目錄
搭建流程時，我們把各個模塊腳本都寫好了，現在通過編寫主程序將模塊串起來，那么怎么樣依次（或者並行）將任務自動投遞到集群呢？就是說這一步運行完之后，下一步自動運行。我們當然可以在腳本中設一個標志，反復檢查這一個標志是否出現來決定是否運行下一步，但這種方法太原始，太多弊端了，耗內存，無法並行，且不可預料的出錯。那么，有沒有相應的工具來管理集群任務投遞？有，python的drmaa包可以實現。
1. drmaa簡介
Distributed Resource Management Application API (DRMAA)，即分布式資源管理應用程序API，是一種高級 開放網格論壇（Open_Grid_Forum）應用程序接口規范，用於向分布式資源管理（DRM）系統（例如集群或網格計算提交和控制作業）。API的范圍涵蓋了應用程序提交，控制和監視DRM系統中執行資源上的作業所需的所有高級功能。DRMAA API已在Sun的Grid Engine（SGE）和Condor等作業管理調度系統中實現。關於SGE可參考我的推文：集群SGE作業調度系統
C、C++、Perl、Python等程序語言都開發有相應的drmaa包來實現SGE集群的任務管理。這里記錄下drmaa-python：
Github：drmaa-python
PyPi：https://pypi.org/project/drmaa/
2. 安裝和配置
要求：Python2.7+；與DRMAA兼容的集群，如SGE。
#安裝
pip install drmaa
#設置路徑
export SGE_ROOT=/path/to/gridengine #SGE安裝的路徑
export SGE_CELL=default
#設置庫
export DRMAA_LIBRARY_PATH=/usr/lib/libdrmaa.so.1.0
#libdrmaa.so.1.0 C動態庫，是libdrmaa-dev包的一部分
3. 示例
3.1 開始和終止會話
Session
#!/usr/bin/env python
import drmaa
def main():
"""Create a drmaa session and exit"""
with drmaa.Session() as s: #自動初始化，組織工作提交
print('A session was started successfully')
#with結束自動exit()，大部分函數都要在exit()前執行，如runJob/wait，getContact可在exit()后。
if __name__=='__main__':
main()
使用可重新連接的會話，可以將DRMAA庫初始化為上一個會話，從而允許該庫訪問該會話的作業列表.
#!/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) #初始化上個session
print('Session was restarted successfullly')
s.exit()
if __name__=='__main__':
main()
3.2 運行工作
假設已知當前目錄有一個sleeper.sh腳本，后接兩個參數：
#!/bin/bash
echo "Hello world, the answer is $1"
sleep 3s
echo "$2 Bye world!"
drmaa將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(存儲提交作業的信息結構)
jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh') #設置remoteCommand屬性，找到要運行的程序。
#路徑默認為用戶的主目錄，相對路徑用workingDirectory屬性
jt.args = ['42', 'Simon says:'] #執行文件的參數
jt.joinFiles=True
jobid = s.runJob(jt) #將分配給作業的ID放入我們傳遞給的字符數組中runJob()
print('Your job has been submitted with ID %s' % jobid)
# jobid = s.runBulkJobs(jt, 1, 30, 2) #提交一個數組作業
# print('Your jobs have been submitted with IDs %s' % jobid)
print('Cleaning up')
s.deleteJobTemplate(jt) #刪除作業模板，釋放作業模板保留的DRMAA內存，但對提交的作業沒有影響
if __name__=='__main__':
main()
3.3 等待工作
即等待任務完成
#!/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) #調用wait()等待作業結束
print('Job: {0} finished with status {1}'.format(retval.jobId, retval.hasExited))
#以下是提交多個作業的等待處理，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()返回一個JobInfo元組，其具有下面的屬性： jobId，hasExited，hasSignal，terminatedSignal，hasCoreDump， wasAborted，exitStatus，resourceUsage
synchronize()的第3個參數是該synchronize()的調用是否在工作后清除。工作完成后，它會留下一些統計信息，如退出狀態和用途，直到wait() 或synchronize()的處理狀態變為True。確保每一項任務對這兩個函數之一調用是很有必要的，否則可能引起內存泄漏。如果想要每一項任務恢復統計信息，可將synchronize()設置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，每一項工作等待一次
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) #刪除剛提交的作業
print('Cleaning up')
s.deleteJobTemplate(jt)
if __name__=='__main__':
main()
還可以用control()來暫停，恢復，保留或釋放工作。control()還可用於控制未通過DRMAA提交的作業，可以將任何有效的SGE作業ID傳遞control()為要刪除的作業ID。
3.5 查詢工作狀態
#!/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()獲取作業的狀態
time.sleep(5)
print('Cleaning up')
s.deleteJobTemplate(jt)
if __name__=='__main__':
main() #確定工作狀態並報告
其他更多關於JobInfo，JobTemplate，Session等方法的屬性可參考：https://drmaa-python.readthedocs.io/en/latest/drmaa.html
4. 應用
4.1 寫一個簡單應用
#!/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) #系統 stat 的調用，返回stat結構
os.chmod(self.__script, st.st_mode | stat.S_IEXEC | stat.S_IXGRP) #S_IEXEC是S_IXUSR同義詞，所有者具有執行權限；S_IXGRP，組具有執行權限
jt = self.__session.createJobTemplate() ##分配工作模板
jt.remoteCommand = self.__script #remoteCommand屬性找到要執行的腳本
jt.workingDirectory = self.__workdir #設定當前工作目錄
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 #傳遞給jt的指令
jobid =self.__session.runJob(jt) #將分配給作業的ID傳遞給的字符數組
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) #設為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 應用示例2
說明：用MEGAN做微生物物種注釋時，blast nr得到的結果太多，一次性注釋太久，因此將其拆分開來。Linux環境中使用MEGAN注釋需要調用xvfb-run（相當於一個wrapper， 給應用程序提供虛擬的 X server），但xvfb不能並行，當我同時運行多個注釋時，MEGAN生成的臨時文件rma會發生沖突，因而無法同時得到注釋結果。不能並行就只能串行，但我拆分了上百份文件，不可能手動一個個投遞，如何一個個任務依次運行呢？可以用drmaa寫個循環。
#繼承上面的SGE類
def check_status(retval,running_log,path,email):
if(retval.exitStatus != 0): #出錯的要發郵件通知
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): #手工終止的不需要發郵件通知
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() #立即寫到文件中。
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): #拆分的一百份任務
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