What is Merlin?

Merlin is a distributed task queue system designed to facilitate the large scale execution of HPC ensembles, like those needed to build machine learning models of complex simulations.

Where can I get help with Merlin?

In addition to this documentation, the Merlin developers can be reached at merlin@llnl.gov. You can also reach out to the merlin user group mailing list: merlin-users@listserv.llnl.gov.

Setup & Installation

How can I build Merlin?

Merlin can be installed via pip in a python virtual environment or via spack.

See Getting started.

Do I have to build Merlin?

If you’re at LLNL and want to run on LC, you can use one of the public deployments. For more information, check out the LLNL access page in confluence.

What are the setup instructions at LLNL?

See “Do I have to build Merlin”

How do I reconfigure for different servers?

The server configuration is set in ~/.merlin/app.yaml. Details can be found here.

Component Technology

What underlying libraries does Merlin use?

What security features are in Merlin?

Merlin encrypts network traffic of step results, implying that all results are encrypted with a unique user-based key, which is auto-generated and placed in ~/.merlin/. This allows for multiple users to share a results database. This is important since some backends, like redis do not allow for multiple distinct users.

What is celery?

Celery is an asynchronous task/job queue based on distributed message passing. It is focused on real-time operation, but supports scheduling as well. See Celery’s GitHub page and Celery’s website for more details.

What is maestro?

Maestro is a tool and library for specifying and conducting general workflows. See Maestro’s GitHub page for more details.

Designing and Building Workflows

yaml specification file

Where are some example workflows?

$ merlin example list

How do I launch a workflow?

To launch a workflow locally, use merlin run --local <spec>. To launch a distributed workflow, use merlin run-workers <spec>, and merlin run <spec>. These may be done in any order.

How do I describe workflows in Merlin?

A Merlin workflow is described with a yaml specification file.

What is a DAG?

DAG is an acronym for ‘directed acyclic graph’. This is the way your workflow steps are represented as tasks.

What if my workflow can’t be described by a DAG?

There are certain workflows that cannot be explicitly defined by a single DAG; however, in our experience, many can. Furthermore, those workflows that cannot usually do employ DAG sub-components. You probably can gain much of the functionality you want by combining a DAG with control logic return features (like step restart and additional calls to merlin run).

How do I implement workflow looping / iteration?

Combining exit $(MERLIN_RETRY) with max_retries can allow you to loop a single step. Entire workflow looping / iteration can be accomplished by finishing off your DAG with a final step that makes another call to merlin run.

Can steps be restarted?

Yes. To build this into a workflow, use exit $(MERLIN_RETRY) within a step to retry a failed cmd section. The max number of retries in given step can be specified with the max_retries field.

Alternatively, use exit $(MERLIN_RESTART) to run the optional <step>.run.restart section.

To delay a retry or restart directive, add the retry_delay field to the step. Note: retry_delay only works in server mode (ie not --local mode).

To restart failed steps after a workflow is done running, see How do I re-run failed steps in a workflow?.

How do I put a time delay in before a restart or retry?

Add the retry_delay field to the step. This specifies how many seconds before the task gets run after the restart. Set this value to large enough for your problem to finish.

See the merlin example restart_delay example for syntax.

Note: retry_delay only works in server mode (ie not --local mode).

I have a long running batch task that needs to restart, what should I do?

Before your allocation ends, use $(MERLIN_RESTART) or $(MERLIN_RETRY) but with a retry_delay on your step for longer that your allocation has left. The server will hold onto the step for that long (in seconds) before releasing it, allowing your batch allocation to end without the worker grabbing the step right away.

For instance, your step could look something like this

name: batch_task
description: A long running task that needs to restart
    cmd: |
        # Run my code, but end 60 seconds before my allocation
        my_code --end_early 60s
        if [ -e restart_needed_flag ]; then
            exit $(MERLIN_RESTART)
    retry_delay: 120 # wait at least 2 minutes before restarting

How do I mark a step failure?

Each step is ultimately designated as: * a success $(MERLIN_SUCCESS) – writes a MERLIN_FINISHED file to the step’s workspace directory * a soft failure $(MERLIN_SOFT_FAIL) – allows the workflow to continue * a hard failure $(MERLIN_HARD_FAIL) – stops the whole workflow by shutting down all workers on that step

Normally this happens behinds the scenes, so you don’t need to worry about it. To hard-code this into your step logic, use a shell command such as exit $(MERLIN_HARD_FAIL).


The $(MERLIN_HARD_FAIL) exit code will shutdown all workers connected to the queue associated with the failed step. To shutdown all workers use the $(MERLIN_STOP_WORKERS) exit code

To rerun all failed steps in a workflow, see How do I re-run failed steps in a workflow?. If you really want a previously successful step to be re-run, you can first manually remove the MERLIN_FINISHED file.

What fields can be added to steps?

Steps have a name, description, and run field, as shown below.

name: <string>
description: <string>
    cmd: <shell command for this step>

Also under run, the following fields are optional:

    depends: <list of step names>
    task_queue: <task queue name for this step>
    shell: <e.g., /bin/bash, /usr/bin/env python3>
    max_retries: <integer>
    retry_delay: <integer: seconds>
    nodes: <integer>
    procs: <integer>

How do I specify the language used in a step?

You can add the field shell under the run portion of your step to change the language you write your step in. The default is /bin/bash, but you can do things like /usr/bin/env python as well. Use merlin example feature_demo to see an example of this.

Running Workflows

$ merlin run <yaml file>

For more details, see Merlin commands.

How do I set up a workspace without executing step scripts?

$ merlin run --dry <yaml file>

How do I start workers?

$ merlin run-workers <yaml file>

How do I see what workers are connected?

$ merlin query-workers

This command gives you fine control over which workers you’re looking for via a regex on their name, the queue names associated with workers, or even by providing the name of a spec file where workers are defined.

For more info, see Searching for any workers (merlin query-workers).

How do I stop workers?

Interactively outside of a workflow (e.g. at the command line), you can do this with

$ merlin stop-workers

This gives you fine control over which kinds of workers to stop, for instance via a regex on their name, or the queue names you’d like to stop.

From within a step, you can exit with the $(MERLIN_STOP_WORKERS) code, which will issue a time-delayed call to stop all of the workers, or with the $(MERLIN_HARD_FAIL) directive, which will stop all workers connected to the current step. This helps prevent the suicide race condition where a worker could kill itself before removing the step from the workflow, causing the command to be left there for the next worker and creating a really bad loop.

You can of course call merlin stop-workers from within a step, but be careful to make sure the worker executing it won’t be stopped too.

For more tricks, see Stopping workers (merlin stop-workers).

How do I re-run failed steps in a workflow?

$ merlin restart <spec>

What tasks are in my queue?

How do I purge tasks?

$ merlin purge <yaml file>

Why is stuff still running after I purge?

You probably have workers executing tasks. Purging removes them from the server queue, but any currently running or reserved tasks are being held by the workers. You need to shut down these workers first:

$ merlin stop-workers
$ merlin purge <yaml file>

Why am I running old tasks?

You might have old tasks in your queues. Try merlin purge <yaml>. You might also have rogue workers. To find out, try merlin query-workers.

Where do tasks get run?

Can I run different steps from my workflow on different machines?

Yes. Under the merlin block you can specify which machines your workers are allowed on. In order for this to work, you must then use merlin run-workers separately on each of the specified machines.

            machines: [hostA, hostB, hostC]

What is Slurm?

A job scheduler. See Slurm documentation .

What is LSF?

Another job scheduler. See IBM’s LSF documentation .

What is flux?

Flux is a hierarchical scheduler and launcher for parallel simulations. It allows the user to specify the same launch command that will work on different HPC clusters with different default schedulers such as SLURM or LSF. Merlin versions earlier than 1.9.2 used the non-flux native scheduler to launch a flux instance. Subsequent merlin versions can launch the merlin workers using a native flux scheduler. More information can be found at the Flux web page.

Older versions of flux may need the --mpi=none argument if flux is launched on a system using the SLURM scheduler. This argument can be added in the launch_args variable in the batch section.

  type: flux
  launch_args: --mpi=none

What is PBS?

Another job scheduler. See Portable Batch System . This functionality is only available to launch a flux scheduler.

How do I use flux on LC?

The --mpibind=off option is currently required when using flux with a slurm launcher on LC toss3 systems. Set this in the batch section as shown in the example below.

  type: flux
  launch_args: --mpibind=off


$LAUNCHER is a reserved word that may be used in a step command. It serves as an abstraction to launch a job with parallel schedulers like What is Slurm?, What is LSF?, and What is flux?.

How do I use LAUNCHER?

Instead of this:

    cmd: srun -N 1 -n 3 python script.py

Do something like this:

    type: slurm

    cmd: $(LAUNCHER) python script.py
    nodes: 1
    procs: 3

The arguments the LAUNCHER syntax will use:

procs: The total number of MPI tasks

nodes: The total number of MPI nodes

walltime: The total walltime of the run (hh:mm:ss or mm:ss or ss) (not available in lsf)

cores per task: The number of hardware threads per MPI task

gpus per task: The number of GPUs per MPI task

SLURM specific run flags:

slurm: Verbatim flags only for the srun parallel launch (srun -n <nodes> -n <procs> <slurm>)

FLUX specific run flags:

flux: Verbatim flags for the flux parallel launch (flux mini run <flux>)

LSF specific run flags:

bind: Flag for MPI binding of tasks on a node (default: -b rs)

num resource set: Number of resource sets

launch_distribution: The distribution of resources (default: plane:{procs/nodes})

lsf: Verbatim flags only for the lsf parallel launch (jsrun … <lsf>)

What is level_max_dirs?

level_max_dirs is an optional field that goes under the merlin.samples section of a yaml spec. It caps the number of sample directories that can be generated at a single level of a study’s sample hierarchy. This is useful for getting around filesystem constraints when working with massive amounts of data.

Defaults to 25.

What is pgen?

pgen stands for “parameter generator”. It’s a way to override the parameters in the global.parameters spec section, instead generating them programatically with a python script. Merlin offers the same pgen functionality as Maestro.

See this guide for details on using pgen. It’s a Maestro doc, but the exact same flags can be used in conjunction with merlin run.

Where can I learn more about merlin?

Check out our paper on arXiv.