[Bigjob-users] Attempt to run example_manyjob_affinity.py
Andre Luckow
aluckow at cct.lsu.edu
Sat Dec 10 15:52:09 CST 2011
Hi Paula,
did you run grid-proxy-init? Could you set:
export SAGA_VERBOSE=100
in your shell and re-send the log, please?
Thanks!
Andre
On Sat, Dec 10, 2011 at 10:44 PM, Paula Sanematsu
<psanem1 at tigers.lsu.edu> wrote:
> Hi Andre,
>
>> for launching remote jobs you certainly want to use Globus, i.e. GRAM
>> URLs. The bigjob_agent key in the resource_list does not need to be
>> set anymore!
>
>
> When I have this configuration for hotel
>
> resource_list.append( {"resource_url" :
> "gram://hotel.futuregrid.org/jobmanager-pbs", "number_of_processes" : "1",
> "allocation" : "myAllocation", "queue" : "workq", "bigjob_agent":
> ("/N/soft/SAGA/saga/1.5.3/gcc-4.1.2/lib/python2.7.1/site-packages/bigjob/bigjob_agent_launcher.sh"),
> "working_directory": (os.getcwd() + "/agent"), "walltime":10, "affinity" :
> "affinity1"})
>
> I get this error:
>
>
> DEBUG:root:Utilizing ADVERT Backend
> DEBUG:root:Parsing URL: advert://advert.cct.lsu.edu:8080
> DEBUG:root:Server: advert.cct.lsu.edu Port 8080 server_connect_url: None
> DEBUG:root:Initialized Coordination to: advert://advert.cct.lsu.edu:8080/
> (DB: )
> DEBUG:root:initialized BigJob: bigjob:7e9a80dc-2374-11e1-92c3-002215124496
> DEBUG:root:create pilot job entry on backend server:
> bigjob:7e9a80dc-2374-11e1-92c3-002215124496:localhost
> DEBUG:root:create advert entry:
> advert://advert.cct.lsu.edu:8080//bigjob/7e9a80dc-2374-11e1-92c3-002215124496/localhost?
>
> DEBUG:root:update state of pilot job to: Unknown Stopped: False
> DEBUG:root:set pilot state to: Unknown
> Adaptor specific modifications: fork
> Working directory: /N/u/paulasoo/HW06_E3/examples/manySJ_2BJ_diff/agent
>
> use standard proxy
> Submit pilot job to: fork://localhost/
> DEBUG:root:start bigjob at: gram://hotel.futuregrid.org/jobmanager-pbs
>
> DEBUG:root:init BigJob w/: advert://advert.cct.lsu.edu:8080
> DEBUG:root:Utilizing ADVERT Backend
> DEBUG:root:Parsing URL: advert://advert.cct.lsu.edu:8080
> DEBUG:root:Server: advert.cct.lsu.edu Port 8080 server_connect_url: None
> DEBUG:root:Initialized Coordination to: advert://advert.cct.lsu.edu:8080/
> (DB: )
> DEBUG:root:initialized BigJob: bigjob:7f793e3a-2374-11e1-92c3-002215124496
> DEBUG:root:create pilot job entry on backend server:
> bigjob:7f793e3a-2374-11e1-92c3-002215124496:hotel.futuregrid.org
> DEBUG:root:create advert entry:
> advert://advert.cct.lsu.edu:8080//bigjob/7f793e3a-2374-11e1-92c3-002215124496/hotel.futuregrid.org?
>
> DEBUG:root:update state of pilot job to: Unknown Stopped: False
> DEBUG:root:set pilot state to: Unknown
> Adaptor specific modifications: gram
> DEBUG:root:Escape RSL
> Working directory: /N/u/paulasoo/HW06_E3/examples/manySJ_2BJ_diff/agent
> use standard proxy
>
> Traceback (most recent call last):
> File "example_manyjob_affinity.py", line 61, in <module>
> mjs = many_job_affinity_service(resource_list, COORDINATION_URL)
> File
> "/N/u/paulasoo/.bigjob/python/lib/python2.7/site-packages/BigJob-0.3.31-py2.7.egg/bigjob_dynamic/many_job_affinity.py",
> line 19, in __init__
> super(many_job_affinity_service, self).__init__(bigjob_list,
> advert_host)
> File
> "/N/u/paulasoo/.bigjob/python/lib/python2.7/site-packages/BigJob-0.3.31-py2.7.egg/bigjob_dynamic/many_job.py",
> line 59, in __init__
> self.__init_bigjobs()
> File
> "/N/u/paulasoo/.bigjob/python/lib/python2.7/site-packages/BigJob-0.3.31-py2.7.egg/bigjob_dynamic/many_job.py",
> line 74, in __init_bigjobs
> self.__start_bigjob(i)
> File
> "/N/u/paulasoo/.bigjob/python/lib/python2.7/site-packages/BigJob-0.3.31-py2.7.egg/bigjob_dynamic/many_job.py",
> line 104, in __start_bigjob
> ppn)
> File
> "/N/u/paulasoo/.bigjob/python/lib/python2.7/site-packages/BigJob-0.3.31-py2.7.egg/bigjob/bigjob_manager.py",
> line 246, in start_pilot_job
> js = saga.job.service(lrms_saga_url)
> bad_parameter: SAGA(BadParameter): condor_job: Adaptor supports 'condor' and
> 'condorg' URL schemes, 'gram' is not supported.
>
> DEBUG:root:Cancel re-scheduler thread
> Exception AttributeError: "'many_job_affinity_service' object has no
> attribute 'stop'" in <bound method many_job_affinity_service.__del__ of
> 7e9a6c78-2374-11e1-92c3-002215124496> ignored
> Cancel Pilot Job
> stop pilot job: bigjob:7e9a80dc-2374-11e1-92c3-002215124496:localhost
> DEBUG:root:delete pilot job:
> bigjob:7e9a80dc-2374-11e1-92c3-002215124496:localhost
> Cancel Pilot Job
> stop pilot job:
> bigjob:7f793e3a-2374-11e1-92c3-002215124496:hotel.futuregrid.org
> DEBUG:root:delete pilot job:
> bigjob:7f793e3a-2374-11e1-92c3-002215124496:hotel.futuregrid.org
>
>> Please try to submit the job first from the hotel front node. Once you
>> are sure that Globus etc. is working you can do a remote submission.
>> E.g you need to make sure that you use the right BJ version on hotel
>> as well (ie. you need to double-check your PYTHONPATH etc.)
>
>
> I think I have BigJob in Hotel working properly, at least
> example_local_single.py and example_local_multiple worked. My PYTHONPATH is
>
> /gpfs/home/paulasoo/.bigjob/python/lib/python2.7/site-packages/:/gpfs/software/x86_64/el5/hotel/SAGA/saga/1.6/gcc-4.1.2//lib/python2.7/site-packages/:
>
> Thanks,
>
> Paula
>
>> Hope that helps.
>>
>> Best,
>> Andre
>>
>> On Fri, Dec 9, 2011 at 9:21 PM, Paula Sanematsu <psanem1 at tigers.lsu.edu>
>> wrote:
>> > Hi Andre,
>> >
>> >>
>> >> Please change numer_nodes to number_of_processes in line 51:
>> >>
>> >> resource_list.append( {"resource_url" : "fork://localhost/",
>> >> "number_of_processes" : "2", "allocation" : "myAllocation", ...
>> >
>> >
>> > I changed number_nodes to number_of_processes and it now runs. However,
>> > it
>> > seems like it is in a infinite loop, perhaps because my second machine
>> > is
>> > not configured properly? This is the configuration for my second
>> > machine:
>> >
>> > resource_list.append( {"resource_url" : "ssh://hotel.futuregrid.org",
>> > "number_of_processes" : "4", "allocation" : "myAllocation", "queue" :
>> > "workq", "bigjob_agent":
>> >
>> > ("/N/soft/SAGA/saga/1.5.3/gcc-4.1.2/lib/python2.7.1/site-packages/bigjob/bigjob_agent_launcher.sh"),
>> > "working_directory": (os.getcwd() + "/agent"), "walltime":10, "affinity"
>> > :
>> > "affinity1"})
>> >
>> > Here, I used the bigjob_agent_launcher.sh in the directory written above
>> > because it was the only place I could find it. Should I use something
>> > else
>> > for "bigjob_agent"? Also, I'm not sure whether
>> > ssh://hotel.futuregrid.org or
>> > gram://hotel.futuregrid.org/jobmanager-pbs should be used.
>> >
>> > This is the output that keeps coming up:
>> >
>> > Current states: {'New': 2, 'Unknown': 6}
>> > DEBUG:root:Reschedule Thread
>> > DEBUG:root:Big Job:
>> > bigjob:50ec186c-22a2-11e1-9a15-002215124496:localhost
>> > Cores: 0/2 State: Running Terminated: False #Required Cores: 1
>> > DEBUG:root:Big Job:
>> > bigjob:51d0e1cc-22a2-11e1-9a15-002215124496:hotel.futuregrid.org Cores:
>> > 4/4
>> > State: Unknown Terminated: False #Required Cores: 1
>> > DEBUG:root:found no active resource for sub-job => (re-) queue it
>> > DEBUG:root:free_cores: [0, 0] total_free_cores: 0
>> >
>> >>
>> >> Also, the BJ part of CSA is a bit old and contains some bugs. If
>> >> possible, try to install BJ in userspace (as outlined on the Wiki
>> >> page).
>> >>
>> >> It's fixed in BigJob-0.3.31 and SVN.
>> >
>> >
>> > I followed the instructions on the Wiki (b. Python Packaging and
>> > Virtualenv)
>> > and did an update. I looks like I have BigJob-0.3.31.
>> >
>> > Thanks,
>> >
>> > Paula
>> >
>> >
>> > On Thu, Dec 8, 2011 at 3:07 PM, Andre Luckow <aluckow at cct.lsu.edu>
>> > wrote:
>> >>
>> >> Hi Paula,
>> >> there is a small bug in the example:
>> >>
>> >> Please change numer_nodes to number_of_processes in line 51:
>> >>
>> >> resource_list.append( {"resource_url" : "fork://localhost/",
>> >> "number_of_processes" : "2", "allocation" : "myAllocation", ...
>> >>
>> >> Also, the BJ part of CSA is a bit old and contains some bugs. If
>> >> possible, try to install BJ in userspace (as outlined on the Wiki
>> >> page).
>> >>
>> >> It's fixed in BigJob-0.3.31 and SVN.
>> >>
>> >> Best,
>> >> Andre
>> >>
>> >>
>> >> On Thu, Dec 8, 2011 at 9:42 PM, Paula Sanematsu
>> >> <psanem1 at tigers.lsu.edu>
>> >> wrote:
>> >> > Hi,
>> >> >
>> >> > I'm trying to run example_manyjob_affinity.py on Sierra, but it
>> >> > doesn't
>> >> > complete (see my output below). I'm submitting the job from Sierra
>> >> > and
>> >> > would
>> >> > like to use Hotel as my second machine. Could you please advise me on
>> >> > how to
>> >> > proceed?
>> >> >
>> >> > In addition, is there anything wrong with the cct advert service? I
>> >> > could
>> >> > run example_local_single.py, but now it's not working.
>> >> >
>> >> > Thanks,
>> >> >
>> >> > Paula
>> >> >
>> >> > ManyJob load test with 8 jobs.
>> >> > Create manyjob service
>> >> > DEBUG:root:start bigjob at: fork://localhost/
>> >> > DEBUG:root:init BigJob w/: advert://advert.cct.lsu.edu:8080
>> >> > DEBUG:root:['/N/u/paulasoo/HW06_E3/examples/manySJ_2BJ_diff/../',
>> >> > '/N/u/paulasoo/HW06_E3/examples/manySJ_2BJ_diff',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/redis-2.2.4-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/virtualenv-1.6.4-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/threadpool-1.2.7-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/uuid-1.30-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/redis-2.2.4-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/threadpool-1.2.7-py2.7.egg',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/uuid-1.30-py2.7.egg',
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages',
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/2.7/site-packages',
>> >> > '/N/u/paulasoo/HW06_E3/examples/manySJ_2BJ_diff',
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/python27.zip',
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/python2.7',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/python2.7/plat-linux2',
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/python2.7/lib-tk',
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/python2.7/lib-old',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/python2.7/lib-dynload',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/python2.7/site-packages',
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/2.7/site-packages',
>> >> > '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/2.7/site-packages',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob_dynamic',
>> >> >
>> >> >
>> >> > '/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob_dynamic']
>> >> > DEBUG:root:Utilizing ADVERT Backend
>> >> > DEBUG:root:Parsing URL: advert://advert.cct.lsu.edu:8080
>> >> > DEBUG:root:Server: advert.cct.lsu.edu Port 8080 server_connect_url:
>> >> > None
>> >> > DEBUG:root:initialized BigJob:
>> >> > bigjob:6638ce9e-21d6-11e1-ac76-002215124496
>> >> > Traceback (most recent call last):
>> >> > File "example_manyjob_affinity.py", line 61, in <module>
>> >> > mjs = many_job_affinity_service(resource_list, COORDINATION_URL)
>> >> > File
>> >> >
>> >> >
>> >> > "/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob_dynamic/many_job_affinity.py",
>> >> > line 19, in __init__
>> >> > super(many_job_affinity_service, self).__init__(bigjob_list,
>> >> > advert_host)
>> >> > File
>> >> >
>> >> >
>> >> > "/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob_dynamic/many_job.py",
>> >> > line 59, in __init__
>> >> > self.__init_bigjobs()
>> >> > File
>> >> >
>> >> >
>> >> > "/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob_dynamic/many_job.py",
>> >> > line 74, in __init_bigjobs
>> >> > self.__start_bigjob(i)
>> >> > File
>> >> >
>> >> >
>> >> > "/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob_dynamic/many_job.py",
>> >> > line 98, in __start_bigjob
>> >> > bj_dict["number_of_processes"],
>> >> > KeyError: 'number_of_processes'
>> >> > Cancel Pilot Job
>> >> > stop pilot job:
>> >> > DEBUG:root:create advert entry: advert://advert.cct.lsu.edu:8080/
>> >> > DEBUG:root:update state of pilot job to: Done Stopped: True
>> >> > DEBUG:root:delete pilot job:
>> >> >
>> >> > _______________________________________________
>> >> > Bigjob-users mailing list
>> >> > Bigjob-users at mail.cct.lsu.edu
>> >> > https://mail.cct.lsu.edu/mailman/listinfo/bigjob-users
>> >> >
>> >
>> >
>
>
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