @property
+    def slurm_submission_script_remote(self) -> str:
+        return (
+            self.workdir_remote / f"slurm-{self.label}-submit.sh"
+        ).as_posix()
+
+    @property
+    def slurm_stdout(self) -> str:
+        return (self.workdir_remote / f"slurm-{self.label}.out").as_posix()
+
+    @property
+    def slurm_stderr(self) -> str:
+        return (self.workdir_remote / f"slurm-{self.label}.err").as_posix()
+
+    @property
+    def log_files_local(self) -> list[str]:
+        return [task.task_files.log_file_local for task in self.tasks]
+
+
+# def _subprocess_run_or_raise(
+#     full_command: str,
+# ) -> Optional[subprocess.CompletedProcess]:
+#     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"
+#         )
+#         logging.error(error_msg)
+#         raise JobExecutionError(info=error_msg)
+
+
+class RunnerSlurmSSH(BaseRunner):
+    fractal_ssh: FractalSSH
+
+    slurm_user: str
+    shutdown_file: Path
+    common_script_lines: list[str]
+    user_cache_dir: str
+    root_dir_local: Path
+    root_dir_remote: Path
+    slurm_account: Optional[str] = None
+    poll_interval: int
+    python_worker_interpreter: str
+    jobs: dict[str, SlurmJob]
+
+    def __init__(
+        self,
+        *,
+        fractal_ssh: FractalSSH,
+        slurm_user: str,
+        root_dir_local: Path,
+        root_dir_remote: Path,
+        slurm_account: Optional[str] = None,
+        common_script_lines: Optional[list[str]] = None,
+        user_cache_dir: Optional[str] = None,
+        slurm_poll_interval: Optional[int] = None,
+    ) -> None:
+        """
+        Set parameters that are the same for different Fractal tasks and for
+        different SLURM jobs/tasks.
+        """
+
+        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
+        # FIXME: move to little method
+        try:
+            invalid_line = next(
+                line
+                for line in self.common_script_lines
+                if line.startswith("#SBATCH --account=")
+            )
+            raise RuntimeError(
+                "Invalid line in `RunnerSlurmSSH.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
+
+        # Check Python versions
+        settings = Inject(get_settings)
+        self.fractal_ssh = fractal_ssh
+        logger.warning(self.fractal_ssh)
+
+        # It is the new handshanke
+        if settings.FRACTAL_SLURM_WORKER_PYTHON is not None:
+            self.check_remote_python_interpreter()
+
+        # Initialize connection and perform handshake
+        self.root_dir_local = root_dir_local
+        self.root_dir_remote = root_dir_remote
+
+        # # Create folders
+        # original_umask = os.umask(0)
+        # self.root_dir_local.mkdir(parents=True, exist_ok=True, mode=0o755)
+        # os.umask(original_umask)
+        # _mkdir_as_user(
+        #     folder=self.root_dir_remote.as_posix(),
+        #     user=self.slurm_user,
+        # )
+
+        self.user_cache_dir = user_cache_dir
+
+        self.slurm_poll_interval = (
+            slurm_poll_interval or settings.FRACTAL_SLURM_POLL_INTERVAL
+        )
+
+        self.shutdown_file = self.root_dir_local / SHUTDOWN_FILENAME
+
+        self.python_worker_interpreter = (
+            settings.FRACTAL_SLURM_WORKER_PYTHON or sys.executable
+        )
+
+        self.jobs = {}
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        return False
+
+    def is_shutdown(self) -> bool:
+        return self.shutdown_file.exists()
+
+    def scancel_jobs(self) -> None:
+        logger.debug("[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.fractal_ssh.run_command(cmd=scancel_cmd)
+                # _run_command_as_user(
+                #     cmd=scancel_cmd,
+                #     user=self.slurm_user,
+                #     check=True,
+                # )
+            except RuntimeError as e:
+                logger.warning(
+                    "[scancel_jobs] `scancel` command failed. "
+                    f"Original error:\n{str(e)}"
+                )
+
+        logger.debug("[scancel_jobs] END")
+
+    def _submit_single_sbatch(
+        self,
+        func,
+        slurm_job: SlurmJob,
+        slurm_config: SlurmConfig,
+    ) -> str:
+        # Prepare input pickle(s)
+        versions = dict(
+            python=sys.version_info[:3],
+            cloudpickle=cloudpickle.__version__,
+            fractal_server=__VERSION__,
+        )
+        for task in slurm_job.tasks:
+            _args = []
+            _kwargs = dict(parameters=task.parameters)
+            funcser = cloudpickle.dumps((versions, func, _args, _kwargs))
+            with open(task.input_pickle_file_local, "wb") as f:
+                f.write(funcser)
+        # 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 task in slurm_job.tasks:
+            input_pickle_file = task.input_pickle_file_local
+            output_pickle_file = task.output_pickle_file_remote
+            cmdlines.append(
+                (
+                    f"{python_worker_interpreter}"
+                    " -m fractal_server.app.runner."
+                    "executors.slurm_common.remote "
+                    f"--input-file {input_pickle_file} "
+                    f"--output-file {output_pickle_file}"
+                )
+            )
+
+        # ...
+        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(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}",
+                f"#SBATCH --out={slurm_job.slurm_stdout}",
+                f"#SBATCH -D {slurm_job.workdir_remote}",
+            ]
+        )
+        script_lines = slurm_config.sort_script_lines(script_lines)
+        logger.debug(script_lines)
+
+        # Always print output of `uname -n` and `pwd`
+        script_lines.append(
+            '"Hostname: `uname -n`; current directory: `pwd`"\n'
+        )
+
+        # Complete script preamble
+        script_lines.append("\n")
+
+        # Include command lines
+        tmp_list_commands = copy(cmdlines)
+        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)
+
+        # Write submission script
+        # submission_script_contents = "\n".join(preamble_lines + cmdlines)
+        with open(slurm_job.slurm_submission_script_local, "w") as f:
+            f.write(script)
+
+        self.fractal_ssh.send_file(
+            local=slurm_job.slurm_submission_script_local,
+            remote=slurm_job.slurm_submission_script_remote,
+        )
+
+        # Run sbatch
+        submit_command = (
+            f"sbatch --parsable {slurm_job.slurm_submission_script_remote}"
+        )
+        pre_submission_cmds = slurm_config.pre_submission_commands
+        if len(pre_submission_cmds) == 0:
+            sbatch_stdout = self.fractal_ssh.run_command(cmd=submit_command)
+        else:
+            logger.debug(f"Now using {pre_submission_cmds=}")
+            script_lines = pre_submission_cmds + [submit_command]
+            script_content = "\n".join(script_lines)
+            script_content = f"{script_content}\n"
+            script_path_remote = (
+                f"{slurm_job.slurm_script_remote.as_posix()}_wrapper.sh"
+            )
+            self.fractal_ssh.write_remote_file(
+                path=script_path_remote, content=script_content
+            )
+            cmd = f"bash {script_path_remote}"
+            sbatch_stdout = self.fractal_ssh.run_command(cmd=cmd)
+
+        # Submit SLURM job and retrieve job ID
+        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.debug(f"Added {slurm_job.slurm_job_id} to self.jobs.")
+
+    @property
+    def job_ids(self) -> list[str]:
+        return list(self.jobs.keys())
+
+    def _copy_files_from_remote_to_local(self, job: SlurmJob) -> None:
+        # FIXME: This should only transfer archives, not single files
+        """
+        Note: this would differ for SSH
+        """
+        source_target_list = [
+            (job.slurm_log_file_remote, job.slurm_log_file_local)
+        ]
+        for task in job.tasks:
+            source_target_list.extend(
+                [
+                    (
+                        task.output_pickle_file_remote,
+                        task.output_pickle_file_local,
+                    ),
+                    (
+                        task.task_files.log_file_remote,
+                        task.task_files.log_file_local,
+                    ),
+                    (
+                        task.task_files.args_file_remote,
+                        task.task_files.args_file_local,
+                    ),
+                    (
+                        task.task_files.metadiff_file_remote,
+                        task.task_files.metadiff_file_local,
+                    ),
+                ]
+            )
+
+        for source, target in source_target_list:
+            try:
+                self.fractal_ssh.fetch_file(local=target, remote=source)
+                # res = _run_command_as_user(
+                #     cmd=f"cat {source}",
+                #     user=self.slurm_user,
+                #     encoding=None,
+                #     check=True,
+                # )
+                # Write local file
+                # with open(target, "wb") as f:
+                #     f.write(res.stdout)
+                # logger.critical(f"Copied {source} into {target}")
+            except (RuntimeError, FileNotFoundError) as e:
+                logger.warning(
+                    f"SKIP copy {target} into {source}. "
+                    f"Original error: {str(e)}"
+                )
+
+    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:
+            Path(task.input_pickle_file_local).unlink(missing_ok=True)
+            Path(task.output_pickle_file_local).unlink(missing_ok=True)
+
+    def submit(
+        self,
+        func: callable,
+        parameters: dict[str, Any],
+        history_item_id: int,
+        task_files: TaskFiles,
+        slurm_config: SlurmConfig,
+        task_type: TaskTypeType,
+    ) -> tuple[Any, Exception]:
+        workdir_local = task_files.wftask_subfolder_local
+        workdir_remote = task_files.wftask_subfolder_remote
+
+        task_files = TaskFiles(
+            **task_files.model_dump(
+                exclude={"component"},
+            ),
+            component=parameters[_COMPONENT_KEY_],
+        )
+
+        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
+        workdir_local.mkdir(parents=True)
+        self.fractal_ssh.mkdir(
+            folder=workdir_remote.as_posix(),
+            parents=True,
+        )
+
+        # Submission phase
+        slurm_job = SlurmJob(
+            label="0",
+            workdir_local=workdir_local,
+            workdir_remote=workdir_remote,
+            tasks=[
+                SlurmTask(
+                    index=0,
+                    component="0",
+                    parameters=parameters,
+                    workdir_remote=workdir_remote,
+                    workdir_local=workdir_local,
+                    task_files=task_files,
+                )
+            ],
+        )  # TODO: replace with actual values (BASED ON TASKFILES)
+
+        slurm_config.parallel_tasks_per_job = 1
+        self._submit_single_sbatch(
+            func,
+            slurm_job=slurm_job,
+            slurm_config=slurm_config,
+        )
+
+        # LOGFILE = task_files.log_file_local
+
+        # Retrieval phase
+        while len(self.jobs) > 0:
+            if self.is_shutdown():
+                self.scancel_jobs()
+            finished_job_ids = get_finished_jobs_ssh(
+                job_ids=self.job_ids,
+                fractal_ssh=self.fractal_ssh,
+            )
+            for slurm_job_id in finished_job_ids:
+                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]
+                )
+            time.sleep(self.slurm_poll_interval)
+
+        return result, exception
+
+    def multisubmit(
+        self,
+        func: callable,
+        list_parameters: list[dict],
+        history_item_id: int,
+        task_files: TaskFiles,
+        slurm_config: SlurmConfig,
+        task_type: TaskTypeType,
+    ):
+        # self.scancel_jobs()
+
+        self.validate_multisubmit_parameters(
+            list_parameters=list_parameters,
+            task_type=task_type,
+        )
+
+        workdir_local = task_files.wftask_subfolder_local
+        workdir_remote = task_files.wftask_subfolder_remote
+
+        # Create local&remote task subfolders
+        if task_type not in ["compound", "converter_compound"]:
+            workdir_local.mkdir(parents=True)
+            self.fractal_ssh.mkdir(
+                folder=workdir_remote.as_posix(),
+                parents=True,
+            )
+
+        # 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] = {}
+
+        original_task_files = task_files
+        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=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 `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):
+            # TODO: replace with actual values
+            tasks = []
+            for ind_chunk, parameters in enumerate(chunk):
+                component = parameters[_COMPONENT_KEY_]
+                tasks.append(
+                    SlurmTask(
+                        index=(ind_batch * batch_size) + ind_chunk,
+                        component=component,
+                        workdir_local=workdir_local,
+                        workdir_remote=workdir_remote,
+                        parameters=parameters,
+                        zarr_url=parameters["zarr_url"],
+                        task_files=TaskFiles(
+                            **original_task_files.model_dump(
+                                exclude={"component"}
+                            ),
+                            component=component,
+                        ),
+                    ),
+                )
+
+            slurm_job = SlurmJob(
+                label=f"{ind_batch:06d}",
+                workdir_local=workdir_local,
+                workdir_remote=workdir_remote,
+                tasks=tasks,
+            )
+            self._submit_single_sbatch(
+                func,
+                slurm_job=slurm_job,
+                slurm_config=slurm_config,
+            )
+        logger.info(f"END submission phase, {list(self.jobs.keys())=}")
+
+        # Retrieval phase
+        while len(self.jobs) > 0:
+            if self.is_shutdown():
+                self.scancel_jobs()
+            finished_job_ids = get_finished_jobs_ssh(
+                job_ids=self.job_ids,
+                fractal_ssh=self.fractal_ssh,
+            )
+            for slurm_job_id in finished_job_ids:
+                slurm_job = self.jobs.pop(slurm_job_id)
+                self._copy_files_from_remote_to_local(slurm_job)
+                for task in slurm_job.tasks:
+                    result, exception = self._postprocess_single_task(
+                        task=task
+                    )
+                    if exception is None:
+                        results[task.index] = result
+                    else:
+                        exceptions[task.index] = exception
+            time.sleep(self.slurm_poll_interval)
+        return results, exceptions
+
+    def check_remote_python_interpreter(self):
+        settings = Inject(get_settings)
+        cmd = (
+            f"{self.python_worker_interpreter} "
+            "-m fractal_server.app.runner.versions"
+        )
+        stdout = self.fractal_ssh.run_command(cmd=cmd)
+        remote_version = json.loads(stdout.strip("\n"))["fractal_server"]
+        if remote_version != __VERSION__:
+            error_msg = (
+                "Fractal-server version mismatch.\n"
+                "Local interpreter: "
+                f"({sys.executable}): {__VERSION__}.\n"
+                "Remote interpreter: "
+                f"({settings.FRACTAL_SLURM_WORKER_PYTHON}): {remote_version}."
+            )
+            logger.error(error_msg)
+            raise RuntimeError(error_msg)