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

Tristan Glatard tristan.glatard at creatis.insa-lyon.fr
Tue Feb 14 09:46:26 CET 2012 

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]
> *Sent:* 11 February 2012 13:28
> *To:* Lee, Sam (SAM LEE)
> *Cc:* egee-admin at creatis.insa-lyon.fr; 
> 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
Tél : +33 (0) 4 72 43 75 47

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