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Using the OpenShift CLI

This page shows how to use the OpenShift CLI to interact ST4SD.

iPython notebooks make it easy to run and work with virtual experiments. However there is often a need to go deeper, especially for developers. In this case using the OpenShift CLI via a terminal is invaluable.

  • For: Researchers, Developers and Administrators
  • Use-When:
    • Researchers: You want to go deeper into the outputs of a particular workflow using standard terminal tools
    • Developers: Debugging virtual experiments. Inspecting and deleting workflows.
    • Administrators: Inspecting and deleting workflows.
  • Skill Requirements:
    • Being comfortable with working with command-line technologies
    • Some knowledge of OpenShift/K8s CLI tools

Software Requirements

The basic requirements are:

  • Access to an OpenShift instance with the ST4SD stack installed (see first steps for more information)
  • OpenShift command line tools installed

Getting Started


In the following we use

  • component to refer to a task/step in a workflow.
  • workflow to mean a particular encoding of a set of steps
  • workflow instance to mean a particular execution of a workflow

Logging-In to the Cluster

To run from a terminal you first need to login to the OpenShift cluster you want to run on. You can use user/password e.g.

oc login -u $USERNAME $CLUSTER

or copy the login command from the OpenShift console of the cluster you want to run in:

  1. Navigate to the console, login,
  2. Click on your name in upper right corner
  3. Click Copy Login Command
  4. Paste the copied command into the terminal and run it

Running a Workflow

Running from a terminal involves two steps

  1. Writing a short file in YAML that describes the workflow you want to run
    • We call it workflow.yaml here but you can call it anything
  2. Executing oc apply -f workflow.yaml

Here is an example yaml for launching the sum-numbers toy workflow. You can use this as a template for your writing your own workflow yaml. This document gives a detailed description of all the available fields.

You can also try running the sum-numbers workflow via this yaml

oc apply -f docs/examples/sum-numbers.yaml

This currently assumes that various objects in the target ST4SD instance you want to run on have been named following the conventions outlined in the ST4SD installation guide. We hope to remove this requirement shortly.

If the above works it will create a workflow object called sn - this is determined by the value of the name field in the workflow yaml.

I get unchanged

This means someone already has run a workflow with the same name in the same instance of ST4SD. Execute

oc delete workflow sn

to remove the old version and try the apply command again.

The oc delete command does not affect the files that the workflow instance has already generated under the persistent volume storage. However, it does trigger the workflow instance, and any components that are still running, to terminate. It also deletes any Kubernetes objects that have been created by the workflow instance. See Querying a workflow kubernetes object for more information on retrieving the status of a workflow via oc.

Names and Labels

Every kubernetes object has a name given by its name field. This name must be unique as it identifies a specific object. Here will refer to the name of a workflow as WORKFLOW_NAME

A kubernetes object can also have arbitrary labels associated with it. These are given as key-values under the metadata.labels section in a workflow’s yaml. For example in the sum-numbers.yaml file we have:

rest-uid: sn
workflow: sn
name: sn

labels are useful for grouping of objects as they allow you to list all objects with particular label key-value pair.

All labels defined in the workflows yaml are propagated to the pods the workflow creates. This allows us to find all pods created by a workflow instance, for example, by asking for all pods who also have a label workflow:sn. In this document we call the value of the workflow field WORKFLOW_ID

From the example yaml above WORKFLOW_NAME and WORKFLOW_ID can be set independently. This is why we differentiate them. However by convention we assume they will be the same, as this makes life much easier!

Examining Virtual Experiments

Querying a Workflow Kubernetes Object

Once you’ve started a workflow try the following commands

  • oc get workflows
    • Lists all workflows and displays their status (running, finished, failed, or an empty string for workflows which have not started running yet).
  • oc get workflow $WORKFLOW_NAME -o yaml
    • Returns the yaml of the workflow along with current status etc.
    • Example: oc get workflow sn -o yaml
  • oc describe workflow $WORKFLOW_NAME
    • This gives a similar, but shorter, output to get
    • Importantly it also returns the EVENTS associated with the created object - this is a primary way to debug issues.
  • oc get pods -l workflow=$WORKFLOW_ID
    • Lists all the pods in the workflow
    • Example: oc get pods -l workflow=sn
    • The argument -l means has this label key-value pair

When you list the pods of a workflow instance you will see one that is also called WORKFLOW_NAME - this is the primary pod of the instance. Pods for other workflow components that use the Kubernetes backend are called flow-$STAGE-$COMPONENT_NAME-$UNIQUEID

Pods of the sn workflow instance

Examining a Components Logs

Getting the logs of a task is straight-forward:

  • oc logs POD_NAME
    • This outputs the logs of the container running in POD_NAME e.g. oc logs flow-stage1-partialsum2-12290339-dc5vw

Examining a Components Output Directory

All components in a workflow write their output under a directory tree on the target cluster which you can login to and browse around with a terminal. The key piece of information you need here is the INSTANCE_NAME of the executing instance of the workflow, which is also the name of the root of the directory tree. To get this run:

oc describe workflow sn | grep instanceName

This will give output like:

instanceName: sum-numbers-2021-02-09T133047.732342.instance

sum-numbers-2021-02-09T133047.732342.instance is the INSTANCE_DIR_NAME

Then you can do:

  • oc exec $WORKFLOW_NAME -c elaunch-primary /bin/bash
    • Start a shell session in the primary pod of the workflow. From here you can cd to the directory at $INSTANCE_DIR_NAME.
      • e.g you can run cd /tmp/workdir/$INSTANCE_DIR_NAME
    • The output of a workflow component called COMPONENT_NAME in stage X will be at stages/stageX/COMPONENT_NAME
    • This only works while the pod is executing
  • oc debug $WORKFLOW_NAME -c elaunch-primary
    • Start a shell session in a copy of the primary pod of the workflow. From here you can browse to the workflow directory at INSTANCE_DIR_NAME like above
    • e.g you can run cd /tmp/workdir/$INSTANCE_DIR_NAME
    • Tip: The default shell will be sh, however the primary pod also has bash
    • Use this if the pod has finished
  • oc exec $WORKFLOW_NAME -c elaunch-primary -- $INSTANCE_DIR_NAME:
    • Returns a detailed list of the state of the workflow components


Debugging a Workflow Component

Your first step in checking if there is an issue is to run oc describe e.g. oc describe workflow WORKFLOW_NAME or oc describe pod WORKFLOW_NAME. This allows you to check for example:

  • If the pod was scheduled
  • If the pods image was pulled
  • Any issues with mounts
  • If the pod went out-of-memory

If you want to debug deeper you can use

  • oc debug $PODNAME
    • This starts a shell in a copy of $PODNAME. Use this if you want to debug the image the pod was using.
  • oc debug $WORKFLOW_NAME -c elaunch-primary
    • Start a shell in a copy of the primary pod of the workflow (same environment, mounts etc.)
    • As noted above you can browse to the workflow directory at INSTANCE_NAME however you also get access to three useful debug tools

Debug Tools Available in the primary Pod

If you start a shell in the primary pod, via exec or debug you can run the following tools. First cd to the workflow instance directory at INSTANCE_NAME

    • This prints the command line for a component.
    • Useful to check what was actually executed is what you thought it was
    • Example: -s0 MyComponent
    • The prints the state of all the workflow components e.g. who failed, restarted etc.
    • By default, it only prints components with issues
    • Example: einspect -f all
      • Prints status info on all components
    • Executes a component. In case of kubernetes use to reexecute any pod of any component. The same workdir will be used
    • Example: -f -s0 MyComponent
      • Note the -f causes a new pod to be spawned. If you don’t specify it, ST4SD will try to execute MyComponent in the primary pod, which will usually fail due to necessary programs not being present.

Switching from Notebook to Commandline

When you use the RESTApi via notebook to start a workflow it automates the creation of a workflow yaml as described above. Hence, you can still use the command line to work with it.

However note the reverse is not fully true. If you launch from the terminal:

  • you cannot use the start/stop/status functions in the notebook - the workflow is not registered with the RESTApi
  • you can use the st4sd-datastore commands

To work with the command line all you need is to REST UID returned when you submitted the workflow from the notebook. This will be the WORKFLOW_NAME and the WORKFLOW_ID of the workflow instance.

Managing Workflows

The number of Workflows and associated Job and Pod objects in a namespace can easily reach O(1000) and higher. This section describes how to examine, sort and delete these objects.

List and Sort

By default oc get wf only lists workflows name and experiment state in alphabetical order of Name. However this can easily be customized

This document assumes that there is only one kind of "Workflow" object on your cluster. If there are multiple CustomResourceDefinitions that introduce the Workflow object then you must use the full qualifier of the Workflow kind. Instead of "oc get wf" you should run "oc get" (or the shorter form "oc get wc.st4sd").

List workflows with custom-columns showing creation date, exit status and state

oc get wf --output custom-columns=",AGE:metadata.creationTimestamp,EXIT-STATUS:status.exitstatus,STATE:status.experimentstate"

You can create a column for any data in the workflow objects YAML using the appropriate key-path.

Sort workflows by creation date

oc --sort-by=".metadata.creationTimestamp" get wf

Similarly you can sort workflow by any data in the workflow objects YAML using the appropriate key-path.

Combining the above you can list workflows showing creation data, exist-status and state sorted by date

oc --sort-by=".metadata.creationTimestamp" get wf --output custom-columns=",AGE:metadata.creationTimestamp,EXIT-STATUS:status.exitstatus,STATE:status.experimentstate"


The following commands illustrate how you can delete workflow objects This also deletes all Job and Pod objects associated with the workflow

Deleting a Workflow object does not delete the data created by the workflow. The output folder will still exist and the output is still accessible via the st4sd-datastore python API.

Deleting the workflow object will delete it from st4sd-runtime-service: st4sd-runtime-service API calls using the deleted workflows rest-uid will not work.

When deleting Workflows it’s worth reviewing the meaning of experiment-state and exit-status here

Delete all workflows whose experiment-state is finished

oc get wf | awk '/finished/{print $1}' | xargs oc delete wf

Delete all workflows whose experiment-state is failed

oc get wf | awk '/failed/{print $1}' | xargs oc delete wf

Delete all workflows whose exist-status is failed

oc get wf --output custom-columns=",EXIT-STATUS:status.exitstatus" | awk '/Failed/{print $1}' | xargs oc delete wf

Delete component Job and Pod objects associated with workflows whose experiment-state is finished

The oneliner below will not delete the Pod objects that contain the elaunch-primary container (i.e. the entrypoint Pod of the virtual experiment instance). The code just deletes all Job and Pod objects that elaunch-primary created to run the tasks of components. After running it, you will still be able to run oc debug $WORKFLOW_NAME.

oc get wf | awk '/finished/{print $1}' | xargs -n1 -I {} oc delete job -lworkflow={}

Delete all workflows whose name starts with homolumo

oc get wf | awk '/homolumo/{print $1}' | xargs oc delete wf
Future versions of ST4SD will contain utilities to automate garbage collection of Kubernetes objects.