Entrypoint for running all tasks in biobench.

Most of this script is self documenting. Run python benchmark.py --help to see all the options.

Note that you will have to download all the datasets, but each dataset includes its own download script with instructions. For example, see biobench.newt.download for an example.

Design

biobench is designed to make it easy to add both models and tasks that work with other models and tasks.

To add a new model, look at biobench.registry's documentation, which includes a tutorial for adding a new model.

Functions

def main(cfg: str = 'configs/neurips.toml', dry_run: bool = True)

Expand source code

@beartype.beartype
def main(cfg: str = os.path.join("configs", "neurips.toml"), dry_run: bool = True):
    """
    Launch all jobs, using either a local GPU or a Slurm cluster. Then report results and save to disk.

    Args:
        cfg: Path to TOML config file.
        dry_run: If --no-dry-run, actually run experiment.
    """
    cfgs = config.load(cfg)

    if not cfgs:
        logger.warning("No configurations loaded.")
        return

    first = cfgs[0]
    # Verify all configs have consistent execution settings
    for cfg in cfgs[1:]:
        if cfg.slurm_acct != first.slurm_acct:
            raise ValueError("All configs must have the same slurm_acct")
        if cfg.log_to != first.log_to:
            raise ValueError("All configs must have the same log_to directory")
        if cfg.ssl != first.ssl:
            raise ValueError("All configs must have the same ssl setting")

    # 1. Setup executor.
    # 1. Setup executor.
    if first.slurm_acct:
        executor = submitit.SlurmExecutor(folder=first.log_to)
        executor.update_parameters(
            time=30,
            gpus_per_node=1,
            cpus_per_task=8,
            stderr_to_stdout=True,
            partition="debug",
            account=first.slurm_acct,
        )
        # See biobench.third_party_models.get_ssl() for a discussion of this variable.
        if not first.ssl:
            executor.update_parameters(setup=["export BIOBENCH_DISABLE_SSL=1"])
    else:
        executor = submitit.DebugExecutor(folder=first.log_to)
        # See biobench.third_party_models.get_ssl() for a discussion of this variable.
        if not first.ssl:
            os.environ["BIOBENCH_DISABLE_SSL"] = "1"

    db = reporting.get_db(first)

    # 2. Run benchmarks.
    jobs = []
    n_skipped = 0
    for cfg in helpers.progress(cfgs, desc="submitting jobs"):
        for task_name, data_root in cfg.data.to_dict().items():
            # Check that you can get the task_name
            try:
                module = importlib.import_module(f"biobench.{task_name}")
            except ModuleNotFoundError:
                logger.warning("Could not find task '%s'.", task_name)
                continue

            if not data_root:
                continue

            if reporting.already_ran(db, cfg, task_name):
                n_skipped += 1
                continue
            elif dry_run:
                jobs.append(cfg)
            else:
                job = executor.submit(module.benchmark, cfg)
                jobs.append(job)

    if dry_run:
        # Summarize the jobs by model and training examples
        model_counts = collections.defaultdict(int)
        for job_cfg in jobs:
            key = (job_cfg.model.ckpt, job_cfg.n_train)
            model_counts[key] += 1

        # Print summary table
        logger.info("Job Summary:")
        logger.info("%-40s | %-10s | %-5s", "Model", "Train Size", "Count")
        logger.info("-" * 61)
        for (model, n_train), count in sorted(model_counts.items()):
            logger.info("%-40s | %-10d | %-5d", model, n_train, count)
        logger.info("-" * 61)
        logger.info("Total jobs to run: %d", len(jobs))
        return

    logger.info("Submitted %d jobs (skipped %d).", len(jobs), n_skipped)

    # 3. Write results to sqlite.
    for i, future in enumerate(submitit.helpers.as_completed(jobs)):
        err = future.exception()
        if err:
            logger.warning("Error running job: %s: %s", err, err.__cause__)
            continue

        report: reporting.Report = future.result()
        report.write(db)
        logger.info("Finished %d/%d jobs.", i + 1, len(jobs))

    logger.info("Finished.")

Launch all jobs, using either a local GPU or a Slurm cluster. Then report results and save to disk.

Args

cfg

Path to TOML config file.

dry_run

If –no-dry-run, actually run experiment.