Ketrew: Keep Track of Experimental Workflows

Ketrew is:

an OCaml library providing an EDSL API to define complex and convoluted workflows (interdependent steps/programs using a lot of data, with many parameter variations, running on different hosts with various schedulers).
an engine taking care of orchestrating the run of those workflows, and keeping track everything that succeeds, fails, or gets lost. Ketrew can be a standalone application, or use a client-server architecture.

This is the 2.0.0 version of Ketrew, serialized content is backwards compatible with the 1.x.x series but the protocol is not; the EDSL API requires minor changes (all caught by the OCaml compiler). See also the documentation for the master branch.

Build & Install

Ketrew requires at least OCaml 4.02.2 and should be able to build & work on any Unix platform.

From Opam

If you have opam up and running:

opam install ketrew

Then you need at runtime ssh in the $PATH.

This gets you the ketrew executable and the ketrew_pure and ketrew libraries.

Without Opam

See the development documentation to find out how to build Ketrew (and its dependencies) from the sources.

Getting Started

Ketrew is very flexible and hence may seem difficult to understand, let's get a very minimalistic workflow running.

The first time you use Ketrew, you need to configure it, simplest by calling ketrew init, and please choose an authentication token:

rm -fr ~/.ketrew/ # if you had a previous configuration there
ketrew init --with-token my-not-so-secret-token

by default this will configure Ketrew in $HOME/.ketrew/ with a client/server mode not using TLS on port 8756 (see ketrew init --help you can even ask it to generate self-signed TLS certificates). See also the documentation on the configuration file learn how to tweak it.

You can check that the client or the server are configured:

ketrew print-configuration
ketrew print-configuration --configuration-profile server
ketrew print-configuration -P daemon

You may then start a server:

KETREW_PROFILE=daemon ketrew start-server

and then open the GUI:

ketrew gui

which is just trying to load http://127.0.0.1:8756/gui?token=my-not-so-secret-token ☺

You can always stop the server or check its status:

ketrew stop -P daemon
ketrew status -P daemon

The ketrew submit sub-command can create tiny workflows:

ketrew submit --wet-run --tag 1st-workflow --tag command-line --daemonize /tmp/KT,"du -sh $HOME"

The job will appear on the WebUI and you can inspect/restart/kill it.

If you don't like Web UI's you can use the text-based UI:

ketrew interact

The EDSL: Defining Workflows

The previous section uses ketrew submit to launch an extremely simple workflow, to go further we need the EDSL.

Overview

The EDSL is an OCaml library where all the functions are used to build a workflow data-structure. Then, one function: Ketrew.Client.submit is used to submit workflows to the engine.

A workflow is a Graph of “targets”.

There are 3 kinds of links between targets:

dependencies: targets that need to be ensured or run before a target can start,
fallbacks: targets that will be activated if the target fails, and
success-triggers: targets that will be activated only after a target succeeds.

Any OCaml program can use the EDSL (script, compiled, or even inside the toplevel), see the documentation of the EDSL API.

Example

This example is a “single-target” workflow that runs an arbitrary shell command on an LSF-based cluster:

#use "topfind"
#thread
#require "ketrew"
let run_command_with_lsf cmd =
  let module KEDSL = Ketrew.EDSL in
  let host =
    (* `Host.parse` takes an URI and creates a “Host” datastructue: a place to
       run stuff.  *)
    KEDSL.Host.parse
      "ssh://user42@MyLSFCluster/home/user42/ketrew-playground/?shell=bash"
    (* This one is an SSH host, named `MyLSFCluster`.
       The directory `/home/user42/ketrew-playground/` will be used by Ketrew
       to monitor the jobs. *)
  in
  let program =
    (* A “program” is a datastructure representing “extended shell scripts”.
       `Program.sh` creates one out a shell command. *)
    KEDSL.Program.sh cmd in
  let lsf_build_process =
    (* “build process” is a method for making things:
       `lsf` creates a datastructure that represents a job running a `program`
       with the LSF scheduling engine, on the host `host`.  *)
    KEDSL.lsf
      ~queue:"normal-people" ~wall_limit:"1:30"
      ~processors:(`Min_max (1,1)) ~host program
  in
  (* The function `KEDSL.target` creates a node in the workflow graph.
     This one is very simple, it has a name and a build-process,
     and since it doesn't have dependencies or fallbacks, it is a
     “single-node” workflow: *)
  KEDSL.target
     "run_command_with_lsf"
     ~make:lsf_build_process

let () =
  let workflow =
     (* Create the  workflow with the first argument of the command line: *)
     run_command_with_lsf Sys.argv.(1) in
  (* Then, `Client.submit` is the only function that “does” something, it
     submits the workflow to the engine: *)
  Ketrew.Client.submit workflow
  (* If Ketrew is in Standalone mode, this means writing the workflow in the
     database (nothing runs yet, you need to run Ketrew's engine yourself).
     If Ketrew is in Client-Server mode, this means sending the workflow to the
     server over HTTPS. The server will start running the workflow right away.  *)

If you actually have access to an LSF cluster and want to try this workflow, put it in a file my_second_workflow.ml, and simply:

ocaml my_second_workflow.ml 'du -sh $HOME'

To learn more about the EDSL, you can also explore examples of more and more complicated workflows (work-in-progress).

Where to Go Next

From here:

To write workflows for Ketrew, see src/test/Workflow_Examples.ml for examples and the documentation of the EDSL API.
To configure Ketrew use the configuration file documentation.
If you don't want a server running and listening on HTTP(S), Ketrew can run a degraded mode called “standalone.”
You may want to “extend” Ketrew with new ways of running “long-running" computations: see the documentation on plugins, and the examples in the library: like Ketrew.Lsf or in the tests: src/test/dummy_plugin.ml.
You may want to extend Ketrew, or preconfigure it, without configuration files or dynamically loaded libraries: just create your own comand-line app.
If you are using Ketrew in server mode, you may want to know about the commands that the server can understand as it listens on a Unix-pipe.
You may want to call out directly to the HTTP API (i.e. without ketrew as a client).
If you want to help or simply to understand Ketrew see the development documentation, and have a look at the modules like Ketrew.Engine.

License

It's Apache 2.0.

Ketrew: Home

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