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Orchestrate hyper-parameters search with snakemake

Project description

Hyperband on Snakemake

Do you have a medium-scale hyper-parameter search to run, and need a way to orchestrate this process? This is the solution. Based on Hyperband [1] and Snakemake [2], this tool will orchestrate the whole process for you. How is it different from the other implementations you can easily find elsewhere?

  1. The exact configuration used for each hyper-parameter setting is safely stored on disk.
  2. All intermediate results are saved, too.
  3. Thanks to Snakemake, training can be offloaded to a cluster manager such as Slurm (see example below), enabling effortless and massive parallel training.
  4. Even though this tool is written in Python, you can launch training scripts made with any technology: they only need to read a configuration file and write a file with a numerical result.

Saving everything on disk proves advantageous when your hyper-parameter search must run for weeks, as it allows you to check the progress, spot early mistakes, perform further iterations after the process ends (e.g., shoot for the very best configuration through Bayesian optimization, using the hyper-band results to bootstrap that model). Importantly, by decoupling training and search, you do not risk losing all your work because of some random bug that would crash the training process.

Note: to use this tool, you must adapt the included templates to your system. See section Customization below for instructions.


Can be installed via pip:

pip install git+

Or clone the repo, create a conda environment (optional) and install the required packages:

> conda create --file packages.txt -c conda-forge -c bioconda -n hyperband-snakemake
> conda activate hyperband-snakemake


Briefly, Hyperband is a random hyper-parameter search algorithm that smartly allocates budget to promising configurations. This is done by running all configurations with a small budget, then obtaining the top half/third/fourth and running them with two/three/four times larger budget, so that the cost for each stage remains the same. To know whether it is better to start with many configurations and small budget, or fewer initial configuration with larger budget, Hyperband creates several brackets with different trade-offs. A practical example follows.

First, obtain the plan of the hyper-parameter search. Suppose we want to evaluate each hyper-parameter configuration by performing ten-folds cross-validation repeated two times. Further, suppose we want to advance the top third of configurations to the next stage (the suggested option), and can spare 5**3=243 units of budget for each bracket. We set one budget unit to correspond to one training epoch, and know that our model requires 10 seconds (0.0028 hours) to perform one epoch on the dataset. These parameters translate to the following search structure:

> python -m hyperband_snakemake generate 5 3 \
    --repetitions 2 --folds 10 \
    --guaranteed-budget 3 \
    --cost-one-epoch-full-dataset 0.0028 \
    --output-dir my-search \
    --random-seed 123456

Hyperband Search (cost: 426.23)
  Bracket 0 (cost: 73.48)
    Stage 0 - 243 configurations each with budget 1.0 (cost: 12.25)
    Stage 1 - 81 configurations each with budget 3.0 (cost: 12.25)
    Stage 2 - 27 configurations each with budget 9.0 (cost: 12.25)
    Stage 3 - 9 configurations each with budget 27.0 (cost: 12.25)
    Stage 4 - 3 configurations each with budget 81.0 (cost: 12.25)
    Stage 5 - 1 configurations each with budget 243.0 (cost: 12.25)
  Bracket 1 (cost: 67.44)
    Stage 0 - 98 configurations each with budget 3.0 (cost: 14.82)
    Stage 1 - 32 configurations each with budget 9.0 (cost: 14.52)
    Stage 2 - 10 configurations each with budget 27.0 (cost: 13.61)
    Stage 3 - 3 configurations each with budget 81.0 (cost: 12.25)
    Stage 4 - 1 configurations each with budget 243.0 (cost: 12.25)
  Bracket 2 (cost: 64.86)
    Stage 0 - 41 configurations each with budget 9.0 (cost: 18.60)
    Stage 1 - 13 configurations each with budget 27.0 (cost: 17.69)
    Stage 2 - 4 configurations each with budget 81.0 (cost: 16.33)
    Stage 3 - 1 configurations each with budget 243.0 (cost: 12.25)
  Bracket 3 (cost: 73.48)
    Stage 0 - 18 configurations each with budget 27.0 (cost: 24.49)
    Stage 1 - 6 configurations each with budget 81.0 (cost: 24.49)
    Stage 2 - 2 configurations each with budget 243.0 (cost: 24.49)
  Bracket 4 (cost: 73.48)
    Stage 0 - 9 configurations each with budget 81.0 (cost: 36.74)
    Stage 1 - 3 configurations each with budget 243.0 (cost: 36.74)
  Bracket 5 (cost: 73.48)
    Stage 0 - 6 configurations each with budget 243.0 (cost: 73.48)

Where each stage uses the best configurations in the previous stage of the same bracket. The indicated cost is in hours (the same unit as the parameter on the command line), and considers the cross-validation structure (with ten folds, one epoch requires about 90% of the time needed for the full dataset, i.e. nine seconds. One budget unit then equals 2x10x9=180 seconds, which translates to 12). The wall-clock time can be of course reduced with parallel training.

This generator will also create a folder hierarchy under my-search, splitting brackets, stages, and configurations. Each folder will contain one random configuration:

> cat my-search/bracket-2/stage-0/config-16/config
folds: 10
repetitions: 2
cv_seed: 109090
learning_rate: 0.001
C: 0.01
solver: saga
penalty: l1

The whole process can now be run via Snakemake:

snakemake --snakefile my-search/Snakefile

The example provided fits a logistic regression model from scikit-learn to the iris dataset, using one iteration per budget unit. The entire search should require a few minutes (can be sped up via e.g. --cores 8) and result in an accuracy of 98% (averaged across folds and repetitions), visible from one of the last lines of the log:

Job counts:
        count   jobs
        1       find_overall_best
[('my-search/bracket-1/stage-4/config-0/result', -0.9800000000000001), ...

The best configuration is also saved in the search root directory (my-search/config).

Now, paired to each configuration, you find the negative average accuracy (the Snakefile is designed to find the configuration with the minimum result):

> cat my-search/bracket-2/stage-0/config-16/result

And log file:

> cat my-search/bracket-2/stage-0/config-16/log.log
INFO:root:Invoked with configuration file dev/sample-hb/bracket-2/stage-0/config-16/config
INFO:root:Invoked with budget 9
INFO:root:Loaded configuration: {'folds': 10, 'repetitions': 2, 'cv_seed': 109090, 'learning_rate': 0.001, 'C': 0.01, 'solver': 'saga', 'penalty': 'l1'}
INFO:root:Accuracy of repetition 0, fold 0: 0.467
INFO:root:Accuracy of repetition 0, fold 1: 0.533
INFO:root:Accuracy of repetition 0, fold 2: 0.667
INFO:root:Accuracy of repetition 1, fold 7: 0.467
INFO:root:Accuracy of repetition 1, fold 8: 0.533
INFO:root:Accuracy of repetition 1, fold 9: 0.667
INFO:root:Mean accuracy: 0.567

Note that, since we used random seeds throughout, these results should be fully reproducible.

Visualizing search status

Since a Hyperband search can take many days, a simple utility to see the ongoing progress is provided:

> python -m hyperband_snakemake status my-search
Bracket 0 - Stages completed: 0
  Stage 0 - 81 configurations
    | Completed (C) | Failed (F) | In progress (R) | Pending (.) | Total |
    |            12 |        4   |               8 |          57 |    81 |

      ...F. ...C. .CC.. ..CC. ....R
      ..C.. ..C.. ..... CRR.C C...C
      ..RR. .F... .R... RF... CF...
      ...R. .

  Top completed configuration(s):
    1. 0.1508 - Conf. 68
    2. 0.1590 - Conf. 50
    3. 0.1624 - Conf. 56

Bracket 1 - Stages completed: 0

(output truncated)

This will simply scan the directory looking for configuration or result files indicating progress. A configuration is deemed "in progress" if its folder does not contain the result file, but contains files or folders other than the configuration itself, such as log files, TensorBoard's summary folders, etc. A configuration is deemed "failed" if the result file contains nan or inf. Note that configurations that terminated abnormally without writing such a result file, e.g. because of an unhandled exception, are still counted as "in progress". You should check Snakemake's logs to determine whether a configuration is still running or has failed.


In its present state, the generator script creates by default the logistic regression example just explained, but adapting it to your needs is easy. This script uses Jinja2 to render three templates:

  1. The Snakefile, containing the logic to run the script and promote good configurations to the next stage.
  2. The bash launch script that is invoked by the Snakefile and runs the sample training script. The training script should take as arguments the configuration file and the budget, and write the result to a file named result in the same directory as the configuration file (if you are maximizing a metric, write its negation instead).
  3. The random configuration that is read by the training script. Thanks to Jinja2, the actual generation of random parameters is contained in the template file itself. There can be some custom logic, e.g. in the provided example the type of regularization (L1 or L2) is chosen based on the solver (SAGA or LBFGS). You are of course not restricted to any particular type of configuration, as long as it is text-based. For example, you can directly produce a Python configuration file and import it in the training script (if you are using Python, that is). This would save you the effort of writing code to read the configuration and instantiate the specified model.

These templates are rendered and saved in the output directory. This directory is now entirely portable, you just have to update config['base_dir'] in the Snakefile. This variable should contain the path of the output dir, either absolute or relative to where you will run snakemake.

You can pass --template-dir to the generator to make it use your custom templates. Simply create a copy of the provided directory, modify to your needs, and run the search:

> cp -r hyperband_snakemake/templates my-templates
> vim my-templates/config
> vim my-templates/
> vim my-templates/Snakefile
> python --template-dir my-templates ...
> snakemake ...

Running with Slurm

Once you have customized the configuration template, it is quite easy to run a hyperband search on a cluster managed by slurm, you just need to modify the launch script template to invoke srun, like so:

srun --time 24:00:00 --gpus-per-task 1 --cpus-per-task 6 --mem 92G \
    --output "$1/slurm-%j.out" --error "$1/slurm-%j.err" \
    <path-to-python> "$1/config" --output-dir "$1" --max-epochs "$2"

Where <path-to-python> points to the python interpreter in a suitable virtual environment (but note that you are not restricted to use Python!).

Another option is to use sbatch combined with --wait, which has the advantage that you can use a heredoc:

sbatch <options> --wait << EOF
conda activate <env>
python "$1/config" --output-dir "$1" --max-epochs "$2"

Then, use nohup (or tmux, or screen) to fire-and-forget Snakemake from the login node:

> nohup snakemake --snakefile my-search/Snakefile --latency-wait 60 -j 100 > my-search/log.out &

Which will schedule up to 100 jobs at the same time. latency-wait tells Snakemake to wait for the result files for up to 60 seconds before failing the job. It may be necessary to account for possible latencies when the results saved in a networked file-system.


[1]: Li, L., Jamieson, K., DeSalvo, G., Rostamizadeh, A. and Talwalkar, A., 2017. Hyperband: A novel bandit-based approach to hyperparameter optimization. The Journal of Machine Learning Research, 18(1), pp.6765-6816.

[2]: Köster, Johannes and Rahmann, Sven. Snakemake - A scalable bioinformatics workflow engine. Bioinformatics 2012.

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