Help for package crew.aws.batch

Title:

A Crew Launcher Plugin for AWS Batch

Description:

In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.aws.batch' package extends the 'mirai'-powered 'crew' package with a worker launcher plugin for AWS Batch. Inspiration also comes from packages 'mirai' by Gao (2023) https://github.com/r-lib/mirai, 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) https://github.com/mrc-ide/rrq, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>.

Version:

0.1.0

License:

MIT + file LICENSE

URL:

https://wlandau.github.io/crew.aws.batch/, https://github.com/wlandau/crew.aws.batch

BugReports:

https://github.com/wlandau/crew.aws.batch/issues

Depends:

R (≥ 4.0.0)

Imports:

cli (≥ 3.1.0), crew (≥ 1.3.0), paws.common (≥ 0.7.0), paws.compute, paws.management, R6, rlang, tibble, utils

Suggests:

knitr (≥ 1.30), markdown (≥ 1.1), rmarkdown (≥ 2.4), testthat (≥ 3.0.0)

Encoding:

UTF-8

Language:

en-US

Config/testthat/edition:

RoxygenNote:

7.3.3

NeedsCompilation:

Packaged:

2025-09-15 12:31:28 UTC; C240390

Author:

William Michael Landau

[aut, cre], Eli Lilly and Company [cph, fnd]

Maintainer:

William Michael Landau <will.landau.oss@gmail.com>

Repository:

CRAN

Date/Publication:

2025-09-15 12:50:09 UTC

crew.aws.batch: a crew launcher plugin for AWS Batch

Description

Terminate an AWS Batch job.

Description

Not a user-side function. For internal use only.

Usage

crew_aws_batch_job_name(name)

Arguments

name

Character string, an AWS Batch job name, possibly invalid.

Value

Character string, a valid AWS Batch job name.

AWS Batch definition class

Description

AWS Batch definition R6 class

Details

See crew_definition_aws_batch().

IAM policies

In order for the AWS Batch crew job definition class to function properly, your IAM policy needs permission to perform the RegisterJobDefinition, DeregisterJobDefinition, and DescribeJobDefinitions AWS Batch API calls. For more information on AWS policies and permissions, please visit https://docs.aws.amazon.com/IAM/latest/UserGuide/access_policies.html.

Active bindings

job_queue: See crew_definition_aws_batch().
job_definition: See crew_definition_aws_batch().
log_group: See crew_definition_aws_batch().
config: See crew_definition_aws_batch().
credentials: See crew_definition_aws_batch().
endpoint: See crew_definition_aws_batch().
region: See crew_definition_aws_batch().

Methods

Public methods

crew_class_definition_aws_batch$new()
crew_class_definition_aws_batch$validate()
crew_class_definition_aws_batch$register()
crew_class_definition_aws_batch$deregister()
crew_class_definition_aws_batch$describe()
crew_class_definition_aws_batch$submit()

Method `new()`

AWS Batch job definition constructor.

Usage

crew_class_definition_aws_batch$new(
  job_queue = NULL,
  job_definition = NULL,
  log_group = NULL,
  config = NULL,
  credentials = NULL,
  endpoint = NULL,
  region = NULL
)

Arguments

job_queue: See crew_definition_aws_batch().
job_definition: See crew_definition_aws_batch().
log_group: See crew_definition_aws_batch().
config: See crew_definition_aws_batch().
credentials: See crew_definition_aws_batch().
endpoint: See crew_definition_aws_batch().
region: See crew_definition_aws_batch().

Returns

AWS Batch job definition object.

Method `validate()`

Validate the object.

Usage

crew_class_definition_aws_batch$validate()

Returns

NULL (invisibly). Throws an error if a field is invalid.

Method `register()`

Usage

crew_class_definition_aws_batch$register(
  image,
  platform_capabilities = "EC2",
  memory_units = "gigabytes",
  memory = NULL,
  cpus = NULL,
  gpus = NULL,
  seconds_timeout = NULL,
  scheduling_priority = NULL,
  tags = NULL,
  propagate_tags = NULL,
  parameters = NULL,
  job_role_arn = NULL,
  execution_role_arn = NULL
)

Arguments

image: Character of length 1, Docker image used for each job. You can supply a path to an image in Docker Hub or the full URI of an image in an Amazon ECR repository.
platform_capabilities: Optional character of length 1, either "EC2" to run on EC2 or "FARGATE" to run on Fargate.
memory_units: Character of length 1, either "gigabytes" or "mebibytes" to set the units of the memory argument. "gigabytes" is simpler for EC2 jobs, but Fargate has strict requirements about specifying exact amounts of mebibytes (MiB). for details, read https://docs.aws.amazon.com/cli/latest/reference/batch/register-job-definition.html # nolint
memory: Positive numeric of length 1, amount of memory to request for each job.
cpus: Positive numeric of length 1, number of virtual CPUs to request for each job.
gpus: Positive numeric of length 1, number of GPUs to request for each job.
seconds_timeout: Optional positive numeric of length 1, number of seconds until a job times out.
scheduling_priority: Optional nonnegative integer of length 1 between 0 and 9999, priority of jobs. Jobs with higher-valued priorities are scheduled first. The priority only applies if the job queue has a fair share policy. Set to NULL to omit.
tags: Optional character vector of tags.
propagate_tags: Optional logical of length 1, whether to propagate tags from the job or definition to the ECS task.
parameters: Optional character vector of key-value pairs designating parameters for job submission.
job_role_arn: Character of length 1, Amazon resource name (ARN) of the job role.
execution_role_arn: Character of length 1, Amazon resource name (ARN) of the execution role.

Details

The register() method registers a simple job definition using the job definition name and log group originally supplied to crew_definition_aws_batch(). Job definitions created with ⁠$register()⁠ are container-based and use the AWS log driver. For more complicated kinds of jobs, we recommend skipping register(): first call https://www.paws-r-sdk.com/docs/batch_register_job_definition/ to register the job definition, then supply the job definition name to the job_definition argument of crew_definition_aws_batch().

Returns

A one-row tibble with the job definition name, ARN, and revision number of the registered job definition.

Method `deregister()`

Attempt to deregister a revision of the job definition.

Usage

crew_class_definition_aws_batch$deregister(revision = NULL)

Arguments

revision: Finite positive integer of length 1, optional revision number to deregister. If NULL, then only the highest revision number of the job definition is deregistered, if it exists.

Details

Attempt to deregister the job definition whose name was originally supplied to the job_definition argument of crew_definition_aws_batch().

Returns

NULL (invisibly).

Method `describe()`

Describe the revisions of the job definition.

Usage

crew_class_definition_aws_batch$describe(revision = NULL, active = FALSE)

Arguments

revision: Positive integer of length 1, optional revision number to describe.
active: Logical of length 1, whether to filter on just the active job definition.

Returns

A tibble with job definition information. There is one row per revision. Some fields may be nested lists.

Method `submit()`

Submit an AWS Batch job with the given job definition.

Usage

crew_class_definition_aws_batch$submit(
  command = c("sleep", "300"),
  name = paste0("crew-aws-batch-job-", crew::crew_random_name()),
  cpus = NULL,
  gpus = NULL,
  memory_units = "gigabytes",
  memory = NULL,
  seconds_timeout = NULL,
  share_identifier = NULL,
  scheduling_priority_override = NULL,
  tags = NULL,
  propagate_tags = NULL,
  parameters = NULL
)

Arguments

command: Character vector with the command to submit for the job. Usually a Linux shell command with each term in its own character string.
name: Character of length 1 with the job name.
cpus: Positive numeric of length 1, number of virtual CPUs to request for each job.
gpus: Positive numeric of length 1, number of GPUs to request for each job.
memory_units: Character of length 1, either "gigabytes" or "mebibytes" to set the units of the memory argument. "gigabytes" is simpler for EC2 jobs, but Fargate has strict requirements about specifying exact amounts of mebibytes (MiB). for details, read https://docs.aws.amazon.com/cli/latest/reference/batch/register-job-definition.html # nolint
memory: Positive numeric of length 1, amount of memory to request for each job.
seconds_timeout: Optional positive numeric of length 1, number of seconds until a job times out.
share_identifier: Character of length 1 with the share identifier of the job. Only applies if the job queue has a scheduling policy. Read the official AWS Batch documentation for details.
scheduling_priority_override: Optional nonnegative integer of length between 0 and 9999, priority of the job. This value overrides the priority in the job definition. Jobs with higher-valued priorities are scheduled first. The priority applies if the job queue has a fair share policy. Set to NULL to omit.
tags: Optional character vector of tags.
propagate_tags: Optional logical of length 1, whether to propagate tags from the job or definition to the ECS task.
parameters: Optional character vector of key-value pairs designating parameters for job submission.

Details

This method uses the job queue and job definition that were supplied through crew_definition_aws_batch(). Any jobs submitted this way are different from the crew workers that the crew controller starts automatically using the AWS Batch launcher plugin. You may use the submit() method in the definition for different purposes such as testing.

Returns

A one-row tibble with the name, ID, and Amazon resource name (ARN) of the job.

AWS Batch launcher class

Description

AWS Batch launcher R6 class

Details

See crew_launcher_aws_batch().

IAM policies

In order for the AWS Batch crew plugin to function properly, your IAM policy needs permission to perform the SubmitJob and TerminateJob AWS Batch API calls. For more information on AWS policies and permissions, please visit https://docs.aws.amazon.com/IAM/latest/UserGuide/access_policies.html.

AWS arguments

The AWS Batch controller and launcher accept many arguments which start with "aws_batch_". These arguments are AWS-Batch-specific parameters forwarded directly to the submit_job() method for the Batch client in the paws.compute R package

For a full description of each argument, including its meaning and format, please visit https://www.paws-r-sdk.com/docs/batch_submit_job/. The upstream API documentation is at https://docs.aws.amazon.com/batch/latest/APIReference/API_SubmitJob.html and the analogous CLI documentation is at https://docs.aws.amazon.com/cli/latest/reference/batch/submit-job.html.

The actual argument names may vary slightly, depending on which : for example, the aws_batch_job_definition argument of the crew AWS Batch launcher/controller corresponds to the jobDefinition argument of the web API and paws.compute::batch()$submit_job(), and both correspond to the --job-definition argument of the CLI.

Verbosity

Control verbosity with the paws.log_level global option in R. Set to 0 for minimum verbosity and 3 for maximum verbosity.

Super class

crew::crew_class_launcher -> crew_class_launcher_aws_batch

Active bindings

options_aws_batch: See crew_launcher_aws_batch().

Methods

Public methods

crew_class_launcher_aws_batch$new()
crew_class_launcher_aws_batch$validate()
crew_class_launcher_aws_batch$launch_workers()

Inherited methods

Method `new()`

Abstract launcher constructor.

Usage

crew_class_launcher_aws_batch$new(
  name = NULL,
  workers = NULL,
  seconds_interval = NULL,
  seconds_timeout = NULL,
  seconds_launch = NULL,
  seconds_idle = NULL,
  seconds_wall = NULL,
  tasks_max = NULL,
  tasks_timers = NULL,
  reset_globals = NULL,
  reset_packages = NULL,
  reset_options = NULL,
  garbage_collection = NULL,
  tls = NULL,
  processes = NULL,
  r_arguments = NULL,
  options_metrics = NULL,
  options_aws_batch = NULL
)

Arguments

name: See crew_launcher_aws_batch().
workers: See crew_launcher_aws_batch().
seconds_interval: See crew_launcher_aws_batch().
seconds_timeout: See crew_launcher_aws_batch().
seconds_launch: See crew_launcher_aws_batch().
seconds_idle: See crew_launcher_aws_batch().
seconds_wall: See crew_launcher_aws_batch().
tasks_max: See crew_launcher_aws_batch().
tasks_timers: See crew_launcher_aws_batch().
reset_globals: Deprecated. See crew_launcher_aws_batch().
reset_packages: Deprecated. See crew_launcher_aws_batch().
reset_options: Deprecated. See crew_launcher_aws_batch().
garbage_collection: Deprecated. See crew_launcher_aws_batch().
tls: See crew_launcher_aws_batch().
processes: See crew_launcher_aws_batch().
r_arguments: See crew_launcher_aws_batch().
options_metrics: See crew_launcher_aws_batch().
options_aws_batch: See crew_launcher_aws_batch().

Returns

An abstract launcher object.

Method `validate()`

Validate the launcher.

Usage

crew_class_launcher_aws_batch$validate()

Returns

NULL (invisibly). Throws an error if a field is invalid.

Method `launch_workers()`

Launch a local process worker which will dial into a socket.

Usage

crew_class_launcher_aws_batch$launch_workers(call, n)

Arguments

call: Character string, a namespaced call to crew::crew_worker() which will run in the worker and accept tasks.
n: Integer of length 1, number of workers to launch in the array job for the current round of auto-scaling.

Details

The call argument is R code that will run to initiate the worker.

Returns

A handle object to allow the termination of the worker later on.

AWS Batch monitor class

Description

AWS Batch monitor R6 class

Details

See crew_monitor_aws_batch().

IAM policies

In order for the AWS Batch crew monitor class to function properly, your IAM policy needs permission to perform the SubmitJob, TerminateJob, ListJobs, and DescribeJobs AWS Batch API calls. In addition, to download CloudWatch logs with the log() method, your IAM policy also needs permission to perform the GetLogEvents CloudWatch logs API call. For more information on AWS policies and permissions, please visit https://docs.aws.amazon.com/IAM/latest/UserGuide/access_policies.html.

Active bindings

job_queue: See crew_monitor_aws_batch().
job_definition: See crew_monitor_aws_batch().
log_group: See crew_monitor_aws_batch().
config: See crew_monitor_aws_batch().
credentials: See crew_monitor_aws_batch().
endpoint: See crew_monitor_aws_batch().
region: See crew_monitor_aws_batch().

Methods

Public methods

crew_class_monitor_aws_batch$new()
crew_class_monitor_aws_batch$validate()
crew_class_monitor_aws_batch$terminate()
crew_class_monitor_aws_batch$status()
crew_class_monitor_aws_batch$log()
crew_class_monitor_aws_batch$jobs()
crew_class_monitor_aws_batch$active()
crew_class_monitor_aws_batch$inactive()
crew_class_monitor_aws_batch$submitted()
crew_class_monitor_aws_batch$pending()
crew_class_monitor_aws_batch$runnable()
crew_class_monitor_aws_batch$starting()
crew_class_monitor_aws_batch$running()
crew_class_monitor_aws_batch$succeeded()
crew_class_monitor_aws_batch$failed()

Method `new()`

AWS Batch job definition constructor.

Usage

crew_class_monitor_aws_batch$new(
  job_queue = NULL,
  job_definition = NULL,
  log_group = NULL,
  config = NULL,
  credentials = NULL,
  endpoint = NULL,
  region = NULL
)

Arguments

job_queue: See crew_monitor_aws_batch().
job_definition: See crew_monitor_aws_batch().
log_group: See crew_monitor_aws_batch().
config: See crew_monitor_aws_batch().
credentials: See crew_monitor_aws_batch().
endpoint: See crew_monitor_aws_batch().
region: See crew_monitor_aws_batch().

Returns

AWS Batch job definition object.

Method `validate()`

Validate the object.

Usage

crew_class_monitor_aws_batch$validate()

Returns

NULL (invisibly). Throws an error if a field is invalid.

Method `terminate()`

Terminate one or more AWS Batch jobs.

Usage

crew_class_monitor_aws_batch$terminate(
  ids = NULL,
  all = FALSE,
  reason = "cancelled/terminated by crew.aws.batch monitor",
  verbose = TRUE
)

Arguments

ids: Character vector with the IDs of the AWS Batch jobs to terminate. Leave as NULL if all is TRUE.
all: TRUE to terminate all jobs belonging to the previously specified job definition. FALSE to terminate only the job IDs given in the ids argument.
reason: Character of length 1, natural language explaining the reason the job was terminated.
verbose: Logical of length 1, whether to show a progress bar if the R process is interactive and length(ids) is greater than 1.

Returns

NULL (invisibly).

Method `status()`

Get the status of a single job

Usage

crew_class_monitor_aws_batch$status(id)

Arguments

id: Character of length 1, job ID. This is different from the user-supplied job name.

Returns

A one-row tibble with information about the job.

Method `log()`

Get the CloudWatch log of a job.

Usage

crew_class_monitor_aws_batch$log(id, path = stdout(), start_from_head = FALSE)

Arguments

id: Character of length 1, job ID. This is different from the user-supplied job name.
path: Character string or stream (e.g. stdout()), file path or connection passed to the con argument of writeLines() to print the log messages. Set to nullfile() to suppress output (and use the invisibly returned tibble object instead).
start_from_head: Logical of length 1, whether to print earlier log events before later ones.

Details

This method assumes the job has log driver "awslogs" (specifying AWS CloudWatch) and that the log group is the one prespecified in the log_group argument of crew_monitor_aws_batch(). This method cannot use other log drivers such as Splunk, and it will fail if the log group is wrong or missing.

Returns

log() invisibly returns a tibble with log information and writes the messages to the stream or path given by the path argument.

Method `jobs()`

List all the jobs in the given job queue with the given job definition.

Usage

crew_class_monitor_aws_batch$jobs(
  status = c("submitted", "pending", "runnable", "starting", "running", "succeeded",
    "failed")
)

Arguments

status: Character vector of job states. Results are limited to these job states.

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `active()`

List active jobs: submitted, pending, runnable, starting, or running (not succeeded or failed).

Usage

crew_class_monitor_aws_batch$active()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `inactive()`

List inactive jobs: ones whose status is succeeded or failed (not submitted, pending, runnable, starting, or running).

Usage

crew_class_monitor_aws_batch$inactive()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `submitted()`

List jobs whose status is "submitted".

Usage

crew_class_monitor_aws_batch$submitted()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `pending()`

List jobs whose status is "pending".

Usage

crew_class_monitor_aws_batch$pending()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `runnable()`

List jobs whose status is "runnable".

Usage

crew_class_monitor_aws_batch$runnable()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `starting()`

List jobs whose status is "starting".

Usage

crew_class_monitor_aws_batch$starting()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `running()`

List jobs whose status is "running".

Usage

crew_class_monitor_aws_batch$running()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `succeeded()`

List jobs whose status is "succeeded".

Usage

crew_class_monitor_aws_batch$succeeded()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Method `failed()`

List jobs whose status is "failed".

Usage

crew_class_monitor_aws_batch$failed()

Details

The output only includes jobs under the job queue and job definition that were supplied through crew_monitor_aws_batch().

Returns

A tibble with one row per job and columns with job information.

Create a controller with an AWS Batch launcher.

Description

Create an R6 object to submit tasks and launch workers on AWS Batch workers.

Usage

crew_controller_aws_batch(
  name = NULL,
  workers = 1L,
  host = NULL,
  port = NULL,
  tls = crew::crew_tls(mode = "automatic"),
  tls_enable = NULL,
  tls_config = NULL,
  serialization = NULL,
  profile = crew::crew_random_name(),
  seconds_interval = 0.5,
  seconds_timeout = 60,
  seconds_launch = 1800,
  seconds_idle = 300,
  seconds_wall = Inf,
  retry_tasks = NULL,
  tasks_max = Inf,
  tasks_timers = 0L,
  reset_globals = TRUE,
  reset_packages = FALSE,
  reset_options = FALSE,
  garbage_collection = FALSE,
  crashes_error = NULL,
  processes = NULL,
  r_arguments = c("--no-save", "--no-restore"),
  crashes_max = 5L,
  backup = NULL,
  options_metrics = crew::crew_options_metrics(),
  options_aws_batch = crew.aws.batch::crew_options_aws_batch(),
  aws_batch_config = NULL,
  aws_batch_credentials = NULL,
  aws_batch_endpoint = NULL,
  aws_batch_region = NULL,
  aws_batch_job_definition = NULL,
  aws_batch_job_queue = NULL,
  aws_batch_share_identifier = NULL,
  aws_batch_scheduling_priority_override = NULL,
  aws_batch_parameters = NULL,
  aws_batch_container_overrides = NULL,
  aws_batch_node_overrides = NULL,
  aws_batch_retry_strategy = NULL,
  aws_batch_propagate_tags = NULL,
  aws_batch_timeout = NULL,
  aws_batch_tags = NULL,
  aws_batch_eks_properties_override = NULL
)

Arguments

name

Character string, name of the launcher. If the name is NULL, then a name is automatically generated when the launcher starts.

workers

Maximum number of workers to run concurrently when auto-scaling, excluding task retries and manual calls to launch(). Special workers allocated for task retries do not count towards this limit, so the number of workers running at a given time may exceed this maximum. A smaller number of workers may run if the number of executing tasks is smaller than the supplied value of the workers argument.

host

IP address of the mirai client to send and receive tasks. If NULL, the host defaults to nanonext::ip_addr()[1].

port

TCP port to listen for the workers. If NULL, then an available ephemeral port is automatically chosen. Controllers running simultaneously on the same computer (as in a controller group) must not share the same TCP port.

tls

A TLS configuration object from crew_tls().

tls_enable

Deprecated on 2023-09-15 in version 0.4.1. Use argument tls instead.

tls_config

Deprecated on 2023-09-15 in version 0.4.1. Use argument tls instead.

serialization

Either NULL (default) or an object produced by mirai::serial_config() to control the serialization of data sent to workers. This can help with either more efficient data transfers or to preserve attributes of otherwise non-exportable objects (such as torch tensors or arrow tables). See ?mirai::serial_config for details.

profile

Character string, compute profile for mirai::daemons().

seconds_interval

Number of seconds between polling intervals waiting for certain internal synchronous operations to complete. In certain cases, exponential backoff is used with this argument passed to seconds_max in a crew_throttle() object.

seconds_timeout

Number of seconds until timing out while waiting for certain synchronous operations to complete, such as checking mirai::info().

seconds_launch

Seconds of startup time to allow. A worker is unconditionally assumed to be alive from the moment of its launch until seconds_launch seconds later. After seconds_launch seconds, the worker is only considered alive if it is actively connected to its assign websocket.

seconds_idle

Maximum number of seconds that a worker can idle since the completion of the last task. If exceeded, the worker exits. But the timer does not launch until tasks_timers tasks have completed. See the idletime argument of mirai::daemon(). crew does not excel with perfectly transient workers because it does not micromanage the assignment of tasks to workers, so please allow enough idle time for a new worker to be delegated a new task.

seconds_wall

Soft wall time in seconds. The timer does not launch until tasks_timers tasks have completed. See the walltime argument of mirai::daemon().

retry_tasks

Deprecated on 2025-01-13 (crew version 0.10.2.9002).

tasks_max

Maximum number of tasks that a worker will do before exiting. Also determines how often the controller auto-scales. See the Auto-scaling section for details.

tasks_timers

Number of tasks to do before activating the timers for seconds_idle and seconds_wall. See the timerstart argument of mirai::daemon().

reset_globals

TRUE to reset global environment variables between tasks, FALSE to leave them alone.

reset_packages

TRUE to detach any packages loaded during a task (runs between each task), FALSE to leave packages alone. In either case, the namespaces are not detached.

reset_options

TRUE to reset global options to their original state between each task, FALSE otherwise. It is recommended to only set reset_options = TRUE if reset_packages is also TRUE because packages sometimes rely on options they set at loading time. for this and other reasons, reset_options only resets options that were nonempty at the beginning of the task. If your task sets an entirely new option not already in options(), then reset_options = TRUE does not delete the option.

garbage_collection

TRUE to run garbage collection after each task task, FALSE to skip.

crashes_error

Deprecated on 2025-01-13 (crew version 0.10.2.9002).

processes

Deprecated on 2025-08-27 (crew version 1.2.1.9009).

r_arguments

Optional character vector of command line arguments to pass to Rscript (non-Windows) or Rscript.exe (Windows) when starting a worker. Example: r_arguments = c("--vanilla", "--max-connections=32").

crashes_max

In rare cases, a worker may exit unexpectedly before it completes its current task. If this happens, pop() returns a status of "crash" instead of "error" for the task. The controller does not automatically retry the task, but you can retry it manually by calling push() again and using the same task name as before. (However, targets pipelines running crew do automatically retry tasks whose workers crashed.)

crashes_max is a non-negative integer, and it sets the maximum number of allowable consecutive crashes for a given task. If a task's worker crashes more than crashes_max times in a row, then pop() throws an error when it tries to return the results of the task.

backup

An optional crew controller object, or NULL to omit. If supplied, the backup controller runs any pushed tasks that have already reached crashes_max consecutive crashes. Using backup, you can create a chain of controllers with different levels of resources (such as worker memory and CPUs) so that a task that fails on one controller can retry using incrementally more powerful workers. All controllers in a backup chain should be part of the same controller group (see crew_controller_group()) so you can call the group-level pop() and collect() methods to make sure you get results regardless of which controller actually ended up running the task.

Limitations of backup: * crashes_max needs to be positive in order for backup to be used. Otherwise, every task would always skip the current controller and go to backup. * backup cannot be a controller group. It must be an ordinary controller.

options_metrics

Either NULL to opt out of resource metric logging for workers, or an object from crew_options_metrics() to enable and configure resource metric logging for workers. For resource logging to run, the autometric R package version 0.1.0 or higher must be installed.

options_aws_batch

List of options from crew_options_aws_batch(). The job definition and job queue must be specified in crew_options_aws_batch(). crew_options_aws_batch() also allows you to request vCPUs, GPUs, and memory for the jobs.

aws_batch_config

Deprecated. Use options_aws_batch instead.

aws_batch_credentials

Deprecated. Use options_aws_batch instead.

aws_batch_endpoint

Deprecated. Use options_aws_batch instead.

aws_batch_region

Deprecated. Use options_aws_batch instead.

aws_batch_job_definition

Deprecated. Use options_aws_batch instead.

aws_batch_job_queue

Deprecated. Use options_aws_batch instead.

aws_batch_share_identifier

Deprecated. Use options_aws_batch instead.

aws_batch_scheduling_priority_override

Deprecated. Use options_aws_batch instead.

aws_batch_parameters

Deprecated. Use options_aws_batch instead.

aws_batch_container_overrides

Deprecated. Use options_aws_batch instead.

aws_batch_node_overrides

Deprecated. Use options_aws_batch instead.

aws_batch_retry_strategy

Deprecated. Use options_aws_batch instead.

aws_batch_propagate_tags

Deprecated. Use options_aws_batch instead.

aws_batch_timeout

Deprecated. Use options_aws_batch instead.

aws_batch_tags

Deprecated. Use options_aws_batch instead.

aws_batch_eks_properties_override

Deprecated. Use options_aws_batch instead.

IAM policies

AWS arguments

Verbosity

Control verbosity with the paws.log_level global option in R. Set to 0 for minimum verbosity and 3 for maximum verbosity.

Examples

if (identical(Sys.getenv("CREW_EXAMPLES"), "true")) {
controller <- crew_controller_aws_batch(
  aws_batch_job_definition = "YOUR_JOB_DEFINITION_NAME",
  aws_batch_job_queue = "YOUR_JOB_QUEUE_NAME"
)
controller$start()
controller$push(name = "task", command = sqrt(4))
controller$wait()
controller$pop()$result
controller$terminate()
}

Create an AWS Batch job definition object.

Description

Create an R6 object to manage a job definition for AWS Batch jobs.

Usage

crew_definition_aws_batch(
  job_queue,
  job_definition = paste0("crew-aws-batch-job-definition-", crew::crew_random_name()),
  log_group = "/aws/batch/job",
  config = NULL,
  credentials = NULL,
  endpoint = NULL,
  region = NULL
)

Arguments

job_queue

Character vector of names of AWS Batch job queues. As of crew.aws.batch version 0.0.8 and above, you can supply more than one job queue. Methods like jobs() and active() will query all the job queues given.

job_definition

Character of length 1, name of the AWS Batch job definition. The job definition might or might not exist at the time crew_definition_aws_batch() is called. Either way is fine.

log_group

Character of length 1, AWS Batch CloudWatch log group to get job logs. The default log group is often "/aws/batch/job", but not always. It is not easy to get the log group of an active job or job definition, so if you have a non-default log group and you do not know its name, please consult your system administrator.

config

Optional named list, config argument of paws.compute::batch() with optional configuration details.

credentials

Optional named list. credentials argument of paws.compute::batch() with optional credentials (if not already provided through environment variables such as AWS_ACCESS_KEY_ID).

endpoint

Optional character of length 1. endpoint argument of paws.compute::batch() with the endpoint to send HTTP requests.

region

Character of length 1. region argument of paws.compute::batch() with an AWS region string such as "us-east-2". Serves as the region for both AWS Batch and CloudWatch. Tries to default to paws.common::get_config()$region, then to Sys.getenv("AWS_REGION") if unsuccessful, then Sys.getenv("AWS_REGION"), then Sys.getenv("AWS_DEFAULT_REGION").

Value

An R6 job definition object.

IAM policies

Create an AWS Batch launcher object.

Description

Create an R6 AWS Batch launcher object.

Usage

crew_launcher_aws_batch(
  name = NULL,
  workers = 1L,
  seconds_interval = 0.5,
  seconds_timeout = 60,
  seconds_launch = 1800,
  seconds_idle = 300,
  seconds_wall = Inf,
  tasks_max = Inf,
  tasks_timers = 0L,
  reset_globals = NULL,
  reset_packages = NULL,
  reset_options = NULL,
  garbage_collection = NULL,
  crashes_error = NULL,
  tls = crew::crew_tls(mode = "automatic"),
  processes = NULL,
  r_arguments = c("--no-save", "--no-restore"),
  options_metrics = crew::crew_options_metrics(),
  options_aws_batch = crew.aws.batch::crew_options_aws_batch(),
  aws_batch_config = NULL,
  aws_batch_credentials = NULL,
  aws_batch_endpoint = NULL,
  aws_batch_region = NULL,
  aws_batch_job_definition = NULL,
  aws_batch_job_queue = NULL,
  aws_batch_share_identifier = NULL,
  aws_batch_scheduling_priority_override = NULL,
  aws_batch_parameters = NULL,
  aws_batch_container_overrides = NULL,
  aws_batch_node_overrides = NULL,
  aws_batch_retry_strategy = NULL,
  aws_batch_propagate_tags = NULL,
  aws_batch_timeout = NULL,
  aws_batch_tags = NULL,
  aws_batch_eks_properties_override = NULL
)

Arguments

name

Character string, name of the launcher. If the name is NULL, then a name is automatically generated when the launcher starts.

workers

seconds_interval

seconds_timeout

Number of seconds until timing out while waiting for certain synchronous operations to complete, such as checking mirai::info().

seconds_launch

seconds_idle

seconds_wall

Soft wall time in seconds. The timer does not launch until tasks_timers tasks have completed. See the walltime argument of mirai::daemon().

tasks_max

Maximum number of tasks that a worker will do before exiting. Also determines how often the controller auto-scales. See the Auto-scaling section for details.

tasks_timers

Number of tasks to do before activating the timers for seconds_idle and seconds_wall. See the timerstart argument of mirai::daemon().

reset_globals

Deprecated on 2025-05-30 (crew version 1.1.2.9004). Please use the reset_globals option of crew_controller() instead.

reset_packages

Deprecated on 2025-05-30 (crew version 1.1.2.9004). Please use the reset_packages option of crew_controller() instead.

reset_options

Deprecated on 2025-05-30 (crew version 1.1.2.9004). Please use the reset_options option of crew_controller() instead.

garbage_collection

Deprecated on 2025-05-30 (crew version 1.1.2.9004). Please use the garbage_collection option of crew_controller() instead.

crashes_error

Deprecated on 2025-01-13 (crew version 0.10.2.9002).

tls

A TLS configuration object from crew_tls().

processes

Deprecated on 2025-08-27 (crew version 1.2.1.9009).

r_arguments

options_metrics

options_aws_batch

aws_batch_config

Deprecated. Use options_aws_batch instead.

aws_batch_credentials

Deprecated. Use options_aws_batch instead.

aws_batch_endpoint

Deprecated. Use options_aws_batch instead.

aws_batch_region

Deprecated. Use options_aws_batch instead.

aws_batch_job_definition

Deprecated. Use options_aws_batch instead.

aws_batch_job_queue

Deprecated. Use options_aws_batch instead.

aws_batch_share_identifier

Deprecated. Use options_aws_batch instead.

aws_batch_scheduling_priority_override

Deprecated. Use options_aws_batch instead.

aws_batch_parameters

Deprecated. Use options_aws_batch instead.

aws_batch_container_overrides

Deprecated. Use options_aws_batch instead.

aws_batch_node_overrides

Deprecated. Use options_aws_batch instead.

aws_batch_retry_strategy

Deprecated. Use options_aws_batch instead.

aws_batch_propagate_tags

Deprecated. Use options_aws_batch instead.

aws_batch_timeout

Deprecated. Use options_aws_batch instead.

aws_batch_tags

Deprecated. Use options_aws_batch instead.

aws_batch_eks_properties_override

Deprecated. Use options_aws_batch instead.

Value

An R6 AWS Batch launcher object.

IAM policies

AWS arguments

Verbosity

Control verbosity with the paws.log_level global option in R. Set to 0 for minimum verbosity and 3 for maximum verbosity.

Submit an AWS Batch job.

Description

Not a user-side function. For internal use only.

Usage

crew_launcher_aws_batch_launch(args_client, args_submit)

Arguments

args_client

Named list of arguments to paws.compute::batch().

args_submit

Named list of arguments to paws.compute::batch()$submit_job().

Details

This utility is its own separate exported function specific to the launcher and not shared with the job definition or monitor classes. It generates the paws.compute::batch() client within itself instead of a method inside the class. This is all because it needs to run on a separate local worker process and it needs to accept exportable arguments.

Value

HTTP response from submitting the job.

Create an AWS Batch monitor object.

Description

Create an R6 object to list, inspect, and terminate AWS Batch jobs.

Usage

crew_monitor_aws_batch(
  job_queue,
  job_definition,
  log_group = "/aws/batch/job",
  config = NULL,
  credentials = NULL,
  endpoint = NULL,
  region = NULL
)

Arguments

job_queue

job_definition

Character string, name of the AWS Batch job definition.

log_group

config

Optional named list, config argument of paws.compute::batch() with optional configuration details.

credentials

Optional named list. credentials argument of paws.compute::batch() with optional credentials (if not already provided through environment variables such as AWS_ACCESS_KEY_ID).

endpoint

Optional character of length 1. endpoint argument of paws.compute::batch() with the endpoint to send HTTP requests.

region

IAM policies

AWS Batch options

Description

Options for the AWS Batch controller.

Usage

crew_options_aws_batch(
  job_definition = "example",
  job_queue = "example",
  cpus = NULL,
  gpus = NULL,
  memory = NULL,
  memory_units = "gigabytes",
  config = list(),
  credentials = list(),
  endpoint = NULL,
  region = NULL,
  share_identifier = NULL,
  scheduling_priority_override = NULL,
  parameters = NULL,
  container_overrides = NULL,
  node_overrides = NULL,
  retry_strategy = NULL,
  propagate_tags = NULL,
  timeout = NULL,
  tags = NULL,
  eks_properties_override = NULL,
  verbose = FALSE
)

Arguments

job_definition

Character of length 1, name of the AWS Batch job definition to use. There is no default for this argument, and a job definition must be created prior to running the controller. Please see https://docs.aws.amazon.com/batch/ for details.

To create a job definition, you will need to create a Docker-compatible image which can run R and crew. You may which to inherit from the images at https://github.com/rocker-org/rocker-versioned2.

job_queue

Character of length 1, name of the AWS Batch job queue to use. There is no default for this argument, and a job queue must be created prior to running the controller. Please see https://docs.aws.amazon.com/batch/ for details.

cpus

Positive numeric scalar, number of virtual CPUs to request per job. Can be NULL to go with the defaults in the job definition. Ignored if container_overrides is not NULL.

gpus

Positive numeric scalar, number of GPUs to request per job. Can be NULL to go with the defaults in the job definition. Ignored if container_overrides is not NULL.

memory

Positive numeric scalar, amount of random access memory (RAM) to request per job. Choose the units of memory with the memory_units argument. Fargate instances can only be certain discrete values of mebibytes, so please choose memory_units = "mebibytes" in that case. The memory argument can be NULL to go with the defaults in the job definition. Ignored if container_overrides is not NULL.

memory_units

Character string, units of memory of the memory argument. Can be "gigabytes" or "mebibytes". Fargate instances can only be certain discrete values of mebibytes, so please choose memory_units = "mebibytes" in that case.

config

Named list, config argument of paws.compute::batch() with optional configuration details.

credentials

Named list. credentials argument of paws.compute::batch() with optional credentials (if not already provided through environment variables such as AWS_ACCESS_KEY_ID).

endpoint

Character of length 1. endpoint argument of paws.compute::batch() with the endpoint to send HTTP requests.

region

Character of length 1. region argument of paws.compute::batch() with an AWS region string such as "us-east-2".

share_identifier

NULL or character of length 1. For details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

scheduling_priority_override

NULL or integer of length 1. For details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

parameters

NULL or a nonempty list. For details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

container_overrides

NULL or a nonempty named list of fields to override in the container specified in the job definition. Any overrides for the command field are ignored because crew.aws.batch needs to override the command to run the crew worker. For more details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

node_overrides

NULL or a nonempty named list. For more details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

retry_strategy

NULL or a nonempty named list. For more details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

propagate_tags

NULL or a logical of length 1. For more details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

timeout

NULL or a nonempty named list. For more details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

tags

NULL or a nonempty named list. For more details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

eks_properties_override

NULL or a nonempty named list. For more details, visit https://www.paws-r-sdk.com/docs/batch_submit_job/ and the "AWS arguments" sections of this help file.

verbose

TRUE to print informative console messages, FALSE otherwise.

Value

A classed list of options for the controller.

Retryable options

Retryable options are deprecated in crew.aws.batch as of 2025-01-27 (version ⁠0.0.8⁠).

crew.aws.batch: a crew launcher plugin for AWS Batch

Description

Terminate an AWS Batch job.

Description

Usage

Arguments

Value

AWS Batch definition class

Description

Details

IAM policies

Active bindings

Methods

Public methods

Method new()

Usage

Arguments

Returns

Method validate()

Usage

Returns

Method register()

Usage

Arguments

Details

Returns

Method deregister()

Usage

Arguments

Details

Returns

Method describe()

Usage

Arguments

Returns

Method submit()

Usage

Arguments

Details

Returns

See Also

AWS Batch launcher class

Description

Details

IAM policies

AWS arguments

Verbosity

Super class

Active bindings

Methods

Public methods

Method new()

Usage

Arguments

Returns

Method validate()

Usage

Returns

Method launch_workers()

Usage

Arguments

Details

Returns

See Also

AWS Batch monitor class

Description

Details

IAM policies

Active bindings

Methods

Public methods

Method new()

Usage

Arguments

Returns

Method validate()

Usage

Returns

Method terminate()

Usage

Method `new()`

Method `validate()`

Method `register()`

Method `deregister()`

Method `describe()`

Method `submit()`

Method `new()`

Method `validate()`

Method `launch_workers()`

Method `new()`

Method `validate()`

Method `terminate()`

Method `status()`

Method `log()`

Method `jobs()`

Method `active()`

Method `inactive()`

Method `submitted()`

Method `pending()`

Method `runnable()`

Method `starting()`

Method `running()`

Method `succeeded()`

Method `failed()`