Supported runtime properties and how to set them-genomics-阿里云帮助中心

This topic describes the runtime properties that the gene analysis platform supports and compares the Alibaba Cloud backend with other computing backends. The gene analysis platform uses Workflow Description Language (WDL) for analysis applications. The `runtime` section in each task defines the resources that a computing job requires.

Supported runtime properties

Important

The runtime settings for the gene analysis platform have limits. For more information, see Limits.

cpu

Default: 2. This property specifies the number of cores that the computing job requires.

Example:

runtime {
  cpu: 2
}

memory

Default: "4G". This property specifies the amount of memory to allocate to the computing job.

Example:

runtime {
  memory: "4G"
}

instanceType

Optional. If you set this property, it overrides the `cpu` and `memory` properties. This property specifies an Alibaba Cloud ECS instance type for the job's execution environment. For a list of all ECS instance types, see Instance family. To check whether the gene analysis platform supports a specific instance type, you can contact the product team or submit a ticket. We recommend that you specify resources using the `cpu` and `memory` properties.

Example:

runtime {
  instanceType: "ecs.c6.xlarge"
}

disk

Default: "40 GB". This property specifies the size of the disk that is mounted in the job's execution environment. This disk is used to store input and output files. The default disk type is a Capacity NAS file system. To use other disk types, see the `disks` parameter.

runtime {
  disk: "40 GB"
}

disks

Default: "local-disk 40 nas_cap". This property specifies the size and type of the disk that is mounted in the job's execution environment. The disk is used to store input and output files.

Note: If you do not specify the `disk` or `disks` parameters, a 40 GB Capacity NAS file system is used by default.

The value of the `disks` property is a comma-separated list of disk specifications. Each disk is described by a space-separated trituple, such as "local-disk 40 nas_cap". The trituple consists of the following parts:

Mount target. The value is fixed to `local-disk`.
Disk size in GB.
Disk type. The supported types are `nas_cap`, `nas_per`, and `cloud_essd`. These types represent Capacity NAS file system, Performance NAS file system, and ESSD PL0, respectively.

Example:

runtime {
  disks: "local-disk 100 cloud_essd"
}

docker

This property specifies the Docker image for the computing job. Only images from Alibaba Cloud Container Registry are supported.

Example:

runtime {
  docker: "registry-vpc.cn-shenzhen.aliyuncs.com/easy-gene/genomes-in-the-cloud:1.0"
}

timeout

This property specifies the maximum runtime for the job in seconds. The value must be a positive integer. If you do not specify a timeout, the job runs until it completes or fails. If the runtime exceeds the specified timeout, the job is terminated, its resources are released, and an error is reported in the console.

Example:

runtime {
  timeout: 36000
}

env

This property lets you mount an Object Storage Service (OSS) bucket to the `/easygene_data` path inside the container. This provides direct access to data in OSS.

Example:

#1. In the WDL runtime, specify the bucket to mount in the container. 
# The bucket is mounted to the fixed path /easygene_data.
#Note: The bucket cannot be in a different account or region.
runtime {
  env: {
    "BUCKET":"test"
  }
}

#2. Then, directly use the files under /easygene_data in the WDL.
#To skip the download, change the input File type to String in the original WDL. 
#For example, if the OSS path is oss://test/dir/1.fq.
#When you mount the 'test' bucket, the path to this file inside the container is /easygene_data/dir/1.fq.
input{
  #File fastq = "oss://test/dir/1.fq"
  #Replace with:
  String fastq = "/easygene_data/dir/1.fq"
}

Comparison with other community computing backends

	Alibaba Cloud Gene Analysis Platform	HPC	Local environment
cpu	✅	✅	✅
memory	✅	✅	✅
instanceType	"ecs.c6.xlarge"	❌	❌
disks	✅	✅	✅
docker	✅	✅	✅

Important

The basic runtime properties for computing tasks on the Alibaba Cloud Gene Analysis Platform are consistent with community standards. This consistency allows applications to run seamlessly in local, High-Performance Computing (HPC), and cloud environments. The platform also provides the `instanceType` extension to support specific hardware requirements, such as GPUs and FPGAs.