From c44a98c9a300e0f24091d431f1f3776adf43b6bb Mon Sep 17 00:00:00 2001 From: Fabian Zills <46721498+PythonFZ@users.noreply.github.com> Date: Fri, 28 Apr 2023 13:30:00 +0100 Subject: [PATCH] Run less code outside works (#31) * make args pickable * update to callback * remove return value * cleanup option * prepare release * lint * extract function * remove defaults * remove DVC todo * poetry update --- README.md | 11 +- dask4dvc/cli/main.py | 26 ++- dask4dvc/dvc_repro.py | 90 +++++---- poetry.lock | 432 ++++++++++++++++++++--------------------- pyproject.toml | 2 +- tests/test_dask4dvc.py | 2 +- 6 files changed, 277 insertions(+), 286 deletions(-) diff --git a/README.md b/README.md index dede509..8e1d7f9 100644 --- a/README.md +++ b/README.md @@ -7,21 +7,19 @@ [DVC](dvc.org) provides tools for building and executing the computational graph locally through various methods. The `dask4dvc` package combines [Dask Distributed](https://distributed.dask.org/) with DVC to make it easier to use with HPC managers like [Slurm](https://github.com/SchedMD/slurm). -The `dask4dvc` package will try to run the DVC graph in parallel. +The `dask4dvc repro` package will run the DVC graph in parallel where possible. +Currently, `dask4dvc run` will not run stages per experiment sequentially. -> :warning: This is an experimental package **not** affiliated in any way with iterative or DVC. ``dask4dvc`` will disbale a few of the checks that DVC implements. Do not make changes to your workspace during the runtime of `dask4dvc`. +> :warning: This is an experimental package **not** affiliated in any way with iterative or DVC. ## Usage Dask4DVC provides a CLI similar to DVC. - `dvc repro` becomes `dask4dvc repro`. -- `dvc queue start --jobs 1` becomes `dask4dvc run` +- `dvc queue start` becomes `dask4dvc run` You can follow the progress using `dask4dvc --dashboard`. -> `dask4dvc run --parallel` is available for `dvc queue start --jobs ` but it currently leads to the failure of some experiments. - -> The `dask4dvc` error messages are currently really sparse. For better error messages please use the DVC commands. ### SLURM Cluster @@ -45,6 +43,7 @@ cluster.adapt() with this setup you can then run `dask4dvc repro --address 127.0.0.1:31415` on the example port `31415`. You can also use config files with `dask4dvc repro --config myconfig.yaml`. +All `dask.distributed` Clusters should be supported. ```yaml default: diff --git a/dask4dvc/cli/main.py b/dask4dvc/cli/main.py index ea9f92c..839f040 100644 --- a/dask4dvc/cli/main.py +++ b/dask4dvc/cli/main.py @@ -43,7 +43,9 @@ def clean() -> None: @app.command() def repro( - targets: typing.List[str] = typer.Argument(None), + targets: typing.List[str] = typer.Argument( + None, help="Name of stages to reproduce. Leave emtpy to run the full graph." + ), address: str = typer.Option(None, help=Help.address), leave: bool = typer.Option(True, help=Help.leave), config: str = typer.Option(None, help=Help.config), @@ -52,6 +54,7 @@ def repro( option: typing.List[str] = typer.Option( None, "-o", "--option", help="Additional dvc repro options" ), + cleanup: bool = typer.Option(True, help="Remove temporary experiments when done"), ) -> None: """Replicate 'dvc repro' command using dask.""" if len(option) != 0: @@ -72,22 +75,17 @@ def repro( client.cluster.adapt(minimum=1, maximum=max_workers) log.info(client) - mapping, experiments, cleanup_data = dvc_repro.parallel_submit( - client, repo, stages - ) - # check if futures are succesful - dask.distributed.Future + mapping, experiments = dvc_repro.parallel_submit(client, repo, stages) wait_for_futures(client, mapping) - for cleanup in cleanup_data: - dvc_repro.collect_and_cleanup(**cleanup) if all(x.status == "finished" for x in mapping.values()): log.info("All stages finished successfully") # dvc.cli.main(["exp", "apply", experiments[-1]]) dask.distributed.wait( client.submit(subprocess.check_call, ["dvc", "repro", *targets]) ) - dvc_repro.remove_experiments(experiments) + if cleanup: + dvc_repro.remove_experiments(experiments) if not leave: _ = input("Press Enter to close the client") @@ -95,14 +93,16 @@ def repro( @app.command() def run( - targets: typing.List[str] = typer.Argument(None), + targets: typing.List[str] = typer.Argument( + None, help="Name of the DVC experiments to reproduce. Leave emtpy to run all." + ), address: str = typer.Option(None, help=Help.address), leave: bool = typer.Option(True, help=Help.leave), config: str = typer.Option(None, help=Help.config), max_workers: int = typer.Option(None, help=Help.max_workers), dashboard: bool = typer.Option(False, help=Help.dashboard), ) -> None: - """Run a DVC experiment.""" + """Replicate 'dvc queue start' using dask.""" if len(targets) == 0: targets = None @@ -119,12 +119,10 @@ def run( client.cluster.adapt(minimum=1, maximum=max_workers) log.info(client) - mapping, _, cleanup_data = dvc_repro.experiment_submit(client, repo, targets) + mapping, _ = dvc_repro.experiment_submit(client, repo, targets) wait_for_futures(client, mapping) # dvc_repro.remove_experiments(experiments) - for cleanup in cleanup_data: - dvc_repro.collect_and_cleanup(**cleanup) if not leave: _ = input("Press Enter to close the client") diff --git a/dask4dvc/dvc_repro.py b/dask4dvc/dvc_repro.py index 0a415aa..b898e27 100644 --- a/dask4dvc/dvc_repro.py +++ b/dask4dvc/dvc_repro.py @@ -1,5 +1,6 @@ """Dask4DVC to DVC repo interface.""" import dataclasses +import functools import logging import subprocess import typing @@ -10,7 +11,7 @@ import dvc.repo from dvc.repo.experiments.executor.local import TempDirExecutor from dvc.repo.experiments.queue import tasks -from dvc.repo.experiments.queue.base import QueueEntry +from dvc.repo.experiments.queue.base import BaseStashQueue, QueueEntry from dvc.repo.reproduce import _get_steps from dvc.stage import PipelineStage @@ -105,89 +106,86 @@ def remove_experiments(experiments: typing.List[str] = None) -> None: def collect_and_cleanup( - entry_dict: dict, executor: TempDirExecutor, infofile: str + future: dask.distributed.Future, entry_dict: dict, infofile: str ) -> None: """Collect the results of a finished experiment and clean up.""" try: tasks.collect_exp(proc_dict=None, entry_dict=entry_dict) finally: - executor.cleanup(infofile) + entry = QueueEntry.from_dict(entry_dict) + with dvc.repo.Repo(entry.dvc_root) as repo: + executor = BaseStashQueue.init_executor( + repo.experiments, + entry, + TempDirExecutor, + location="dvc-task", + ) + executor.cleanup(infofile) + + +def submit_to_dask( + client: dask.distributed.Client, infofile: str, entry: QueueEntry, successors: list +) -> dask.distributed.Future: + """Submit a queued experiment to run with Dask.""" + future = client.submit( + exec_run, + infofile=infofile, + successors=successors, + pure=False, + key=entry.name, + ) + + future.add_done_callback( + functools.partial( + collect_and_cleanup, + entry_dict=dataclasses.asdict(entry), + infofile=infofile, + ) + ) + return future def parallel_submit( client: dask.distributed.Client, repo: dvc.repo.Repo, stages: typing.Dict[PipelineStage, str], -) -> typing.Tuple[ - typing.Dict[PipelineStage, dask.distributed.Future], - typing.List[str], - typing.List[dict], -]: +) -> typing.Tuple[typing.Dict[PipelineStage, dask.distributed.Future], typing.List[str],]: """Submit experiments in parallel.""" mapping = {} queue_entries = get_all_queue_entries(repo) experiments = [] - cleanup_data = [] - for stage in stages: log.debug(f"Preparing experiment '{stages[stage]}'") entry, infofile = queue_entries[stages[stage]] - executor = tasks.setup_exp(dataclasses.asdict(entry)) + tasks.setup_exp(dataclasses.asdict(entry)) # we use get here, because some stages won't be queued, such as dependency files successors = [ mapping.get(successor) for successor in repo.index.graph.successors(stage) ] - mapping[stage] = client.submit( - exec_run, - infofile=infofile, - successors=successors, - pure=False, - key=entry.name, - ) + mapping[stage] = submit_to_dask(client, infofile, entry, successors) - cleanup_data.append( - { - "executor": executor, - "infofile": infofile, - "entry_dict": dataclasses.asdict(entry), - } - ) experiments.append(entry.name) - return mapping, experiments, cleanup_data + return mapping, experiments def experiment_submit( client: dask.distributed.Client, repo: dvc.repo.Repo, experiments: typing.List[str] -) -> typing.Tuple[ - typing.Dict[str, dask.distributed.Future], typing.List[str], typing.List[dict] -]: +) -> typing.Tuple[typing.Dict[str, dask.distributed.Future], typing.List[str]]: """Submit experiments in parallel.""" queue_entries = get_all_queue_entries(repo) if experiments is None: experiments = list(queue_entries.keys()) mapping = {} print(f"Submitting experiments: {experiments}") - cleanup_data = [] + for experiment in experiments: log.critical(f"Preparing experiment '{experiment}'") entry, infofile = queue_entries[experiment] - executor = tasks.setup_exp(dataclasses.asdict(entry)) + tasks.setup_exp(dataclasses.asdict(entry)) - mapping[experiment] = client.submit( - exec_run, - infofile=infofile, - successors=[], - pure=False, - key=entry.name, - ) - cleanup_data.append( - { - "executor": executor, - "infofile": infofile, - "entry_dict": dataclasses.asdict(entry), - } - ) - return mapping, list(mapping.keys()), cleanup_data + mapping[experiment] = submit_to_dask(client, infofile, entry, None) + + return mapping, list(mapping.keys()) diff --git a/poetry.lock b/poetry.lock index 04ec91e..9d383e2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -313,14 +313,14 @@ python-dateutil = ">=2.7.0" [[package]] name = "astroid" -version = "2.15.3" +version = "2.15.4" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false python-versions = ">=3.7.2" files = [ - {file = "astroid-2.15.3-py3-none-any.whl", hash = "sha256:f11e74658da0f2a14a8d19776a8647900870a63de71db83713a8e77a6af52662"}, - {file = "astroid-2.15.3.tar.gz", hash = "sha256:44224ad27c54d770233751315fa7f74c46fa3ee0fab7beef1065f99f09897efe"}, + {file = "astroid-2.15.4-py3-none-any.whl", hash = "sha256:a1b8543ef9d36ea777194bc9b17f5f8678d2c56ee6a45b2c2f17eec96f242347"}, + {file = "astroid-2.15.4.tar.gz", hash = "sha256:c81e1c7fbac615037744d067a9bb5f9aeb655edf59b63ee8b59585475d6f80d8"}, ] [package.dependencies] @@ -1537,19 +1537,20 @@ tests = ["dvc[testing]", "flaky (==3.7.0)", "mypy (==0.910)", "pylint (==2.15.9) [[package]] name = "dvc-objects" -version = "0.21.1" +version = "0.21.2" description = "dvc objects" category = "main" optional = false python-versions = ">=3.8" files = [ - 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