[Bigjob-users] [saga-users] Local installation of SAGA and running example of BIGJOB

Wed Dec 7 11:50:13 CST 2011

Sorry, I forgot to do adaptor configuration. Too many machines!! I'm
attaching new errors along with the files. I'll try it on sierra as
india gave similar errors (and it's down).

Start Pilot Job/BigJob at: fork://localhost
DEBUG:root:init BigJob w/: advert://localhost/?dbtype=sqlite3
DEBUG:root:['/home/kkadam/../', '/home/kkadam',
'/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/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/external/python/2.7.1/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',
'/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/2.7/site-packages',
'/home/kkadam',
'/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']
DEBUG:root:Utilizing ADVERT Backend
DEBUG:root:Parsing URL: advert://localhost/?dbtype=sqlite3
DEBUG:root:Server: localhost Port None server_connect_url: None
DEBUG:root:initialized BigJob: bigjob:c17323dc-20f9-11e1-94f1-a4badb0c3696
DEBUG:root:create pilot job entry on backend server:
bigjob:c17323dc-20f9-11e1-94f1-a4badb0c3696:localhost
DEBUG:root:create advert entry:
advert://localhost/bigjob/c17323dc-20f9-11e1-94f1-a4badb0c3696/localhost
Traceback (most recent call last):
  File "example_local_single.py", line 113, in <module>
    main()
  File "example_local_single.py", line 79, in main
    processes_per_node)
  File "/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob/bigjob_manager.py",
line 154, in start_pilot_job
    self.coordination.set_pilot_state(self.pilot_url,
str(saga.job.Unknown), False)
  File "/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/coordination/bigjob_coordination_advert.py",
line 67, in set_pilot_state
    pilot_dir = saga.advert.directory(saga.url(pilot_url),
saga.advert.Create | saga.advert.CreateParents |
saga.advert.ReadWrite)
saga.no_success: SAGA(NoSuccess): default_advert: Unable to establish
connection to database_connection: dbname='advertdb' host='localhost'
password='SAGA_client' port='5432' user='SAGA' Cannot establish
connection to the database: could not connect to server: Connection
refused
	Is the server running on host "localhost" and accepting
	TCP/IP connections on port 5432?

Cancel Pilot Job
stop pilot job: bigjob:c17323dc-20f9-11e1-94f1-a4badb0c3696:localhost
DEBUG:root:delete pilot job:
bigjob:c17323dc-20f9-11e1-94f1-a4badb0c3696:localhost

Thanks,
-Kundan

On Wed, Dec 7, 2011 at 11:22 AM, pradeep kumar Mantha
<pmanth2 at tigers.lsu.edu> wrote:
> Hi!
>
>   Could you please let us know what coordination URL you are using in the
> example.
>
>   If you followed the  Advert adaptor configuration under bigjob tutorial.
>    Please let us know what is the content of $HOME/.saga.ini
> & $HOME/saga_adaptors/saga_adaptor_default_advert.ini
>
> There is a problem accessing advert service from compute nodes on alamo. A
> ticket has been raised for Futuregrid.  So I suggest you to use Sierra or
> India in the mean while.
>
> thanks
> pradeep.
>
>
>
>
>
> On Wed, Dec 7, 2011 at 11:04 AM, Kundan Kadam <kkadam1 at tigers.lsu.edu>
> wrote:
>>
>> Thanks all for prompt reply!! I'll try to keep SAGA and BIGJOB
>> questions only to respective mailing-list from now on.
>>
>> SAGA
>> I'll install python-boost on my account. I'll get in touch with you in
>> case of any problems. Thanks again!!
>>
>>
>> BIGJOB
>> I'm on alamo. I load SAGA in my environment and run the example file,
>> output is as follows.
>>
>> $ /N/soft/SAGA/external/python/2.7.1/gcc-4.1.2//bin/python
>> example_local_single.py
>>
>> Start Pilot Job/BigJob at: fork://localhost
>> DEBUG:root:init BigJob w/: advert://localhost/?dbtype=sqlite3
>> DEBUG:root:['/home/kkadam/../', '/home/kkadam',
>>
>> '/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/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/external/python/2.7.1/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',
>> '/N/soft/SAGA/external/python/2.7.1/gcc-4.1.2/lib/2.7/site-packages',
>> '/home/kkadam',
>> '/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']
>> DEBUG:root:Utilizing ADVERT Backend
>> DEBUG:root:Parsing URL: advert://localhost/?dbtype=sqlite3
>> DEBUG:root:Server: localhost Port None server_connect_url: None
>> DEBUG:root:initialized BigJob: bigjob:eee22e8a-20f4-11e1-ad65-a4badb0c3696
>> DEBUG:root:create pilot job entry on backend server:
>> bigjob:eee22e8a-20f4-11e1-ad65-a4badb0c3696:localhost
>> DEBUG:root:create advert entry:
>> advert://localhost/bigjob/eee22e8a-20f4-11e1-ad65-a4badb0c3696/localhost
>> Traceback (most recent call last):
>>  File "example_local_single.py", line 113, in <module>
>>    main()
>>  File "example_local_single.py", line 79, in main
>>    processes_per_node)
>>  File
>> "/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/bigjob/bigjob_manager.py",
>> line 154, in start_pilot_job
>>    self.coordination.set_pilot_state(self.pilot_url,
>> str(saga.job.Unknown), False)
>>  File
>> "/N/soft/SAGA/saga/1.6/gcc-4.1.2/lib/python2.7/site-packages/BigJob-0.3.2-py2.7.egg/coordination/bigjob_coordination_advert.py",
>> line 67, in set_pilot_state
>>    pilot_dir = saga.advert.directory(saga.url(pilot_url),
>> saga.advert.Create | saga.advert.CreateParents |
>> saga.advert.ReadWrite)
>> saga.no_success: SAGA(NoSuccess): default_advert: Unable to establish
>> connection to database_connection: dbname='advertdb' host='localhost'
>> password='<password>' port='5432' user='<username>' Cannot establish
>> connection to the database: could not connect to server: Connection
>> refused
>>        Is the server running on host "localhost" and accepting
>>        TCP/IP connections on port 5432?
>>
>>
>> Cancel Pilot Job
>> stop pilot job: bigjob:eee22e8a-20f4-11e1-ad65-a4badb0c3696:localhost
>> DEBUG:root:delete pilot job:
>> bigjob:eee22e8a-20f4-11e1-ad65-a4badb0c3696:localhost
>>
>>
>>
>> Thanks,
>> -Kundan
>>
>>
>>
>>
>> On Tue, Dec 6, 2011 at 2:17 PM, Melissa Romanus
>> <melissa.romanus at rutgers.edu> wrote:
>> > Hi Andre,
>> >
>> > This topic interests me as well. Are there tutorials for using ssh to
>> > launch bigjob on the website?
>> >
>> > -Melissa
>> >
>> > On Tue, Dec 6, 2011 at 2:59 PM, Andre Luckow <andre.luckow at gmail.com>
>> > wrote:
>> >> Hi Kundan,
>> >> Can you sent the complete error. Are you using ssh to launch BJ; then
>> >> you
>> >> need to setup certificate based authentication.
>> >>
>> >> Best,
>> >> Andre
>> >>
>> >>
>> >> On Tuesday, December 6, 2011, Kundan Kadam <kkadam1 at tigers.lsu.edu>
>> >> wrote:
>> >>> This is embarrassing but I am having trouble installing SAGA locally
>> >>> on any of the Futuregrid machines. I could only install SAGA core on
>> >>> hotel, but none of the python bindings or adapters. Problem is
>> >>> location of python, even when it is apparently correct, there's an
>> >>> error saying boost python flags/ headers not found. Am I missing
>> >>> something obvious or should I contact Futuregrid support?
>> >>>
>> >>> However I could get the the preinstalled SAGA loaded into my
>> >>> environment.
>> >>> (using
>> >>> http://www.saga-project.org/documentation/deployment/xsede-fg) I got
>> >>> the BIGJOB installed.  (Using method b of
>> >>> http://faust.cct.lsu.edu/trac/bigjob/wiki/install) And apparently it
>> >>> works because I can say import saga and import bigjob in python
>> >>> without errors.
>> >>>
>> >>> Problem is running examples. (example_local_single.py etc) The
>> >>> tutorial (http://faust.cct.lsu.edu/trac/bigjob/wiki/Tutorials) says
>> >>> just to run it without modifying the file. But it gives an error
>> >>> saying "Are you sure you have access to localhost?" or similar. Do I
>> >>> need to configure the framework before that somehow?
>> >>>
>> >>> At the moment the machines are down for monthly maintainance.
>> >>>
>> >>> Thanks,
>> >>> -Kundan
>> >>> _______________________________________________
>> >>> saga-users mailing list
>> >>> saga-users at cct.lsu.edu
>> >>> https://mail.cct.lsu.edu/mailman/listinfo/saga-users
>> >>>
>> >>
>> >> _______________________________________________
>> >> saga-users mailing list
>> >> saga-users at cct.lsu.edu
>> >> https://mail.cct.lsu.edu/mailman/listinfo/saga-users
>> >>
>> _______________________________________________
>> Bigjob-users mailing list
>> Bigjob-users at mail.cct.lsu.edu
>> https://mail.cct.lsu.edu/mailman/listinfo/bigjob-users
>
>
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