Workflow Syntax and Execution Runtime

This section introduces the YAML syntax used by Popper, describes the workflow execution runtime and shows how to execute workflows in alternative container engines.

Syntax

A Popper workflow file looks like the following:

steps:
- uses: docker://alpine:3.9
  args: ["ls", "-la"]

- uses: docker://alpine:3.11
  args: ["echo", "second step"]

options:
  env:
    FOO: BAR
  secrets:
  - TOP_SECRET

A workflow specification contains one or more steps in the form of a YAML list named steps. Each item in the list is a dictionary containing at least a uses attribute, which determines the docker image being used for that step. An options dictionary specifies options that are applied to the workflow.

Workflow steps

The following table describes the attributes that can be used for a step. All attributes are optional with the exception of the uses attribute.

Attribute	Description
`uses`	required A string with the name of the image that will be executed for that step. For example, `uses: docker://node:10`. See "Referencing images in a step" section below for more examples.
`id`	optional Assigns an identifier to the step. By default, steps are assigned a numeric ID corresponding to the order of the step in the list, with `'1'` identifying the first step.
`runs`	optional A list of strings that specifies the command to run in the container. If `runs` is omitted, the command specified in the `Dockerfile`'s `ENTRYPOINT` instruction will execute. Use the `runs` attribute when the `Dockerfile` does not specify an `ENTRYPOINT` or you want to override the `ENTRYPOINT` command. The `runs` attribute does not invoke a shell by default. Using `runs: "echo $VAR"` will NOT print the value stored in `$VAR`, but will instead print `\"\$VAR.\"`. To use environment variables with the `runs` instruction, you must include a shell to expand the variables, for example: `runs: ["sh", "-c", "echo $VAR"]`. If the value of `runs` refers to a local script, the path is relative to the workspace folder (see The Workspace section below).
`args`	optional A list of strings representing the arguments to pass to the command. For example, `args: ["--flag", "--arg", "value"]`. If the value of `args` refers to a local script, the path is relative to the workspace folder (see The Workspace section below). Similarly to the `runs` attribute, if an environment variable is being referenced, in order for this reference to be valid, a shell must be invoked (in the `runs` attribute) in order to expand the value of the variable.
`env`	optional A dictionary of environment variables to set inside the container's runtime environment. For example: `env: {VAR1: FOO, VAR2: bar}`. In order to access these environment variables from a script that runs inside the container, make sure the script runs a shell (e.g. `bash`) in order to perform variable substitution.
`secrets`	optional A list of strings representing the names of secret variables to define in the environment of the container for the step. For example, `secrets: ["SECRET1", "SECRET2"]`.
`skip_pull`	optional A boolean value that determines whether to pull the image before executing the step. By default this is `false`. If the given container image already exist (e.g. because it was built by a previous step in the same workflow), assigning `true` skips downloading the image from the registry.
`dir`	optional A string representing an absolute path inside the container to use as the working directory. By default, this is `/workspace`.
`options`	optional Container configuration options. For instance: `options: {ports: {8888:8888}, interactive: True, tty: True}`. Currently only supported for the docker runtime. See the parameters of `client.containers.runs()` in the Docker Python SDK for the full list of options

Referencing images in a step

A step in a workflow can reference a container image defined in a Dockerfile that is part of the same repository where the workflow file resides. In addition, it can also reference a Dockerfile contained in public Git repository. A third option is to directly reference an image published a in a container registry such as DockerHub. Here are some examples of how you can refer to an image on a public Git repository or Docker container registry:

Template	Description
`./path/to/dir`	The path to the directory that contains the `Dockerfile`. This is a relative path with respect to the workspace directory (see The Workspace section below). Example: `./path/to/myimg/`.
`{url}/{user}/{repo}@{ref}`	A specific branch, ref, or SHA in a public Git repository. If `url` is ommited, `github.com` is used by default. Example: `https://bitbucket.com/popperized/ansible@master`.
`{url}/{user}/{repo}/{path}@{ref}`	A subdirectory in a public Git repository at a specific branch, ref, or SHA. Example: `git@gitlab.com:popperized/geni/build-context@v2.0`.
`docker://{image}:{tag}`	A Docker image published on Docker Hub. Example: `docker://alpine:3.8`.
`docker://{host}/{image}:{tag}`	A Docker image in a public registry other than DockerHub. Note that the container engine needs to have properly configured to access the referenced registry in order to download from it. Example: `docker://gcr.io/cloud-builders/gradle`.

It's strongly recommended to include the version of the image you are using by specifying a SHA or Docker tag. If you don't specify a version and the image owner publishes an update, it may break your workflows or have unexpected behavior.

In general, any Docker image can be used in a Popper workflow, but keep in mind the following:

When the runs attribute for a step is used, the ENTRYPOINT of the image is overridden.
The WORKDIR is overridden and /workspace is used instead (see The Workspace section below).
The ARG instruction is not supported, thus building an image from a Dockerfile (public or local) only uses its default value.
While it is possible to run containers that specify USER other than root, doing so might cause unexpected behavior.

Referencing private Github repositories

You can reference Dockerfiles located in private Github repositories by defining a GITHUB_API_TOKEN environment variable that the popper run command reads and uses to clone private repositories. The repository referenced in the uses attribute is assumed to be private and, to access it, an API token from Github is needed (see instructions here). The token needs to have permissions to read the private repository in question. To run a workflow that references private repositories:

export GITHUB_API_TOKEN=access_token_here
popper run -f wf.yml

If the access token doesn't have permissions to access private repositories, the popper run command will fail.

Workflow options

The options attribute can be used to specify env and secrets that are available to all the steps in the workflow. For example:

options:
  env:
    FOO: var1
    BAR: var2
  secrets: [SECRET1, SECRET2]

steps:
- uses: docker://alpine:3.11
  runs: sh
  args: ["-c", "echo $FOO $SECRET1"]

- uses: docker://alpine:3.11
  runs: sh
  args: ["-c", "echo $ONLY_FOR"]
  env:
    ONLY_FOR: this step

The above shows environment variables that are available to all steps that get defined in the options dictionary; it also shows an example of a variable that is available only to a single step (second step). This attribute is optional.

Execution Runtime

This section describes the runtime environment where a workflow executes.

The Workspace

When a step is executed, a folder in your machine is bind-mounted (shared) to the /workspace folder inside the associated container. By default, the folder being bind-mounted is $PWD, that is, the working directory from where popper run is being invoked from. If the -w (or --workspace) flag is given, then the value for this flag is used instead. See the official Docker documentation for more information about how volumes work with containers.

The following diagram illustrates this relationship between the filesystem namespace of the host (the machine where popper run is executing) and the filesystem namespace within container:

                                 Container
                                +----------------------+
                                |  /bin                |
                                |  /etc                |
                                |  /lib                |
 Host                           |  /root               |
+-------------------+   bind    |  /sys                |
|                   |   mount   |  /tmp                |
| /home/me/my/proj <------+     |  /usr                |
| ├─ wf.yml         |     |     |  /var                |
| └─ README.md      |     +------> /workspace          |
|                   |           |  ├── wf.yml          |
|                   |           |  └── README.md       |
+-------------------+           +----------------------+

For example, let's look at a workflow that creates files in the workspace:

steps:
- uses: docker://alpine:3.12
  args: [touch, ./myfile]

The above workflow has only one single step that creates the myfile file in the workspace directory if it doesn't exist, or updates its metadata if it already exists, using the touch command. Assuming the above workflow is stored in a wf.yml file in /home/me/my/proj/, we can run it by first changing the current working directory to this folder:

cd /home/me/my/proj/
popper run -f wf.yml

And this will result in having a new file in /home/me/my/proj/myfile. However, if we invoke the workflow from a different folder, the folder being bind-mounted inside the container is a different one. For example:

cd /home/me/
popper run -f /home/me/my/proj/wf.yml

In the above, the file will be written to /home/me/myfile, because we are invoking the command from /home/me/, and this path is treated as the workspace folder. If we provide a value for the --workspace flag (or its short version -w), the workspace path then changes and thus the file is written to this given location. For example:

cd /
popper run -f /home/me/my/proj/wf.yml -w /home/me/my/proj/

The above writes the /home/me/my/proj/myfile even though Popper is being invoked from /. Note that the above is equivalent to the first example of this subsection, where we first changed the directory to /home/me/my/proj and ran popper run -f wf.yml.

Changing the working directory

To specify a working directory for a step, you can use the dir attribute in the workflow, which takes as value a string representing an absolute path inside the container. This changes where the specified command is executed. For example, adding dir as follows:

steps:
- uses: docker://alpine:3.9
  args: [touch, ./myfile]
  dir: /tmp/

And assuming that it is stored in /home/me/my/proj/wf.yml, invoking the workflow as:

cd /home/me
popper run -f wf.yml -w /home/me/my/proj

Would result in writing myfile in the /tmp folder that is inside the container filesystem namespace, as opposed to writing it to /home/me/my/projc/ (the value given for the --workspace flag). As it is evident in this example, if the directory specified in the dir attribute resides outside the /workspace folder, then anything that gets written to it won't persist after the step ends its execution (see "Filesystem namespaces and persistence" below for more).

For completeness, we show an example of using dir to specify a folder within the workspace:

steps:
- uses: docker://alpine:3.9
  args: [touch, ./myfile]
  dir: /workspace/my/proj/

And executing:

cd /home/me
popper run -f wf.yml

would result in having a file in /home/me/my/proj/myfile.

Filesystem namespaces and persistence

As mentioned previously, for every step Popper bind-mounts (shares) a folder from the host (the workspace) into the /workspace folder in the container. Anything written to this folder persists. Conversely, anything that is NOT written in this folder will not persist after the workflow finishes, and the associated containers get destroyed.

Environment variables

A step can define, read, and modify environment variables. A step defines environment variables using the env attribute. For example, you could set the variables FIRST, MIDDLE, and LAST using this:

steps:
- uses: "docker://alpine:3.9"
  args: ["sh", "-c", "echo my name is: $FIRST $MIDDLE $LAST"]
  env:
    FIRST: "Jane"
    MIDDLE: "Charlotte"
    LAST: "Doe"

When the above step executes, Popper makes these variables available to the container and thus the above prints to the terminal:

my name is: Jane Charlotte Doe

Note that these variables are only visible to the step defining them and any modifications made by the code executed within the step are not persisted between steps (i.e. other steps do not see these modifications).

Git Variables

When Popper executes insides a git repository, it obtains information related to Git. These variables are prefixed with GIT_ (e.g. to GIT_COMMIT or GIT_BRANCH).

Exit codes and statuses

Exit codes are used to communicate about a step's status. Popper uses the exit code to set the workflow execution status, which can be success, neutral, or failure:

Exit code	Status	Description
`0`	`success`	The step completed successfully and other tasks that depends on it can begin.
`78`	`neutral`	The configuration error exit status (`EX_CONFIG`) indicates that the step terminated but did not fail. For example, a filter step can use a `neutral` status to stop a workflow if certain conditions aren't met. When a step returns this exit status, Popper terminates all concurrently running steps and prevents any future steps from starting. The associated check run shows a `neutral` status, and the overall check suite will have a status of `success` as long as there were no failed or cancelled steps.
All other	`failure`	Any other exit code indicates the step failed. When a step fails, all concurrent steps are cancelled and future steps are skipped. The check run and check suite both get a `failure` status.

Container Engines

By default, Popper workflows run in Docker on the machine where popper run is being executed (i.e. the host machine). This section describes how to execute in other container engines. See next section for information on how to run workflows on resource managers such as SLURM and Kubernetes.

To run workflows on other container engines, an --engine <engine> flag for the popper run command can be given, where <engine> is one of the supported ones. When no value for this flag is given, Popper executes workflows in Docker. Below we briefly describe each container engine supported, and lastly describe how to pass engine-specific configuration options via the --conf flag.

Docker

Docker is the default engine used by the popper run. All the container configuration for the docker engine is supported by Popper. Popper also supports running workflows on remote docker daemons by use of the DOCKER_HOST, DOCKER_TLS_VERIFY and DOCKER_CERT_PATH variables, as explained in the official documentation. For example:

export DOCKER_HOST="ssh://myuser@hostname"
popper run -f wf.yml

The above runs the workflow on the hostname machine instead of locally. It assumes the following:

myuser has passwordless access to hostname, otherwise the password to the machine is requested.
The myuser account can run docker on the remote machine.

Singularity

Popper can execute a workflow in systems where Singularity 3.2+ is available. To execute a workflow in Singularity containers:

popper run --engine singularity

Limitations

The use of ARG in Dockerfiles is not supported by Singularity.
The --reuse flag of the popper run command is not supported.

Host

There are situations when executing a command directly on the host where the popper command is running. This is done by making use of the special sh value for the uses attribute. This value instructs Popper to execute the command or script given in the runs attribute directly on the host. For example:

steps:
- uses: "sh"
  runs: ["ls", "-la"]

- uses: "sh"
  runs: "./path/to/my/script.sh"
  args: ["some", "args", "to", "the", "script"]

In the first step above, the ls -la command is executed on the workspace folder (see "The Workspace" section). The second one shows how to execute a script. Note that the command or script specified in the runs attribute are NOT executed in a shell. If you need a shell, you have to explicitly invoke one, for example:

steps:
- uses: sh
  runs: [bash, -c, 'sleep 10 && true && exit 0']

The obvious downside of running a step on the host is that, depending on the command being executed, the workflow might not be portable.

Custom engine configuration

Other than bind-mounting the /workspace folder, Popper runs containers with any default configuration provided by the underlying engine. However, a --conf flag is provided by the popper run command to specify custom options for the underlying engine in question (see here for more).

Alternatively, to restrict a configuration to a specific step in a workflow, set the desired parameters in the step's options Note: this is currently only supported for the Docker runtime

Resource Managers

By default, workflows are executed locally on the host where Popper is executed from. In addition, workflows can also be executed through other resource managers. The resource manager can be specified either through the --resource-manager/-r option, or specified in the configuration file given via the --config/-c flag. If neither of them are provided, the steps are run in the host machine by default.

Kubernetes

Popper enables leveraging the compute and storage capabilities of the cloud by allowing running workflows on Kubernetes clusters. Users need to have access to a cluster config file in order to run workflows on Kubernetes. This file can be provided by a system administrator.

Popper provisions all the required resources and orchestrates the entire workflow execution. When a workflow is executed, Popper first creates a persistent volume claim, spawns an init pod and uses it to copy the workflow context (packed in the form of a .tar.gz file) into the persistent volume and then unpacks the context there. Subsequently, Popper tears down the init pod and executes the steps of a workflow in separate pods of their own. After the execution of each step, the respective pods are deleted but the persistent volume claim is not deleted so that it can be reused by subsequent workflow executions.

For running workflows on Kubernetes, several configuration options can be passed to the Kubernetes resource manager through the Popper configuration file to customize the execution environment. All the available configuration options have been described below:

namespace: The namespace within which to provision resources like PVCs and Pods for workflow execution. If not provided the default namespace will be used.
persistent_volume_name: Any pre-provisioned persistent volume like an NFS or EBS volume can be supplied through this option. Popper will then claim storage space from the supplied persistent volume. In the default case, a HostPath persistent volume of 1GB with a name of the form pv-hostpath-popper-<workflowid> will be created by Popper automatically.
volume_size: The amount of storage space to claim from a persistent volume for use by a workflow. The default is 500MB.
pod_host_node: The node on which to restrict the deployment of all the pods. This option is important when a HostPath persistent volume is used. In this case, users need to restrict all the pods to a particular node. If this option is not provided, Popper will leave the task of scheduling the pods upon Kubernetes. The exception to this is, when both the pod_host_node and persistent_volume_name options are not provided, Popper will try to find out a pod and schedule all the pods (init-pods + step-pods) on that node to use the HostPath persistent volume of 1GB which will be automatically created.
hostpathvol_path: The path to use for creating a HostPath volume. If not provided, /tmp will be used.
hostpathvol_size: The size of the HostPath volume. If not provided, 1GB will be used.

To run workflows on Kubernetes:

$ popper run -f wf.yml -r kubernetes

Limitations

A workflow cannot build local Dockerfiles. In order to work around this issue, a workflow can build an image using BuildKit or Kaniko as explained here.

SLURM

Popper workflows can run on HPC (Multi-Node environments) using Slurm as the underlying resource manager to distribute the execution of a step to several nodes. You can get started with running Popper workflows through Slurm by following the example below.

NOTE: Set the POPPER_CACHE_DIR environment variable to /path/to/shared/.cache while running a workflow on multiple nodes.

Let's consider a workflow sample.yml like the one shown below.

steps:
- id: one
  uses: docker://alpine:3.9
  args: ["echo", "hello-world"]

- id: two
  uses: popperized/bin/sh@master
  args: ["ls", "-l"]

To run all the steps of the workflow through SLURM resource manager, use the --resource-manager or -r option of the popper run subcommand to specify the resource manager.

popper run -f sample.yml -r slurm

This runs the workflow on a single compute node in the cluster which is also the default scenario when no specific configuration is provided.

To have more finer control on which steps to run through SLURM resource manager, the specifications can be provided through the config file as shown below.

We create a config file called config.yml with the following contents.

engine:
  name: docker
  options:
    privileged: True
    hostname: example.local

resource_manager:
  name: slurm
  options:
    two:
      nodes: 2

Now, we execute popper run with this config file as follows:

popper run -f sample.yml -c config.yml

This runs the step one locally in the host and step two through SLURM on any 2 compute nodes. If singularity is used as the container engine, then by default the steps would run using MPI as SLURM jobs. This behaviour can be overriden by passing mpi: false in the configuration of the step for which MPI is not required.

Life of a Workflow

This section explains what popper does when it executes a workflow. We will break down what popper does behind the scenes when executing the following sample workflow, which can be found here:

steps:
# download CSV file with data on global CO2 emissions
- id: download
  uses: docker://byrnedo/alpine-curl:0.1.8
  args: [-LO, https://github.com/datasets/co2-fossil-global/raw/master/global.csv]

# obtain the transpose of the global CO2 emissions table
- id: get-transpose
  uses: docker://getpopper/csvtool:2.4
  args: [transpose, global.csv, -o, global_transposed.csv]

Each step of a workflow has the following stages:

1. Look at `uses` attribute and pull/build image

Each step of a workflow must specify the DockerFile or Docker image it will use to create a container with a uses line. For example, the first step of our example workflow contains the following line:

uses: docker://byrnedo/alpine-curl:0.1.8

These statements may refer to a Dockerfile inside the same repository as the workflow; a Dockerfile inside an external, public repository or container registry; or an image in a registry.

The example uses line above would result in the following output from Popper:

[download] docker pull byrnedo/alpine-curl:0.1.8

This line indicates that the necessary image was successfully pulled by docker. If the image needs to be built from a Dockerfile, it will do so at this stage.

Popper would run this command under the hood if the engine used is Docker:

docker pull byrnedo/alpine-curl:0.1.8

and it would run this command if the engine is singularity:

singularity pull popper_download_f20ab8c9.sif docker://byrnedo/alpine-curl:0.1.8

The workings and limitations of uses and other possible attributes for a workflow are outlined here.

2. Configure and create container

Popper instantiates containers in the underlying engine (with Docker as the default) using basic configurations options. The underlying engine configuration can be modified using a configuration file. Learn more about configuring the engine here.

In the example workflow, the first step contains the following lines, one for the id (which is used as the name of the step) and one for the args:

id: download

args: [-LO, https://github.com/datasets/co2-fossil-global/raw/master/global.csv]

Using these inputs, Popper executes the following command for a Docker build:

docker create name=popper_download_f20ab8c9 byrnedo/alpine-curl:0.1.8 -LO https://github.com/datasets/co2-fossil-global/raw/master/global.csv

This creates a docker container from the image given by the uses line with inputs from the args line, and with a name created using the id given in the id line and the id number of our specific workflow.

3. Launch container

Popper launches the container, waits for it to be done, and then prints the resulting output.

In the example workflow, the first step is run with the following commands when running in Docker and Singularity engines, respectively:

docker start

singularity run popper_download_f20ab8c9.sif (-LO, https://github.com/datasets/co2-fossil-global/raw/master/global.csv)

This produces the following output:

[download] docker start
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   144    0   144    0     0    500      0 --:--:-- --:--:-- --:--:--   500
100  6453  100  6453    0     0  10509      0 --:--:-- --:--:-- --:--:-- 25709
Step 'download' ran successfully !

4. Move on to next step

The above three stages comprise a single step in a workflow's execution. As workflows can be made up of multiple steps, the workflow continues its execution by progressing to its next step, which contains its own uses and configurations for its containers and operations. Thus, your average workflow looks something like this:

steps:
- id: <optional step name>
  uses: <some local/public repository or container registry>
  args: [<command>, ..., <command>]

- id: <Optional step name>
  uses: <some local/public repository or container registry>
  args: [<command>, ..., <command>]
  .
  .
  .

The workflow repeats the same three stages for each step in the process. Consequently, the next step of our example workflow produces the following output:

[get-transpose] docker pull getpopper/csvtool:2.4
[get-transpose] docker create name=popper_get-transpose_f20ab8c9 image=getpopper/csvtool:2.4 command=['transpose', 'global.csv', '-o', 'global_transposed.csv']
[get-transpose] docker start
Step 'get-transpose' ran successfully !
Workflow finished successfully.

Once the workflow has executed all of its outlined steps, its lifecycle is complete!

Conclusion

Hopefully this section has clarified how a Popper workflow iterates through its steps to simplify any workflow into a simple popper run call. Not only does it allow you to run fewer commands per run, it also runs the correct commands for different engines based on whether you're using Docker or Singularity.

Thus, Popper can be a useful tool for increasing efficiency on any workflow-heavy project!

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cn_workflows.md

cn_workflows.md

Workflow Syntax and Execution Runtime

Syntax

Workflow steps

Referencing images in a step

Referencing private Github repositories

Workflow options

Execution Runtime

The Workspace

Changing the working directory

Filesystem namespaces and persistence

Environment variables

Git Variables

Exit codes and statuses

Container Engines

Docker

Singularity

Limitations

Host

Custom engine configuration

Resource Managers

Kubernetes

Limitations

SLURM

Life of a Workflow

1. Look at `uses` attribute and pull/build image

2. Configure and create container

3. Launch container

4. Move on to next step

Conclusion

Files

cn_workflows.md

Latest commit

History

cn_workflows.md

File metadata and controls

Workflow Syntax and Execution Runtime

Syntax

Workflow steps

Referencing images in a step

Referencing private Github repositories

Workflow options

Execution Runtime

The Workspace

Changing the working directory

Filesystem namespaces and persistence

Environment variables

Git Variables

Exit codes and statuses

Container Engines

Docker

Singularity

Limitations

Host

Custom engine configuration

Resource Managers

Kubernetes

Limitations

SLURM

Life of a Workflow

1. Look at uses attribute and pull/build image

2. Configure and create container

3. Launch container

4. Move on to next step

Conclusion

1. Look at `uses` attribute and pull/build image