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Rabbit storage for containerized applications

Note

This RFC contains outdated information. For the most up-to-date details, please refer to the User Containers documentation.

For Rabbit to provide storage to a containerized application there needs to be some mechanism. The remainder of this RFC proposes that mechanism.

Actors

There are several actors involved:

  • The AUTHOR of the containerized application
  • The ADMINISTRATOR who works with the author to determine the application requirements for execution
  • The USER who intends to use the application using the 'container' directive in their job specification
  • The RABBIT software that interprets the #DWs and starts the container during execution of the job

There are multiple relationships between the actors:

  • AUTHOR to ADMINISTRATOR: The author tells the administrator how their application is executed and the NNF storage requirements.
  • Between the AUTHOR and USER: The application expects certain storage, and the #DW must meet those expectations.
  • ADMINISTRATOR to RABBIT: Admin tells Rabbit how to run the containerized application with the required storage.
  • Between USER and RABBIT: User provides the #DW container directive in the job specification. Rabbit validates and interprets the directive.

Proposal

The proposal below outlines the high level behavior of running containers in a workflow:

  1. The AUTHOR writes their application expecting NNF Storage at specific locations. For each storage requirement, they define:
    1. a unique name for the storage which can be referenced in the 'container' directive
    2. the required mount path or mount path prefix
    3. other constraints or storage requirements (e.g. minimum capacity)
  2. The AUTHOR works with the ADMINISTRATOR to define:
    1. a unique name for the program to be referred by USER
    2. the pod template or MPI Job specification for executing their program
    3. the NNF storage requirements described above.
  3. The ADMINISTRATOR creates a corresponding NNF Container Profile Kubernetes custom resource with the necessary NNF storage requirements and pod specification as described by the AUTHOR
  4. The USER who desires to use the application works with the AUTHOR and the related NNF Container Profile to understand the storage requirements
  5. The USER submits a WLM job with the #DW container directive variables populated
  6. WLM runs the workflow and drives it through the following stages...
    1. Proposal: RABBIT validates the #DW container directive by comparing the supplied values to those listed in the NNF Container Profile. If the workflow fails to meet the requirements, the job fails
    2. PreRun: RABBIT software:
      1. duplicates the pod template specification from the Container Profile and patches the necessary Volumes and the config map. The spec is used as the basis for starting the necessary pods and containers
      2. creates a config map reflecting the storage requirements and any runtime parameters; this is provided to the container at the volume mount named nnf-config, if specified
    3. The containerized application(s) executes. The expected mounts are available per the requirements and celebration occurs. The pods continue to run until:
    4. a pod completes successfully (any failed pods will be retried)
    5. the max number of pod retries is hit (indicating failure on all retry attempts)
      1. Note: retry limit is non-optional per Kubernetes configuration
      2. If retries are not desired, this number could be set to 0 to disable any retry attempts
    6. PostRun: RABBIT software:
    7. marks the stage as Ready if the pods have all completed successfully. This includes a successful retry after preceding failures
    8. starts a timer for any running pods. Once the timeout is hit, the pods will be killed and the workflow will indicate failure
    9. leaves all pods around for log inspection

Container Assignment to Rabbit Nodes

During Proposal, the USER must assign compute nodes for the container workflow. The assigned compute nodes determine which Rabbit nodes run the containers.

Container Definition

Containers can be launched in two ways:

  1. MPI Jobs
  2. Non-MPI Jobs

MPI Jobs are launched using mpi-operator. This uses a launcher/worker model. The launcher pod is responsible for running the mpirun command that will target the worker pods to run the MPI application. The launcher will run on the first targeted NNF node and the workers will run on each of the targeted NNF nodes.

For Non-MPI jobs, mpi-operator is not used. This model runs the same application on each of the targeted NNF nodes.

The NNF Container Profile allows a user to pick one of these methods. Each method is defined in similar, but different fashions. Since MPI Jobs use mpi-operator, the MPIJobSpec is used to define the container(s). For Non-MPI Jobs a PodSpec is used to define the container(s).

An example of an MPI Job is below. The data.mpiSpec field is defined:

kind: NnfContainerProfile
apiVersion: nnf.cray.hpe.com/v1alpha1
data:
  mpiSpec:
    mpiReplicaSpecs:
      Launcher:
        template:
          spec:
            containers:
            - command:
              - mpirun
              - dcmp
              - $(DW_JOB_foo_local_storage)/0
              - $(DW_JOB_foo_local_storage)/1
              image: ghcr.io/nearnodeflash/nnf-mfu:latest
              name: example-mpi
      Worker:
        template:
          spec:
            containers:
            - image: ghcr.io/nearnodeflash/nnf-mfu:latest
              name: example-mpi
    slotsPerWorker: 1
...

An example of a Non-MPI Job is below. The data.spec field is defined:

kind: NnfContainerProfile
apiVersion: nnf.cray.hpe.com/v1alpha1
data:
  spec:
    containers:
    - command:
      - /bin/sh
      - -c
      - while true; do date && sleep 5; done
      image: alpine:latest
      name: example-forever
...

In both cases, the spec is used as a starting point to define the containers. NNF software supplements the specification to add functionality (e.g. mounting #DW storages). In other words, what you see here will not be the final spec for the container that ends up running as part of the container workflow.

Security

The workflow's UID and GID are used to run the container application and for mounting the specified fileystems in the container. Kubernetes allows for a way to define permissions for a container using a Security Context.

mpirun uses ssh to communicate with the worker nodes. ssh requires that UID is assigned to a username. Since the UID/GID are dynamic values from the workflow, work must be done to the container's /etc/passwd to map the UID/GID to a username. An InitContainer is used to modify /etc/passwd and mount it into the container.

Communication Details

The following subsections outline the proposed communication between the Rabbit nodes themselves and the Compute nodes.

Rabbit-to-Rabbit Communication

Non-MPI Jobs

Each rabbit node can be reached via <hostname>.<subdomain> using DNS. The hostname is the Rabbit node name and the workflow name is used for the subdomain.

For example, a workflow name of foo that targets rabbit-node2 would be rabbit-node2.foo.

Environment variables are provided to the container and ConfigMap for each rabbit that is targeted by the container workflow:

NNF_CONTAINER_NODES=rabbit-node2 rabbit-node3
NNF_CONTAINER_SUBDOMAIN=foo
NNF_CONTAINER_DOMAIN=default.svc.cluster.local

kind: ConfigMap
apiVersion: v1
data:
  nnfContainerNodes:
    - rabbit-node2
    - rabbit-node3
  nnfContainerSubdomain: foo
  nnfContainerDomain: default.svc.cluster.local

DNS can then be used to communicate with other Rabbit containers. The FQDN for the container running on rabbit-node2 is rabbit-node2.foo.default.svc.cluster.local.

MPI Jobs

For MPI Jobs, these hostnames and subdomains will be slightly different due to the implementation of mpi-operator. However, the variables will remain the same and provide a consistent way to retrieve the values.

Compute-to-Rabbit Communication

For Compute to Rabbit communication, the proposal is to use an open port between the nodes, so the applications could communicate using IP protocol. The port number would be assigned by the Rabbit software and included in the workflow resource's environmental variables after the Setup state (similar to workflow name & namespace). Flux should provide the port number to the compute application via an environmental variable or command line argument. The containerized application would always see the same port number using the hostPort/containerPort mapping functionality included in Kubernetes. To clarify, the Rabbit software is picking and managing the ports picked for hostPort.

This requires a range of ports to be open in the firewall configuration and specified in the rabbit system configuration. The fewer the number of ports available increases the chances of a port reservation conflict that would fail a workflow.

Example port range definition in the SystemConfiguration:

apiVersion: v1
items:
  - apiVersion: dws.cray.hpe.com/v1alpha1
    kind: SystemConfiguration
      name: default
      namespace: default
    spec:
      containerHostPortRangeMin: 30000
      containerHostPortRangeMax: 40000
      ...

Example

For this example, let's assume I've authored an application called foo. This application requires Rabbit local GFS2 storage and a persistent Lustre storage volume.

Working with an administrator, my application's storage requirements and pod specification are placed in an NNF Container Profile foo:

kind: NnfContainerProfile
apiVersion: v1alpha1
metadata:
    name: foo
    namespace: default
spec:
    postRunTimeout: 300
    maxRetries: 6
    storages:
    - name: DW_JOB_foo-local-storage
      optional: false
    - name: DW_PERSISTENT_foo-persistent-storage
      optional: false
    spec:
        containers:
        - name: foo
          image: foo:latest
          command:
          - /foo
          ports:
          - name: compute
            containerPort: 80

Say Peter wants to use foo as part of his job specification. Peter would submit the job with the directives below:

#DW jobdw name=my-gfs2 type=gfs2 capacity=1TB

#DW persistentdw name=some-lustre

#DW container name=my-foo profile=foo                 \
    DW_JOB_foo-local-storage=my-gfs2                  \
    DW_PERSISTENT_foo-persistent-storage=some-lustre

Since the NNF Container Profile has specified that both storages are not optional (i.e. optional: false), they must both be present in the #DW directives along with the container directive. Alternatively, if either was marked as optional (i.e. optional: true), it would not be required to be present in the #DW directives and therefore would not be mounted into the container.

Peter submits the job to the WLM. WLM guides the job through the workflow states:

  1. Proposal: Rabbit software verifies the #DW directives. For the container directive my-foo with profile foo, the storage requirements listed in the NNF Container Profile are foo-local-storage and foo-persistent-storage. These values are correctly represented by the directive so it is valid.
  2. Setup: Since there is a jobdw, my-gfs2, Rabbit software provisions this storage.

  3. Pre-Run:

    1. Rabbit software generates a config map that corresponds to the storage requirements and runtime parameters.

          kind: ConfigMap
    apiVersion: v1
    metadata:
        name: my-job-container-my-foo
    data:
        DW_JOB_foo_local_storage:             mount-type=indexed-mount
        DW_PERSISTENT_foo_persistent_storage: mount-type=mount-point
        ...

    2. Rabbit software creates a pod and duplicates the foo pod spec in the NNF Container Profile and fills in the necessary volumes and config map.

          kind: Pod
    apiVersion: v1
    metadata:
        name: my-job-container-my-foo
    template:
        metadata:
            name: foo
            namespace: default
        spec:
            containers:
            # This section unchanged from Container Profile
            - name: foo
              image: foo:latest
              command:
                - /foo
              volumeMounts:
              - name: foo-local-storage
                mountPath: <MOUNT_PATH>
              - name: foo-persistent-storage
                mountPath: <MOUNT_PATH>
              - name: nnf-config
                mountPath: /nnf/config
              ports:
                - name: compute
                  hostPort: 9376 # hostport selected by Rabbit software
                  containerPort: 80

            # volumes added by Rabbit software
            volumes:
            - name: foo-local-storage
              hostPath:
                path: /nnf/job/my-job/my-gfs2
            - name: foo-persistent-storage
              hostPath:
                path: /nnf/persistent/some-lustre
            - name: nnf-config
              configMap:
                name: my-job-container-my-foo

            # securityContext added by Rabbit software - values will be inherited from the workflow
            securityContext:
              runAsUser: 1000
              runAsGroup: 2000
              fsGroup: 2000

    3. Rabbit software starts the pods on Rabbit nodes

    4. Post-Run
    5. Rabbit waits for all pods to finish (or until timeout is hit)
    6. If all pods are successful, Post-Run is marked as Ready
    7. If any pod is not successful, Post-Run is not marked as Ready

Special Note: Indexed-Mount Type for GFS2 File Systems

When using a GFS2 file system, each compute is allocated its own Rabbit volume. The Rabbit software mounts a collection of mount paths with a common prefix and an ending indexed value.

Application AUTHORS must be aware that their desired mount-point really contains a collection of directories, one for each compute node. The mount point type can be known by consulting the config map values.

If we continue the example from above, the foo application expects the foo-local-storage path of /foo/local to contain several directories

$ ls /foo/local/*

node-0
node-1
node-2
...
node-N

Node positions are not absolute locations. WLM could, in theory, select 6 physical compute nodes at physical location 1, 2, 3, 5, 8, 13, which would appear as directories /node-0 through /node-5 in the container path.

Symlinks will be added to support the physical compute node names. Assuming a compute node hostname of compute-node-1 from the example above, it would link to node-0, compute-node-2 would link to node-1, etc.

Additionally, not all container instances could see the same number of compute nodes in an indexed-mount scenario. If 17 compute nodes are required for the job, WLM may assign 16 nodes to run one Rabbit, and 1 node to another Rabbit.