cromwell SGE配置

支持平台

cromwell安装后可以直接进行单机，单节点的任务投递。

java -jar cromwell.jar run pipeline.wdl -i pipeline.json

但是 cromwell 不仅支持本地计算机任务调度，同时支持集群/云计算作业管理系统。cromwell针对包含 SGE、AWS、Docker 在内的等多种平台和容器均提供了配置文件模板，可以通过简单的配置实现基于各平台的调度。

• Cloud Providers

  • AWS: Amazon Web Services (documentation)
  • TES: is a backend that submits jobs to a server with protocol defined by GA4GH (documentation)
  • PAPIv2: Google Pipelines API backend (version 2!) (documentation)

• Containers

  • Docker: an example backend that only runs workflows with docker in every command
  • Singularity: run Singularity containers locally (documentation)
  • Singularity+Slurm: An example using Singularity with SLURM (documentation)
  • TESK is the same, but intended for Kubernetes. See the TES docs at the bottom.
  • udocker: to interact with udocker locally documentation
  • udocker+Slurm: to interact with udocker on SLURM (documentation)

• Workflow Managers

  • HtCondor: a workload manager at UW-Madison (documentation)
  • LSF: the Platform Load Sharing Facility backend (documentation)
  • SGE: a backend for Sungrid Engine (documentation)
  • slurm: SLURM workload manager (documentation)

集群配置

SGE

官方针对不同的集群/云作业管理系统提供了相关的配置文件（https://github.com/broadinstitute/cromwell/tree/develop/cromwell.example.backends），但是本质都是讲调度命令嵌入其中。
**作业调度系统的配置文件并非完整的配置文件，必须添加到 [cromwell.examples.conf](https://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/cromwell.examples.confhttps://github.com/broadinstitute/cromwell/blob/develop/cromwell.example.backends/cromwell.examples.conf) 的 backend 部分才可以正常工作**

# cromwell.sge.config
# 完整配置文件
include required(classpath("application"))

backend {
default = SGE
  providers {
    SGE {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
      config {
        concurrent-job-limit = 5


        runtime-attributes = """
        Int cpu = 1
        Float? memory_gb
        String? sge_queue
        String? sge_project
        """

        submit = """
        qsub \
        -terse \
        -V \
        -b y \
        -N ${job_name} \
        -wd ${cwd} \
        -o ${out}.qsub \
        -e ${err}.qsub \
        -pe smp ${cpu} \
        ${"-l mem_free=" + memory_gb + "g"} \
        ${"-q " + sge_queue} \
        /usr/bin/env bash ${script}
        """

        kill = "qdel ${job_id}"
        check-alive = "qstat -j ${job_id}"
        job-id-regex = "(\\d+)"


      }
    }
  }
}

使用sge进行任务投递

java -Dconfig.file=cromwell.examples.conf -jar /home/liubo4/software/cromwell-84.jar run helloword.wdl -i helloword.wdl.input.json

SGE&docker

# cromwell.sge.docker.config
# 完整配置文件
include required(classpath("application"))

backend {
default = SGE
  providers {
    SGE {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
      config {
        concurrent-job-limit = 5


        runtime-attributes = """
        Int cpu = 1
        Float? memory_gb
        String? sge_queue
        String? sge_project
        """

        submit = """
        qsub \
        -terse \
        -V \
        -b y \
        -N ${job_name} \
        -wd ${cwd} \
        -o ${out}.qsub \
        -e ${err}.qsub \
        -pe smp ${cpu} \
        ${"-l mem_free=" + memory_gb + "g"} \
        ${"-q " + sge_queue} \
        /usr/bin/env bash ${script}
        """

        kill = "qdel ${job_id}"
        check-alive = "qstat -j ${job_id}"
        job-id-regex = "(\\d+)"


      }
    }
  }
}

reference

Cromwell ReadtheDoc SGE
Cromwell Example Backends
[https://blog.csdn.net/tanzuozhev/article/details/120629170]