How can I get qstat to give me full job names?
I know qstat -r gives detailed information about the task, but it's too much and the resource requirements are included.
The qstat -r output is like:
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:
Right now my only option is to grep the output as I need:
$ 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
Can I do it better to have a nicer output?
This on is a bit messy, but it works as a simple solution to have in the command history. All standard tools. Output is pretty much the same as what you get from a normal qstat call, but you won't get the headers:
One-liner:
qstat -xml | tr '\n' ' ' | sed 's#<job_list[^>]*>#\n#g' \
| sed 's#<[^>]*>##g' | grep " " | column -t
Description of commands:
List jobs as XML:
qstat -xml
Remove all newlines:
tr '\n' ' '
Add newline before each job entry in the list:
sed 's#<job_list[^>]*>#\n#g'
Remove all XML stuff:
sed 's#<[^>]*>##g'
Hack to add newline at the end:
grep " "
Columnize:
column -t
Example output
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
This script works pretty well. It looks like it is from cambridge. http://www.hep.ph.ic.ac.uk/~dbauer/grid/myqstat.py
For 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)
For 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)
Maybe an easier solution: set SGE_LONG_JOB_NAMES to -1, and qstat will figure out the size of the name column:
export SGE_LONG_JOB_NAMES=-1
qstat -u username
Works for me.
Cheers!
I am currently writing my own qstat wrapper in order to get a clean, useful and customizable output.
Here is the github repository. The project has grown too much for the code to be pasted in this message.
It comes with an installer and should work without any problem with both Python 2.7 and 3 (the installation script makes the modifications if needed). qjobs -h provides some help on the available options. I will write a more complete documentation in the following days on the github wiki.
I will update this message as often as possible to stick to the current state of the project. Please feel free to comment here (or on github) to ask for features/report problems.
In the near future, I will try to add a fully interactive mode to browse the job list more easily. Of course, the classic text output will be still available (it could be useful to e-mail the output, or for a quick check of the pending/running jobs).
Example output
Command qjobs gives:
5599109 short_name r 2015-06-25 10:27:39 queue1
5599110 jobName r 2015-06-25 10:35:39 queue2
5599111 a_long_job_name qw 2015-06-25 10:40:39
5599112 foo qw 2015-06-25 10:40:39
5599113 bar qw 2015-06-25 10:40:39
5599114 baz qw 2015-06-25 10:40:39
5599115 beer qw 2015-06-25 10:40:39
tot: 7
r: 2 qw: 5
Command qjobs -o gives:
tot: 7
r: 2 qw: 5
Command qjobs -o inek -t gives (e is elapsed time since start/sub time, the format is customizable using the Format Spec. Mini-Language of Python; k is complete queue name, with domain):
5598985 SpongeBob 522:02 (21.75 days) queue1@node23.domain.fake
5598987 ping_java 521:47 (21.74 days) queue1@node39.domain.fake
5598988 run3.14 521:46 (21.74 days) queue2@node40.domain.fake
5598990 strange_job_42 521:42 (21.74 days) queue3@node36.domain.fake
5598991 coffee-maker 521:39 (21.74 days) queue2@node34.domain.fake
5598992 dumbtask 521:29 (21.73 days) queue1@node14.domain.fake
qjobs -i gives a complete list of the available 'items'. Each of this item is available as:
- a column output (with
-o ITEMS); - as a criteria to count the job and produces total output, with
-t(e.g.-t sto count by state as in the two first examples); - as a criteria to sort the job with
-s, default is-s ipsmeaning that the job list is sorted by ID, then by priority and finally by state before being printed.
The result of qjobs -i is:
i: job id
p: job priority
n: job name
o: job owner
s: job state
t: job start/submission time
e: elapsed time since start/submission
q: queue name without domain
d: queue domain
k: queue name with domain
r: requested queue(s)
l: number of slots used
Thanks to JLT for nice simple code. I've expanded it a bit to fit my needs and make it look nice.
Sample Output:
Job ID Job Name Owner Status
------ ------------------------------------ ------ ------
201716 AtacSilN100400K mtsige R
201771 IsoOnGrap400K mtsige R
202067 AtacOnSilica400K mtsige R
202100 AtacGrapN100400K mtsige R
202135 AtacOnSilc400K mtsige R
202145 AtacOnGrap400K mtsige R
202152 AtacOnGraphN3360K mtsige R
202161 AtacticSilicaN10 mtsige R
202163 AtacGrapN10 mtsige R
202169 AtacSilcN10 mtsige R
202192 wallpmma07 am110 R
202193 wallpmma03 am110 R
202194 att03wpm_95solps am110 R
202202 AtacticSilicaN3 mtsige R
203260 8test18_trop_2p ico R
203359 parseAll_Bob/Sub951By50/Cyl20A_atom1 oge1 R
203360 parseAll_Bob/Sub951By50/Cyl30A_atom1 oge1 R
203361 parseAll_Bob/Sub951By50/Cyl30A_atom2 oge1 R
Code:
#!/opt/bin/python3
import os
import xml.etree.ElementTree as ET
#Fields
fields=['Job_Id','Job_Name','Job_Owner','job_state']
names=['Job ID','Job Name','Owner','Status']
#Get job info
f = os.popen('qstat -x')
tree = ET.parse(f)
root = tree.getroot()
n_fields=len(fields)
jobs=[[job.find(field).text for field in fields] for job in root]
max_lengths=[len(name) for name in names]
sep=' '
#Identify max characer length per field
for j in jobs:
for i in range(n_fields):
#Chop off anything after and including '@' or '.' from all fields
if j[i].find('@')>0:
j[i]=j[i][:j[i].find('@')]
if j[i].find('.')>0:
j[i]=j[i][:j[i].find('.')]
if(len(j[i])>max_lengths[i]):
max_lengths[i]=len(j[i])
#Field names
for i in range(n_fields):
print('{s:^{length}}'.format(s=names[i],length=max_lengths[i]),end=sep)
print()
#Dashes
for i in range(n_fields):
print('-'*max_lengths[i],end=sep)
print()
#Jobs
for j in jobs:
for i in range(n_fields):
if j[i].find('@')>0:
j[i]=j[i][:j[i].find('@')]
print('{s:<{length}}'.format(s=j[i],length=max_lengths[i]),end=sep)
print()
For me the script of Physical Chemist didn't work so I wrote a very simple script using the xml.tree.ElementTree module which i regard as somewhat easier than xml.dom.minidom
import os
import xml.etree.ElementTree as ET
f = os.popen('qstat -x')
tree = ET.parse(f)
root = tree.getroot()
print "Job_Id walltime state nodes Job_Name"
print "------ -------- ----- --------------- --------------------------"
for job in root:
print job.find('Job_Id').text, " ",
print job.find('resources_used').find('walltime').text, " ",
print job.find('job_state').text, " ",
print job.find('Resource_List').find('nodes').text, " ",
print job.find('Job_Name').text
A poor KISS solution :
qstat -xml -f -u \* | fgrep JB_name | wc -l
python code
import xmltodict
import subprocess as sp
import pandas as pd
qstat_xml = sp.check_output(['qstat','--xml'], stderr=sp.STDOUT) # read xml
stat_dict = xmltodict.parse(qstat_xml) # convert to dict
job_list = stat_dict['Data']['Job'] # select job_list
job_df = pd.DataFrame(job_list) # convert to dataframe
print('columns', job_df.columns) # print available columns
column_list = ['Job_Id', 'Job_Name']
selection_df = job_df[column_list] # select columns
print(selection_df)
来源：https://stackoverflow.com/questions/26104116/qstat-and-long-job-names