Coclobas is a scheduler for HPC-like jobs accessible through HTTP.
It can be setup with three kinds of configurations:
- Using Kubernetes and the Google Container Engine,
i.e. using a Kubernetes “eleastic” cluster setup with
gcloudand submitting jobs as Kubernetes “pods”.
- Using the server's machine as a one-node cluster and submitting jobs as docker containers given a maximal number of jobs.
- (Experimental) using an AWS-Batch job queue with Docker containers.
Coclobas provides logging facilities (e.g. maintaining logs long after Kubernetes disposes of them).
Finally, it makes it easy to submit arbitrary scripts to be run in any Docker container, which makes it easier than using raw Kubernetes or Docker to submit arbitrarily complex jobs.
ketrew package is present, Coclobas comes with a Ketrew plugin
and a build of the Ketrew binary with the plugin already loaded in (for
Coclobas 0.0.1 is in
opam (supports GKE/Kubernetes and local-docker modes).
You can just use Opam to get things going quickly:
opam pin add coclobas https://github.com/hammerlab/coclobas.git
Or you may clone this repo and:
In GKE/Kubernetes mode,
must be installed (and authenticated) with the Coclobas server.
In Local/Docker mode,
docker must be present (and accessible to the Coclobas
In AWS-Batch mode, the
aws command line application must be present (and
it must be recent enough to have
aws batch enabled).
You first need to create a “root” directory, see:
coclobas configure --help
Example 1: GKE/Kubernetes mode:
coclobas config --root $root \ --cluster-kind gke \ --gke-cluster-name "my-coclotest-cluster" \ --gcloud-zone "us-east1-c" \ --max-nodes 5
Example 2: Local/Docker mode:
coclobas config --root $root \ --cluster-kind local-doker \ --max-nodes 5
Example 3: AWS-Batch mode:
coclobas config --root $root \ --cluster-kind aws-batch \ --aws-queue awsuser-jq01 \ --min-sleep 4 \ --max-update-errors 4 \ --max-nodes 4
Start The Server
Now that Coclobas has a configuration (this information is stored in the
--root, so you can have many possible Coclobas servers configured, all in
different directories), you'll want to start it:
coclobas start-server --root $root --port 8999
You can use this
curl http://127.0.0.1:8999/status to see if Coclobas is ready
to go (if it says
Initializing usually it means that it is setting up a
GKE-cluster which takes a few minutes).
The most common way of submitting jobs is through the Ketrew plugin, see
In GKE/Kubernetes mode:
workflow_node without_product ~name:"Coclobas that uses the GKE/Kubernetes" ~make:( Coclobas_ketrew_backend.Plugin.kubernetes_program ~base_url:"http://127.0.0.1:8999/" ~image:"ubuntu" ~volume_mounts:[ `Nfs ( Coclobas.Kube_job.Specification.Nfs_mount.make ~host:"nfs-server.example.com" ~path:"/path/inside/nfs-server" ~point:"/mount/point/" ()) ] Program.( chain [ shf "hostname"; shf "du -sh /mount/point"; shf "sleep 60"; ] ) )
In Local/Docker mode:
workflow_node without_product ~name:"Coclobas test of local-docker jobs" ~make:( Coclobas_ketrew_backend.Plugin.local_docker_program ~base_url:"http://127.0.0.1:8999/" ~image:"ubuntu" ~volume_mounts:[ `Local ("/usr/bin", "/hostusrbin") ] Program.( exec ["find"; "/hostusrbin"] ) )
Querying the Server
All the “job inspection” features are available through the Ketrew UIs as “backend queries.”
One can also directly query the server through the command line,
coclobas client --help, for example:
coclobas client --server http://127.0.0.1:8999 list
If you have any questions, you may submit an issue, or join the authors on the public “Slack” channel of the Hammer Lab:
It's Apache 2.0.