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Kubernetes

REANA supports Kubernetes as a primary and default job execution backend alongside HTCondor and Slurm.

If step does not contain compute_backend specification, it will be executed on the default backend.

   # Serial example
   ...
   steps:
      - name: reana_demo_helloworld_htcondorcern
        environment: 'python:2.7-slim'
        compute_backend: kubernetes
        commands:
            - python "${helloworld}"

Custom memory limit

When jobs exceed the cluster memory limits, you will get out of memory (OOM) error and job gets OOMKilled. To avoid OOM error, you can increase the memory limits per workflow step to make an efficient use of the available resources. Note that you can also decrease the memory limit to increment the chances of jobs being scheduled earlier if the cluster is busy.

To set the memory limit of a job you can specify kubernetes_memory_limit in the specification of each workflow step.

Read more about the expected memory values on Kubernetes official documentation

You can configure the steps in the respective specifications for Serial, Yadage, CWL and Snakemake workflow engines.

Serial workflow

You can set kubernetes_memory_limit in every step of workflow specification.

   ...
   steps:
      - name: reana_demo_helloworld_memory_limit
        environment: 'python:2.7-slim'
        compute_backend: kubernetes
        kubernetes_memory_limit: '8Gi'
        commands:
            - python helloworld.py

Yadage workflow

You can set kubernetes_memory_limit in every step under environment.resources.

   ...
   stages:
   - name: reana_demo_helloworld_memory_limit
      dependencies: [init]
      scheduler:
        scheduler_type: 'singlestep-stage'
        parameters:
          helloworld: {step: init, output: helloworld}
        step:
          process:
            process_type: 'string-interpolated-cmd'
            cmd: 'python "{helloworld}"'
          environment:
            environment_type: 'docker-encapsulated'
            image: 'python'
            imagetag: '2.7-slim'
            resources:
              - compute_backend: kubernetes
              - kubernetes_memory_limit: '8Gi'

CWL workflow

You can set kubernetes_memory_limit in every step under hints.reana.

   ...
   steps:
    first:
      hints:
        reana:
          compute_backend: kubernetes
          kubernetes_memory_limit: '8Gi'
      run: helloworld_memory_limit.tool
      in:
        helloworld: helloworld_memory_limit
      out: [result]

Snakemake workflow

You can set kubernetes_memory_limit in every rule under resources.

  ...
  rule helloworld:
    input:
        helloworld=config["helloworld"],
        inputfile=config["inputfile"],
    params:
        sleeptime=config["sleeptime"]
    output:
        "results/greetings.txt"
    resources:
        compute_backend="kubernetes",
        kubernetes_memory_limit="8Gi"
    container:
        "docker://python:2.7-slim"
    ...