qstat和长工作名称

Question

我怎样才能qstat给我完整的工作名称？

我知道qstat -r提供有关任务的详细信息,但它太多了,并且包含了资源要求.

该qstat -r输出是这样的:

 131806 0.25001 tumor_foca ajalali      qw    09/29/2014 15:49:41                                    1 2-100:1
       Full jobname:     tumor_focality-TCGA-THCA-ratboost_linear_svc
       Hard Resources:   distribution=wheezy (0.000000)
                         h_rt=72000 (0.000000)
                         mem_free=15G (0.000000)
                         h_vmem=15G (0.000000)
                         h_stack=256M (0.000000)
       Soft Resources:   
 131807 0.25001 vital_stat ajalali      qw    09/29/2014 15:49:41                                    1 2-100:1
       Full jobname:     vital_status-TCGA-LGG-ratboost_linear_svc
       Hard Resources:   distribution=wheezy (0.000000)
                         h_rt=72000 (0.000000)
                         mem_free=15G (0.000000)
                         h_vmem=15G (0.000000)
                         h_stack=256M (0.000000)
       Soft Resources:   

现在我唯一的选择就是根据grep需要输出:

$ qstat -r | grep "Full jobname" -B1
--
 131806 0.25001 tumor_foca ajalali      qw    09/29/2014 15:49:41                                    1 2-100:1
       Full jobname:     tumor_focality-TCGA-THCA-ratboost_linear_svc
--
 131807 0.25001 vital_stat ajalali      qw    09/29/2014 15:49:41                                    1 2-100:1
       Full jobname:     vital_status-TCGA-LGG-ratboost_linear_svc

我能做得更好,以获得更好的输出吗？

Answer 1

这有点凌乱,但它可以作为命令历史记录中的简单解决方案.所有标准工具.输出与普通qstat调用的输出几乎相同,但是你不会得到标题:

一内胆:

qstat -xml | tr '\n' ' ' | sed 's#<job_list[^>]*>#\n#g' \
  | sed 's#<[^>]*>##g' | grep " " | column -t

命令描述:

将作业列为XML:

qstat -xml

删除所有换行符:

tr '\n' ' '

在列表中的每个作业条目之前添加换行符:

sed 's#<job_list[^>]*>#\n#g'

删除所有XML内容:

sed 's#<[^>]*>##g'

哈克最后添加换行符:

grep " "

Columnize:

column -t

示例输出

351996  0.50502  ProjectA_XXXXXXXXX_XXXX_XXXXXX                user123  r   2015-06-25T15:38:41  xxxxx-sim01@xxxxxx02.xxxxx.xxx  1
351997  0.50502  ProjectA_XXX_XXXX_XXX                         user123  r   2015-06-25T15:39:26  xxxxx-sim01@xxxxxx23.xxxxx.xxx  1
351998  0.50502  ProjectA_XXXXXXXXXXXXX_XXXX_XXXX              user123  r   2015-06-25T15:40:26  xxxxx-sim01@xxxxxx14.xxxxx.xxx  1
351999  0.50502  ProjectA_XXXXXXXXXXXXXXXXX_XXXX_XXXX          user123  r   2015-06-25T15:42:11  xxxxx-sim01@xxxxxx19.xxxxx.xxx  1
352001  0.50502  ProjectA_XXXXXXXXXXXXXXXXXXXXXXX_XXXX_XXXX    user123  r   2015-06-25T15:42:11  xxxxx-sim01@xxxxxx11.xxxxx.xxx  1
352008  0.50501  runXXXX69                                     usr1     r   2015-06-25T15:49:04  xxxxx-sim01@xxxxxx17.xxxxx.xxx  1
352009  0.50501  runXXXX70                                     usr1     r   2015-06-25T15:49:04  xxxxx-sim01@xxxxxx01.xxxxx.xxx  1
352010  0.50501  runXXXX71                                     usr1     r   2015-06-25T15:49:04  xxxxx-sim01@xxxxxx06.xxxxx.xxx  1
352011  0.50501  runXXXX72                                     usr1     r   2015-06-25T15:49:04  xxxxx-sim01@xxxxxx21.xxxxx.xxx  1
352012  0.50501  runXXXX73                                     usr1     r   2015-06-25T15:49:04  xxxxx-sim01@xxxxxx13.xxxxx.xxx  1
352013  0.50501  runXXXX74                                     usr1     r   2015-06-25T15:49:04  xxxxx-sim01@xxxxxx11.xxxxx.xxx  1

Answer 2

也许更简单的解决方案：将 SGE_LONG_JOB_NAMES 设置为 -1，qstat 将计算出名称列的大小：

export SGE_LONG_JOB_NAMES=-1
qstat -u username

为我工作。

干杯!

Answer 3

这个脚本效果很好.它看起来像是来自剑桥.http://www.hep.ph.ic.ac.uk/~dbauer/grid/myqstat.py

对于Python 3:

#!/usr/bin/python
import xml.dom.minidom
import os
import sys
import string    

f=os.popen('qstat -u \* -xml -r')

dom=xml.dom.minidom.parse(f)


jobs=dom.getElementsByTagName('job_info')
run=jobs[0]

runjobs=run.getElementsByTagName('job_list')


def fakeqstat(joblist):
    for r in joblist:
        try:
            jobname=r.getElementsByTagName('JB_name')[0].childNodes[0].data
            jobown=r.getElementsByTagName('JB_owner')[0].childNodes[0].data
            jobstate=r.getElementsByTagName('state')[0].childNodes[0].data
            jobnum=r.getElementsByTagName('JB_job_number')[0].childNodes[0].data
            jobtime='not set'
            if(jobstate=='r'):
                jobtime=r.getElementsByTagName('JAT_start_time')[0].childNodes[0].data
            elif(jobstate=='dt'):
                jobtime=r.getElementsByTagName('JAT_start_time')[0].childNodes[0].data
            else:
                jobtime=r.getElementsByTagName('JB_submission_time')[0].childNodes[0].data

            print(jobnum, '\t', jobown.ljust(16), '\t', jobname.ljust(16),'\t', jobstate,'\t',jobtime)
        except Exception as e:
            print(e)

fakeqstat(runjobs)

对于Python 2:

#!/usr/bin/python
import xml.dom.minidom
import os
import sys
import string
#import re


f=os.popen('qstat -u \* -xml -r')

dom=xml.dom.minidom.parse(f)


jobs=dom.getElementsByTagName('job_info')
run=jobs[0]

runjobs=run.getElementsByTagName('job_list')


def fakeqstat(joblist):
        for r in joblist:
                jobname=r.getElementsByTagName('JB_name')[0].childNodes[0].data
                jobown=r.getElementsByTagName('JB_owner')[0].childNodes[0].data
                jobstate=r.getElementsByTagName('state')[0].childNodes[0].data
                jobnum=r.getElementsByTagName('JB_job_number')[0].childNodes[0].data
                jobtime='not set'
                if(jobstate=='r'):
                        jobtime=r.getElementsByTagName('JAT_start_time')[0].childNodes[0].data
                elif(jobstate=='dt'):
                        jobtime=r.getElementsByTagName('JAT_start_time')[0].childNodes[0].data
                else:
                        jobtime=r.getElementsByTagName('JB_submission_time')[0].childNodes[0].data



                print  jobnum, '\t', jobown.ljust(16), '\t', jobname.ljust(16),'\t', jobstate,'\t',jobtime


fakeqstat(runjobs)