November 30, 2021

REANA 0.8.0 is released

We are glad to announce the release of REANA 0.8.0, a major update allowing users to run Snakemake workflows, allowing administrators to set and monitor CPU and Disk quotas for users, and more!

What’s new for the users?

Support for running Snakemake workflows

One of the most notable new features of REANA 0.8 release series is the support for running Snakemake workflows. Snakemake joins CWL and Yadage as another workflow specification language that you can use to write complex computational workflows:

# Snakefile
rule all:
    input:
        "results/data.root",
        "results/plot.png"

rule gendata:
    input:
        gendata_tool=config["gendata"]
    output:
        "results/data.root"
    params:
        events=config["events"]
    container:
        "docker://reanahub/reana-env-root6:6.18.04"
    shell:
        "mkdir -p results && root -b -q '{input.gendata_tool}({params.events},\"{output}\")'"

rule fitdata:
    input:
        fitdata_tool=config["fitdata"],
        data="results/data.root"
    output:
        "results/plot.png"
    container:
        "docker://reanahub/reana-env-root6:6.18.04"
    shell:
        "root -b -q '{input.fitdata_tool}(\"{input.data}\",\"{output}\")'"

Please see the dedicated blog post about how to use Snakemake with REANA.

Upgrade of CWL workflow engine

The Common Workflow Language engine was upgraded from cwltool version 1 to version 3 and the compliance with the CWL reference test suite has been improved. This allows using many new CWL constructs in your workflows.

CPU and Disk quota accounting

Optionally, the REANA cluster may have CPU and Disk quota accounting feature turned on. The new command reana-client quota-show will allow seeing your quota limits and current usage:

$ reana-client quota-show --resource cpu --report limit
No limit.

$ reana-client quota-show --resource disk --report limit
No limit.

If the quota accounting feature is turned on, the quota-show command will also allow displaying current usage:

$ reana-client quota-show  --resource cpu --report usage -h
36s

$ reana-client quota-show  --resource disk --report usage -h
2.61 GiB

If the feature is enabled, the REANA web interface will indicate disk usage in your workflow list:

quota-in-workflow-list

The overall quota consumption can be tracked on your profile page:

quota-in-profile

Improved workflow validation

The reana-client validate command has been improved to include a possibility to validate the workflow against the remote REANA cluster you would like to use. The new option is named --server-capabilities:

$ cd my-analysis
$ reana-client validate --server-capabilities

The option will cover the scenarios where your workflow definition can be theoretically correct, but the remote REANA cloud does not support the desired feature. One example is the optional compute_backend declaration. If you would like to set compute_backend to htcondorcern in order to instruct the REANA cluster to use the HTCondor high-throughput compute backend for some job, but the remote REANA cluster where you are connected to does not support it, you would be warned about the mismatch.

Improved list command filtering

The reana-client list command’s performance has been optimised. If you have a large number of workflows, the list will execute much faster.

The default output focuses on tracking the status of the workflows. If you would like to track the workflow progress or the workspace disk usage, please use new options --include-progress and --include-workspace-size.

The list command also adds a possibility to filter workflows by name or by status via the new --filter option. This can be convenient if you work on several projects (“project-a”, “project-b”, …) and have run many workflows such as “project-a.1”, “project-a.2”, up to “project-z.1”. If you are interested in listing the status of workflow runs from the “project-p” group only, you can use:

$ reana-client list --filter name=project-p

You can also filter workflows based on the workflow status. For example, let us display only those workflow runs that failed:

$ reana-client list --filter status=failed

The filtering options can be combined in which case the filters will be applied one after another as they appear in the command line. For example, showing “running” workflows from “project-p” only:

$ reana-client list --filter status=running --filter name=project-p

The other reana-client commands, notably ls allowing to list files and du allowing to get information about disk usage, were also enriched with the --filter option.

Inspecting run times of individual jobs

The reana-client logs command was improved to show the started and finished time for each individual job in the workflow:

$ reana-client logs -w my-analysis.42
...
==> Step: gendata
==> Workflow ID: 4455a6b2-3d94-4694-ae99-e493327cd53f
==> Compute backend: Kubernetes
==> Job ID: reana-run-job-6f57f1c8-8edf-4840-9423-b638e664bf57
==> Docker image: reanahub/reana-env-root6:6.18.04
==> Command: mkdir -p results && root -b -q 'code/gendata.C(20000,"results/data.root")'
==> Status: finished
==> Started: 2021-11-26T12:46:17
==> Finished: 2021-11-26T12:46:23
==> Logs:
...

If you would like to see a brief overview of all the steps of the workflow in one go, you can simply grep the ‘==>’ string in the logs command output:

$ reana-client logs -w my-analysis.42 | grep '^==>'
==> Workflow engine logs
==> Job logs
==> Step: gendata
==> Workflow ID: 4455a6b2-3d94-4694-ae99-e493327cd53f
==> Compute backend: Kubernetes
==> Job ID: reana-run-job-6f57f1c8-8edf-4840-9423-b638e664bf57
==> Docker image: reanahub/reana-env-root6:6.18.04
==> Command: mkdir -p results && root -b -q 'code/gendata.C(20000,"results/data.root")'
==> Status: finished
==> Started: 2021-11-26T12:46:17
==> Finished: 2021-11-26T12:46:23
==> Logs:
==> Step: fitdata
==> Workflow ID: 4455a6b2-3d94-4694-ae99-e493327cd53f
==> Compute backend: Kubernetes
==> Job ID: reana-run-job-2da81be7-5108-41cd-8b7c-ffc0f081b3bd
==> Docker image: reanahub/reana-env-root6:6.18.04
==> Command: root -b -q 'code/fitdata.C("results/data.root","results/plot.png")'
==> Status: finished
==> Started: 2021-11-26T12:46:23
==> Finished: 2021-11-26T12:46:33
==> Logs:

Removal of support for Python 2.7

Following the discontinuation of Python 2.7 official support, REANA 0.8 release series stopped supporting Python 2.7 version. Please upgrade your reana-client installation to use at least Python 3.6.

What’s new for the administrators?

CPU and Disk quota accounting

REANA 0.8 release series allows cluster administrators to set certain CPU and Disk quota usage limits for individual users. This can be set by Helm configuration option quota.enabled.

Please note that if you do enable CPU and Disk quota monitoring, you may want to further configure quota.termination_update_policy to decide whether the CPU and Disk quota usage consumption for users will be calculated immediately after workflow terminates or via a periodic cron jobs.

Improved cluster performance

The cluster performance when running numerous concurrent workflows was considerably improved. We have tested running up to a thousand of concurrent workflows running on clusters of up to three hundred nodes. There are new Helm configuration options that allow fine-tuning REANA cluster components in these conditions, such as:

  • reana_server.environment.REANA_WORKFLOW_SCHEDULING_POLICY allows to set workflow scheduling policy. The value “fifo”, meaning “first-in first-out”, will execute workflows as they are coming. The value “balanced” will look at how many workflows a particular user launches. If user A uses the system heavily, and user B submits new workflows, the system will prefer to schedule the workflow from user B before continuing with workflows of the user A. The “balanced” scheduling policy will also look at the workflow DAG complexity. If a new workflow C would like to launch 10 jobs at the start, and the workflow D only 2 jobs, and the cluster is busy and the current capacity cannot accept more than 4 jobs at the given time, the workflow D would be preferred over workflow C.

  • reana_server.environment.REANA_RATELIMIT_GUEST_USER and reana_server.environment.REANA_RATELIMIT_AUTHENTICATED_USER allow setting REST API rate limit values. If your cluster is very busy, you can use values such as “2000 per second” enabling heavy traffic from running a high amount of concurrent workflows.

  • reana_server.environment.REANA_SCHEDULER_REQUEUE_SLEEP allows setting sleep time between processing queued workflows. The default value of 15 seconds may be too conservative, as the scheduler will pause for 15 seconds before looking at the incoming workflow queue. If you are running a lot of concurrent workflows, you may want to lower it to 1 second or even 0.1 seconds.

  • reana_workflow_controller.environment.REANA_JOB_STATUS_CONSUMER_PREFETCH_COUNT allows tweaking the Rabbit MQ prefetch count for the job status consumer. The default value was tested to behave well up to a thousand of concurrent workflows, so should be probably fine in your setups.

How to upgrade existing REANA 0.7 clusters

If you are a REANA cluster administrator and you would like to upgrade from REANA 0.7.* to REANA 0.8.0, please follow the steps described below.

1. Upgrade the cluster using Helm

$ helm upgrade reana reanahub/reana --version 0.8.0

You may set various Helm values specified above; see also the full list of REANA Helm values.

2. Label the cluster nodes

REANA 0.8 release series uses more cluster node labels which allows separating nodes dedicated to running infrastructure pods, runtime user workflow batch pods, runtime user job pods, and runtime user interactive sessions. Setting the new values allows preventing exceptional situations with user jobs, such as exhausting node memory, from affecting other pods.

We therefore recommend upgrading your cluster node labels. For example, if you have four nodes in the cluster, you can label them as follows:

$ kubectl label node reana-cluster-node-0 reana.io/system=infrastructure
$ kubectl label node reana-cluster-node-1 reana.io/system=runtimebatch
$ kubectl label node reana-cluster-node-2 reana.io/system=runtimejobs
$ kubectl label node reana-cluster-node-3 reana.io/system=runtimesessions

3. Upgrade the database schema

This release introduces several database schema changes to support among others the new quota accounting feature. We thus need to perform database schema upgrade by following the dedicated upgrade documentation:

$ kubectl exec -i -t deployment/reana-server -c rest-api -- reana-db alembic upgrade
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
INFO  [alembic.runtime.migration] Running upgrade  -> c912d4f1e1cc, Quota tables.
INFO  [alembic.runtime.migration] Running upgrade c912d4f1e1cc -> ad93dae04483, Interactive sessions.
INFO  [alembic.runtime.migration] Running upgrade ad93dae04483 -> 4801b98f6408, Job started and finished times.
INFO  [alembic.runtime.migration] Running upgrade 4801b98f6408 -> f84e17bd6b18, Workflow complexity.
INFO  [alembic.runtime.migration] Running upgrade f84e17bd6b18 -> 6568d7cb6710, storing full workflow workspace.

4. Create default quota resources

Due to the new quota accounting feature, it is necessary to create two default resources to measure both CPU and Disk usage:

$ kubectl exec -i -t deployment/reana-server -c rest-api -- reana-db quota create-default-resources
Created resources: ['processing time', 'shared storage']

5. Set the default user quota limits

The last step is to set the quota limits for all the users in the database. By default, let us set the default quota limit, which is 0, meaning that there are limits of usage for users:

$ kubectl exec -i -t deployment/reana-server -c rest-api -- flask reana-admin quota-set-default-limits
Quota limit 0 for 'processing time' successfully set to users ['john.doe@example.org', ....]
Quota limit 0 for 'shared storage' successfully set to users ['john.doe@example.org', ....]

Later on, we could decide to set quota limits per user and per resource by using the command flask reana-admin quota-set.

And we are done with the upgrade! At this point, you should have your REANA cluster fully upgraded to 0.8.0.

Further improvements and bug fixes

REANA 0.8.0 release comes with other minor improvements and bug fixes. Please see the detailed REANA 0.8.0 release notes.

Enjoy!

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