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Add admin doc for aws batch runner

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qiagu
2022-08-18 12:42:38 -07:00
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@@ -16,6 +16,7 @@ Galaxy is known to work with:
* [HTCondor](http://research.cs.wisc.edu/htcondor/)
* [Slurm](https://slurm.schedmd.com/)
* [Galaxy Pulsar](#pulsar) (formerly LWR)
* [AWS Batch](https://aws.amazon.com/batch)
It should also work with [any other DRM](http://www.drmaa.org/implementations.php) which implements a [DRMAA](http://www.drmaa.org) interface. If you successfully run Galaxy with a DRM not listed here, please let us know via an email to the [galaxy-dev mailing list](https://galaxyproject.org/mailing-lists/).
@@ -307,6 +308,63 @@ Torque attributes can be defined in either their short (e.g. [qsub(1B)](http://c
Most options available to `qsub(1b)` and `pbs_submit(3b)` are supported. Exceptions include `-o/Output_Path`, `-e/Error_Path`, and `-N/Job_Name` since these PBS job attributes are set by Galaxy.
## AWS Batch
Runs jobs via the [AWS Batch](https://aws.amazon.com/batch/). Built on top of AWS Elastic Container Service (ECS), AWS Batch enables users to run hundreds of thousands of jobs with simple configuration.
#### Dependencies
AWS Batch job runner requirs AWS Elastic File System (EFS) being mounted as a shared file system that enables Galaxy and job containers to read and write files. In the best pratice, Galaxy is installed an AWS EC2 instance and an EFS is mounted to the EC2 as a local drive. Job-related paths, such as objects, jobs_directory, tool_directory and so on, need to be placed on the EFS drive.
In addition, Galaxy admin needs to configure Batch compute environment, Batch job queue and proper AWS IAM roles, and provision them as destination parameters.
AWS Batch job runner requires [boto3](https://pypi.org/project/boto3/) installed in Galaxy environment.
#### Parameters and Configuration
AWS Batch job runner sends jobs to Batch compute environment that is composed of either Fargate or EC2. While Fargate provides a series of lightweigt compute resources (up to 4 vcpu and 30 GB memeory), the EC2 offers more abroad choices. With `auto_platform` enabled, this runner supports mapping to the best fit type of resources based on the provisioned `vcpu` and `memory`, i.e., Fargate is preferred over EC2 when `vcpu` and `memory` don't go beyond the limits (4 and 30 gb, respectively). If the power of `GPU` is needed for a destination, a job queue built on top of GPU-enabled compute environment must be provisoned.
```xml
<plugins>
<plugin id="aws_batch" type="runner" load="galaxy.jobs.runners.aws:AWSBatchJobRunner">
<!-- Run `aws configure` with aws cli or set params below -->
<!-- <param id="aws_access_key_id">xxxxxxxxx</param>
<param id="aws_secret_access_key">xxxxxxxxxxxxxxxxxxx</param>
<param id="region">us-west-1</param> -->
</plugin>
</plugins>
<destinations>
<destination id="aws_batch_auto" runner="aws_batch">
<param id="docker_enabled">true</param>
<!-- `docker_enabled = true` is always required -->
<param id="job_queue">arn_for_Fargate_job_queue, arn_for_EC2_job_queue</param>
<!-- Fargete and non-GPU EC2 -->
<param id="job_role_arn">arn:aws:iam::xxxxxxxxxxxxxxxxxx</param>
<param id="vcpu">1</param>
<param id="memory">2048</param>
<!-- MB, default is 2048 -->
<param id="efs_filesystem_id">fs-xxxxxxxxxxxxxx</param>
<param id="efs_mount_point">/mnt/efs/fs1</param>
<!-- This is the location where the EFS is mounted -->
<param id="fargate_version">1.4.0</param>
<!-- `fargate_version` is required to use Fargate compute resources -->
<param id="auto_platform">true</param>
</destination>
<destination id="aws_batch_gpu" runner="aws_batch">
<param id="docker_enabled">true</param>
<!-- `docker_enabled = true` is always required -->
<param id="job_queue">arn_for_gpu_job_queue</param>
<!-- Job queue must be built on GPU-specific compute environment -->
<param id="job_role_arn">arn:aws:iam::xxxxxxxxxxxxxxxxxx</param>
<param id="vcpu">4</param>
<param id="memory">20000</param>
<!-- MB, default is 2048 -->
<param id="gpu">1</param>
<param id="efs_filesystem_id">fs-xxxxxxxxxxxxxx</param>
<param id="efs_mount_point">/mnt/efs/fs1</param>
<!-- This is the location where the EFS is mounted -->
</destination>
</destinations>
```
## Submitting Jobs as the Real User
Galaxy runs as a process on your server as whatever user starts the server - usually an account created for the purpose of running Galaxy. Jobs will be submitted to your cluster(s) as this user. In environments where users in Galaxy are guaranteed to be users on the underlying system (i.e. Galaxy is configured to use external authentication), it may be desirable to submit jobs to the cluster as the user logged in to Galaxy rather than Galaxy's system user.