[Gate-users] Fwd: running simulation on gatelab.

Wed Feb 15 09:49:17 CET 2012

Hi Sanghyeb,

Are you able to do this operation on your own for now?
It should be included in some future Gate-Lab version.

Cheers,
Tristan

On 02/15/2012 09:41 AM, Pierre Gueth wrote:
> hi all,
>
> after looking at Sanghyeb simulation, it seems that all the trouble 
> come from non consistent macro encoding (more precisely dos/linux line 
> ending). a little "dos2unix mac/**" fixes the problem.
>
> best regards,
> pierre
>
>
> Le 14/02/2012 09:46, Tristan Glatard a écrit :
>> Hi Sanghyeb,
>>
>> The simulation output file only gives technical information which is 
>> not relevant unless there's something in the error file.
>>
>> The relevant information is in the "application error" and 
>> "application output" files of your jobs. You can find them under tab 
>> "Jobs summary" (2nd tab on the left), then right-click on a job and 
>> "view application output/error". All your jobs failed with 
>> "application error", which means that it is a GATE error, not a 
>> system error.
>>
>> There seem to be a problem with your macro:
>>>    ===  Process: Bremsstrahlung  ===
>>> Particle: e+
>>>     * Model(s):
>>>        - <!> *** Warning *** <!> No model selected!
>>> Particle: e-
>>>     * Model(s):
>>>        - StandardModel
>>>
>>>
>>>
>>>
>>> List of initialized processes:
>>>
>>>
>>>
>>> [Core-0] Initialization of geometry
>>> [Core-0] Initialization of physics
>>> [Core-0] Initialization of actors
>>> > ***** [G4-cerr] ***** COMMAND NOT FOUND <
>>> [Gate] Sorry, error in a macro command : abort.
>>>         Nb of children:       0
>> It should be validated before the GATE-Lab can run it.
>>
>> Cheers,
>> Tristan
>>
>>
>>
>> On 02/14/2012 12:52 AM, Lee, Sam (SAM LEE) wrote:
>>> Thanks for your help.
>>>
>>> I modified my script, and ran it on gatelab. However, I still have 
>>> not been successful. Application execution fails with an error.
>>>
>>> However, there is nothing in the "simulation error" log file. And 
>>> this is what I got from "Simulation output file".
>>>
>>> 2012-02-14 00:36:55,487 [Thread-22] WARN 
>>> fr.insalyon.creatis.gasw.executor.DataManager.run(DataManager.java:94) 
>>> - fr.insalyon.creatis.gasw.GaswException: Unable to replicate 
>>> '/grid/biomed/creatis/vip/data/users/sang_hyeb_lee/myGateSimus/inputs/file-3982686619571.zip' 
>>> from 
>>> 'srm://marsedpm.in2p3.fr/dpm/in2p3.fr/home/biomed/generated/2012-02-14/filef6c67bc1-6cb8-42c0-9a2f-d73df4008612': 
>>> Using grid catalog type: UNKNOWNUsing grid catalog : 
>>> lfc-biomed.in2p3.frVO name: biomedChecksum type: NoneTrying SURL 
>>> srm://marsedpm.in2p3.fr:8446/srm/managerv2?SFN=/dpm/in2p3.fr/home/biomed/generated/2012-02-14/filef6c67bc1-6cb8-42c0-9a2f-d73df4008612 
>>> ...Source SE type: SRMv2Source SRM Request Token: 
>>> e386c43e-06da-4084-b006-474468d00bfcDestination SE type: 
>>> SRMv2[SE][Mkdir][] 
>>> httpg://data-manager.grid.creatis.insa-lyon.fr:8446/srm/managerv2: 
>>> CGSI-gSOAP running on data-manager.grid.creatis.insa-lyon.fr reports 
>>> could not open connection to 
>>> data-manager.grid.creatis.insa-lyon.frDestination SRM Request Token: 
>>> [ERROR]Internal errorlcg_rep: Communication error on send
>>> 2012-02-14 00:36:55,689 [Thread-22] INFO 
>>> fr.insalyon.creatis.gasw.executor.DataManager.replicate(DataManager.java:166) 
>>> - Replicating 
>>> '/grid/biomed/creatis/vip/data/groups/GateLab/releases/current_gate_release.tgz'.
>>> 2012-02-14 00:37:01,884 [Thread-22] WARN 
>>> fr.insalyon.creatis.gasw.executor.DataManager.run(DataManager.java:94) 
>>> - fr.insalyon.creatis.gasw.GaswException: Unable to replicate 
>>> '/grid/biomed/creatis/vip/data/groups/GateLab/releases/current_gate_release.tgz' 
>>> from
>>> .
>>> .
>>>
>>> Am I getting an error because of my script? This script runs fine on 
>>> my desktop. By looking at the log file, It looks like there is 
>>> a communication error in the grid.
>>>
>>> Thanks,
>>> Sanghyeb(Sam) Lee
>>>
>>> PhD Candidate
>>> Department of Electrical Engineering and Computer Science
>>> University of Tennessee, Knoxville
>>>
>>> *From:* Tristan Glatard [tristan.glatard at creatis.insa-lyon.fr 
>>> <mailto:tristan.glatard at creatis.insa-lyon.fr>]
>>> *Sent:* 11 February 2012 13:28
>>> *To:* Lee, Sam (SAM LEE)
>>> *Cc:* egee-admin at creatis.insa-lyon.fr 
>>> <mailto:egee-admin at creatis.insa-lyon.fr>; 
>>> gate-users at lists.opengatecollaboration.org 
>>> <mailto:gate-users at lists.opengatecollaboration.org>
>>> *Subject:* Re: Fwd: [Gate-users] running simulation on gatelab.
>>>
>>> Dear Sam Lee,
>>>
>>> Someone flooded the infrastructure with 3000 12-hour jobs which 
>>> prevented other simulations to start up.
>>>
>>> This has been handled and your jobs are on their way.
>>>
>>> Best regards,
>>> Tristan
>>>
>>> P.S.: you can have an idea of the current load on the GATE-Lab by 
>>> clicking "System load" in the monitor window.
>>>
>>> P.S.2: your jobs are currently failing with the following error.
>>>
>>> [G4-cerr] [GateSystemComponentMessenger]:
>>> [G4-cerr] could not find a volume creator for the name 'module'
>>> [G4-cerr] Attachment request will be ignored!
>>> [G4-cerr]
>>> [G4-cerr] ***** COMMAND NOT FOUND <
>>> > *****
>>> [Gate] Sorry, error in a macro command : abort.
>>> [ ERROR - Sat Feb 11 18:24:34 GMT 2012 ] Exiting with return value 6
>>>
>>> You should either fix your macro or ask to Pierre Gueth 
>>> (pierre.gueth at creatis.insa-lyon.fr 
>>> <mailto:pierre.gueth at creatis.insa-lyon.fr>) if the gate release 
>>> deployed in GATE-Lab can handle it.
>>>
>>> On 02/11/2012 11:32 AM, David Sarrut wrote:
>>>>
>>>>
>>>> ---------- Forwarded message ----------
>>>> From: *Lee, Sam (SAM LEE)* <slee91 at utk.edu <mailto:slee91 at utk.edu>>
>>>> Date: Sat, Feb 11, 2012 at 02:26
>>>> Subject: [Gate-users] running simulation on gatelab.
>>>> To: gate-users <gate-users at lists.opengatecollaboration.org 
>>>> <mailto:gate-users at lists.opengatecollaboration.org>>
>>>>
>>>>
>>>> Hey,
>>>>
>>>> I am trying to run simulation on gatelab. I have successfully 
>>>> loaded my macro files into gatelab. However, it just sits there 
>>>> "QUEUED" for hours. Does anyone know what the usual waiting time 
>>>> is? I have killed simulations and reloaded macro files several 
>>>> times. However, my simulation is being "QUEUED" for several hours. 
>>>> It doesn't start running. Has anyone successfully used gatelab to 
>>>> run simulation?
>>>>
>>>> Thanks,
>>>> Sanghyeb(Sam) Lee
>>>>
>>>> PhD Candidate
>>>> Department of Electrical Engineering and Computer Science
>>>> University of Tennessee, Knoxville
>>>> Personal webpage: www.sergeantlee.com <http://www.sergeantlee.com>
>>>> _______________________________________________
>>>> Gate-users mailing list
>>>> Gate-users at lists.opengatecollaboration.org 
>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>
>>>>
>>>>
>>>> -- 
>>>> David Sarrut, Phd
>>>> Chargé de recherche CNRS
>>>> Laboratoire CREATIS, UMR CNRS 5220, Inserm U 1044
>>>> Centre de lutte contre le cancer Léon Bérard
>>>> 28 rue Laënnec, 69373 Lyon cedex 08
>>>> Tel : 04 78 78 51 51 / 06 74 72 05 42
>>>> http://www.creatis.insa-lyon.fr/rio
>>>> _________________________________
>>>>  "2 + 2 = 5,  for extremely large values of 2"
>>>> _________________________________
>>>>
>>>
>>>
>>> -- 
>>> Tristan Glatard
>>> CNRS researcher, CREATIS
>>> http://www.creatis.insa-lyon.fr/~glatard  <http://www.creatis.insa-lyon.fr/%7Eglatard>
>>> Tél : +33 (0) 4 72 43 75 47
>>
>>
>> -- 
>> Tristan Glatard
>> CNRS researcher, CREATIS
>> http://www.creatis.insa-lyon.fr/~glatard  <http://www.creatis.insa-lyon.fr/%7Eglatard>
>> Tél : +33 (0) 4 72 43 75 47

-- 
Tristan Glatard
CNRS researcher, CREATIS
http://www.creatis.insa-lyon.fr/~glatard
Tél : +33 (0) 4 72 43 75 47

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