python包之drmaa：集群任务管理

目录

• 1. drmaa简介
• 2. 安装和配置
• 3. 示例
  • 3.1 开始和终止会话
  • 3.2 运行工作
  • 3.3 等待工作
  • 3.4 控制工作
  • 3.5 查询工作状态
• 4. 应用
  • 4.1 写一个简单应用
  • 4.2 应用示例2

搭建流程时，我们把各个模块脚本都写好了，现在通过编写主程序将模块串起来，那么怎么样依次（或者并行）将任务自动投递到集群呢？就是说这一步运行完之后，下一步自动运行。我们当然可以在脚本中设一个标志，反复检查这一个标志是否出现来决定是否运行下一步，但这种方法太原始，太多弊端了，耗内存，无法并行，且不可预料的出错。那么，有没有相应的工具来管理集群任务投递？有，python的drmaa包可以实现。

1. drmaa简介

Distributed Resource Management Application API (DRMAA)，即分布式资源管理应用程序API，是一种高级 开放网格论坛（Open_Grid_Forum）应用程序接口规范，用于向分布式资源管理（DRM）系统（例如集群或网格计算提交和控制作业）。API的范围涵盖了应用程序提交，控制和监视DRM系统中执行资源上的作业所需的所有高级功能。DRMAA API已在Sun的Grid Engine（SGE）和Condor等作业管理调度系统中实现。关于SGE可参考我的推文：集群SGE作业调度系统

C、C++、Perl、Python等程序语言都开发有相应的drmaa包来实现SGE集群的任务管理。这里记录下drmaa-python：

Github：drmaa-python

PyPi：https://pypi.org/project/drmaa/

2. 安装和配置

要求：Python2.7+；与DRMAA兼容的集群，如SGE。

#安装
pip install drmaa

#设置路径
export SGE_ROOT=/path/to/gridengine  #SGE安装的路径
export SGE_CELL=default

#设置库
export DRMAA_LIBRARY_PATH=/usr/lib/libdrmaa.so.1.0
#libdrmaa.so.1.0 C动态库，是libdrmaa-dev包的一部分

3. 示例

3.1 开始和终止会话

Session

#!/usr/bin/env python

import drmaa

def main():
   """Create a drmaa session and exit"""
   with drmaa.Session() as s:  #自动初始化，组织工作提交
      print('A session was started successfully')
#with结束自动exit()，大部分函数都要在exit()前执行，如runJob/wait，getContact可在exit()后。
if __name__=='__main__':
   main()

使用可重新连接的会话，可以将DRMAA库初始化为上一个会话，从而允许该库访问该会话的作业列表.

#!/usr/bin/env python

import drmaa

def main():
    """
    Create a session, show that each session has an ID, use session ID to
    disconnect, then reconnect. Finally, exit.
    """
    s = drmaa.Session()
    s.initialize()
    print('A session was started successfully')
    response = s.contact
    print('session contact returns: %s' % response)
    s.exit()
    print('Exited from session')

    s.initialize(response) #初始化上个session
    print('Session was restarted successfullly')
    s.exit()

if __name__=='__main__':
    main()

3.2 运行工作

假设已知当前目录有一个sleeper.sh脚本，后接两个参数：

#!/bin/bash
echo "Hello world, the answer is $1"
sleep 3s
echo "$2 Bye world!"

drmaa将sleeper.sh提交到SGE：

#!/usr/bin/env python

import drmaa
import os

def main():
   """
   Submit a job.
   Note, need file called sleeper.sh in current directory.
   """
   with drmaa.Session() as s:
       print('Creating job template')
       jt = s.createJobTemplate()  #分配工作模板(存储提交作业的信息结构)
       jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh') #设置remoteCommand属性，找到要运行的程序。
        #路径默认为用户的主目录，相对路径用workingDirectory属性
       jt.args = ['42', 'Simon says:']  #执行文件的参数
       jt.joinFiles=True

       jobid = s.runJob(jt)  #将分配给作业的ID放入我们传递给的字符数组中runJob()
       print('Your job has been submitted with ID %s' % jobid)

 #    jobid = s.runBulkJobs(jt, 1, 30, 2) #提交一个数组作业
 #    print('Your jobs have been submitted with IDs %s' % jobid)

       print('Cleaning up')
       s.deleteJobTemplate(jt) #删除作业模板，释放作业模板保留的DRMAA内存，但对提交的作业没有影响

if __name__=='__main__':
   main()

3.3 等待工作

即等待任务完成

#!/usr/bin/env python

import drmaa
import os

def main():
    """
    Submit a job and wait for it to finish.
    Note, need file called sleeper.sh in home directory.
    """
    with drmaa.Session() as s:
        print('Creating job template')
        jt = s.createJobTemplate()
        jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh')
        jt.args = ['42', 'Simon says:']
        jt.joinFiles = True

        jobid = s.runJob(jt)
        print('Your job has been submitted with ID %s' % jobid)

        retval = s.wait(jobid, drmaa.Session.TIMEOUT_WAIT_FOREVER) #调用wait()等待作业结束
        print('Job: {0} finished with status {1}'.format(retval.jobId, retval.hasExited))

#以下是提交多个作业的等待处理，synchronize替代wait
#joblist = s.runBulkJobs(jt, 1, 30, 2)
#print('Your jobs have been submitted with IDs %s' % joblist)
#s.synchronize(joblist, drmaa.Session.TIMEOUT_WAIT_FOREVER, True)

        print('Cleaning up')
        s.deleteJobTemplate(jt)

if __name__=='__main__':
    main()

wait()返回一个JobInfo元组，其具有下面的属性： jobId，hasExited，hasSignal，terminatedSignal，hasCoreDump， wasAborted，exitStatus，resourceUsage

synchronize()的第3个参数是该synchronize()的调用是否在工作后清除。工作完成后，它会留下一些统计信息，如退出状态和用途，直到wait() 或synchronize()的处理状态变为True。确保每一项任务对这两个函数之一调用是很有必要的，否则可能引起内存泄漏。如果想要每一项任务恢复统计信息，可将synchronize()设置False。如下：

joblist = s.runBulkJobs(jt, 1, 30, 2)
print('Your jobs have been submitted with IDs %s' % joblist)

s.synchronize(joblist, drmaa.Session.TIMEOUT_WAIT_FOREVER, False) #False，每一项工作等待一次
for curjob in joblist:
    print('Collecting job ' + curjob)
    retval = s.wait(curjob, drmaa.Session.TIMEOUT_WAIT_FOREVER)
    print('Job: {0} finished with status {1}'.format(retval.jobId,retval.hasExited))

3.4 控制工作

#!/usr/bin/env python

import drmaa
import os

def main():
    """Submit a job, then kill it.
    Note, need file called sleeper.sh in home directory.
    """
    with drmaa.Session() as s:
        print('Creating job template')
        jt = s.createJobTemplate()
        jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh')
        jt.args = ['42', 'Simon says:']
        jt.joinFiles = True

        jobid = s.runJob(jt)
        print('Your job has been submitted with ID %s' % jobid)
        # options are: SUSPEND, RESUME, HOLD, RELEASE, TERMINATE
        s.control(jobid, drmaa.JobControlAction.TERMINATE) #删除刚提交的作业

        print('Cleaning up')
        s.deleteJobTemplate(jt)

if __name__=='__main__':
    main()

还可以用control()来暂停，恢复，保留或释放工作。control()还可用于控制未通过DRMAA提交的作业，可以将任何有效的SGE作业ID传递control()为要删除的作业ID。

3.5 查询工作状态

#!/usr/bin/env python

import drmaa
import time
import os

def main():
    """
    Submit a job, and check its progress.
    Note, need file called sleeper.sh in home directory.
    """
    with drmaa.Session() as s:
        print('Creating job template')
        jt = s.createJobTemplate()
        jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh')
        jt.args = ['42', 'Simon says:']
        jt.joinFiles=True

        jobid = s.runJob(jt)
        print('Your job has been submitted with ID %s' % jobid)

        # Who needs a case statement when you have dictionaries?
        decodestatus = {drmaa.JobState.UNDETERMINED: 'process status cannot be determined',
                        drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active',
                        drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold',
                        drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold',
                        drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
                        drmaa.JobState.RUNNING: 'job is running',
                        drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended',
                        drmaa.JobState.USER_SUSPENDED: 'job is user suspended',
                        drmaa.JobState.DONE: 'job finished normally',
                        drmaa.JobState.FAILED: 'job finished, but failed'}

        for ix in range(10):
            print('Checking %s of 10 times' % ix)
            print decodestatus(s.jobStatus(jobid)) #jobStatus()获取作业的状态
            time.sleep(5)

        print('Cleaning up')
        s.deleteJobTemplate(jt)

if __name__=='__main__':
    main()   #确定工作状态并报告

其他更多关于JobInfo，JobTemplate，Session等方法的属性可参考：https://drmaa-python.readthedocs.io/en/latest/drmaa.html

4. 应用

4.1 写一个简单应用

#!/usr/bin/env python

import drmaa
import os

class SGE():
    def __init__(self):
        self.__sgeProject="Test"
        self.__sgeQueue="test.q"
        self.__maxvmen="1G"
        self.__proc="1"
        self.__script=""
        self.__workdir=""
        self.__session=""
    def setSgeProject(self, p):
        self.__sgeProject=p
    def getSgeProject(self):
        return self.__sgeProject
    def setSgeQueue(self, q):
        self.__sgeQueue=q
    def getSgeQueue(self):
        return self.__sgeQueue
    def setMaxvmem(self, m):
        self.__maxvmem=m
    def setNumproc(self, proc):
        self.__proc=proc
    def getMaxvmem(self):
        return self.__maxvmem
    def setScript(self, s):
        self.__script=s
    def getScript(self):
        return self.__script
    def setWorkDir(self, w):
        self.__workdir=w
    def getWorkDir(self):
        return self.__workdir
    def setSession(self, ss):
        self.__session=ss
    def getSession(self):
        return self.__session

    def submit(self):
        st=os.stat(self.__script)    #系统 stat 的调用，返回stat结构
        os.chmod(self.__script, st.st_mode | stat.S_IEXEC | stat.S_IXGRP)  #S_IEXEC是S_IXUSR同义词，所有者具有执行权限；S_IXGRP，组具有执行权限
        jt = self.__session.createJobTemplate() ##分配工作模板
        jt.remoteCommand = self.__script  #remoteCommand属性找到要执行的脚本
        jt.workingDirectory = self.__workdir  #设定当前工作目录
        par4qsub="".join(["-binding linear:",self.__proc," -P ",self.__sgeProject," -q ",self.__sgeQueue," -cwd -l ","vf=",self.__maxvmem," -l p=",self.__proc])
        print('qsub {0} {1}'.format(par4qsub,self.__script))
        jt.nativeSpecification = par4qsub #传递给jt的指令
        jobid =self.__session.runJob(jt) #将分配给作业的ID传递给的字符数组
        self.__session.deleteJobTemplate(jt)
        return jobid

def main():
    with drmaa.Session() as s:
        sgeObj = SGE()
        sgeObj.setSession(session)
        sgeObj.setSgeProject("SGEProject")
        sgeObj.setSgeQueue("SGEQueue")
        dict_qsub_id={}
        joblist=[]
        cwdir=os.path.join(getcwd())
        sgeObj.setWorkDir(cwdir)
        sgeObj.setScript(os.path.join(cwdir,"test.sh"))
        sgeObj.setMaxvmem("Memory")
        sgeObj.setNumproc("1")
        jobid=sgeObj.submit()
        dict_qsub_id[jobid]=os.path.join(cwdir,"test.sh")
        joblist.append(jobid)

        s.synchronize(joblist, drmaa.Session.TIMEOUT_WAIT_FOREVER, False) #设为false
        for curjob in joblist:
            retval = session.wait(curjob, drmaa.Session.TIMEOUT_WAIT_FOREVER)
            print('Job: {0} finished with status {1}'.format(retval.jobId,retval.hasExited))

if __name__=="__main__":
    main()

4.2 应用示例2

说明：用MEGAN做微生物物种注释时，blast nr得到的结果太多，一次性注释太久，因此将其拆分开来。Linux环境中使用MEGAN注释需要调用xvfb-run（相当于一个wrapper， 给应用程序提供虚拟的 X server），但xvfb不能并行，当我同时运行多个注释时，MEGAN生成的临时文件rma会发生冲突，因而无法同时得到注释结果。不能并行就只能串行，但我拆分了上百份文件，不可能手动一个个投递，如何一个个任务依次运行呢？可以用drmaa写个循环。

#继承上面的SGE类
def check_status(retval,running_log,path,email):
    if(retval.exitStatus != 0):  #出错的要发邮件通知
        running_log.write('{0}\nError job: {1}\n  exitStatus: {2}\n  wasAborted: {3}\n  maxvmem: {4}Gb\n  Qsub_id: {5}\n\n'.format("="*40, path, retval.exitStatus, retval.wasAborted, str(float(retval.resourceUsage['maxvmem'])/1000000000), retval.jobId ))
        running_log.close()
        emailObj = Email()
        emailObj.setReceiver(email)
        emailObj.sendMail('<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body><p>Error job: {0}</p><p>  exitStatus: {1}</p><p>wasAborted: {2}</p><p>maxvmem: {3}</p></body></html>'.format(path, retval.exitStatus, retval.wasAborted, str(float(retval.resourceUsage['maxvmem'])/1000000000) ))
        os._exit(0)
    elif(retval.wasAborted == True):  #手工终止的不需要发邮件通知
        running_log.write('{0}\nAborted job: {1}\n  exitStatus: {2}\n  wasAborted: {3}\n  maxvmem: {4}Gb\n  Qsub_id: {5}\n\n'.format("="*40, path, retval.exitStatus, retval.wasAborted, str(float(retval.resourceUsage['maxvmem'])/1000000000) , retval.jobId))
        running_log.close()
        os._exit(0)
    else:
        running_log.write('{0}\nFinished job: {1}\n  exitStatus: {2}\n  wasAborted: {3}\n  maxvmem: {4}Gb\n  Qsub_id: {5}\n\n'.format("="*40, path, retval.exitStatus, retval.wasAborted, str(float(retval.resourceUsage['maxvmem'])/1000000000), retval.jobId ))
        running_log.flush()   #立即写到文件中。

def main():
    project_dir=os.getcwd()
    running_log=open("running.log", "w")
    qsub_id_log=open("qsub_id.log", "w")
    dict_qsub_id={}
    with drmaa.Session() as session:
        sgeObj = Sge()
        sgeObj.setSession(session)
        for i in range(1,101):  #拆分的一百份任务
            joblist=[]
            subdir="tax_"+str(i)
            cwdir=os.path.join(project_dir,subdir)
            sgeObj.setWorkDir(cwdir)
            shell="run_tax_"+str(i)+".sh"
            sgeObj.setScript(os.path.join(cwdir,shell))
            sgeObj.setMaxvmem("1G")
            sgeObj.setNumproc("1")
            jobid=sgeObj.submit()
            qsub_id_log.write(jobid+"\n")
            qsub_id_log.flush()
            dict_qsub_id[jobid]=os.path.join(cwdir,shell)
            joblist.append(jobid)
            session.synchronize(joblist, drmaa.Session.TIMEOUT_WAIT_FOREVER, False)
            for curjob in joblist:
                retval = session.wait(curjob, drmaa.Session.TIMEOUT_WAIT_FOREVER)
                check_status(retval,running_log,dict_qsub_id[retval.jobId],"123456@qq.com")
        emailObj = Email()
        emailObj.setReceiver("123456@qq.com")
        emailObj.sendMail('<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body><p>Finished job: {0}</p></body></html>'.format(project_dir))
        print ("{0} All work is done! {0}>".format("="*30))
        running_log.close()
        qsub_id_log.close()

if __name__=="__main__":
    main()

Ref：https://drmaa-python.readthedocs.io/en/latest/tutorials.html#starting-and-stopping-a-session