[GE Portal] Fasta- No Text box for 2nd Input file

Sangamesh B forum.san at gmail.com
Sat May 31 07:15:33 BST 2008


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Hi Melvin,

I submitted the job in the following way:

   Selected Submit Jobs. From applications list I selected Sleeper job.
Another window appeared. I edited text box 100 seconds and submitted.

After this, Sun TCP window appears. But without any info about the
job.(Blank page, with no errors)

After login to portal, it should show the the list of jobs (projects) that
were executed earlier. If it shows history of jobs or projects then job
submission happens and produces the output also. In the other case, if it
doesn't show the job history, the job submission willn't happen and SUN TCP
window will be blank

With this experience, I guess that GEP may using some database. Sometimes it
is failing to retrieve the data from database. So job submission  is not
happening.

Thanks,
Sangamesh
On Sat, May 31, 2008 at 7:23 AM, Melvin Koh <Melvin.Koh at sun.com> wrote:

> Sangamesh,
>
> Can you describe what you did to submit the job in GEP? What is the job you
> submitted?
>
> Sangamesh B wrote:
>
>>   Still the problem is not solved. The window "Sun TCP New Project Status"
>> appears without the job-info.
>>
>>   May I know, is this an applet/servlet or html page. Where the code is
>> written for this page so that I can debug it.
>>
>> Thanks,
>> Sangamesh
>>
>> On 5/13/08, *Sangamesh B* <forum.san at gmail.com <mailto:
>> forum.san at gmail.com>> wrote:
>>
>>    After the complete installation of Bio Cluster Grid, the job
>>    submission was not happening. The
>>    "Sun TCP New Project Status" window was blank. Yesterday it was
>>    working for every sleeper job till restarting the system. After
>>    restart, every time it didn't show the  job-info on the window.
>>
>>    Before restart, it produced the output file. After restart, only
>>    folder gets created, but the job doesn't submit. "qstat -f" confirms
>>    this.
>>
>>    Thanks,
>>    Sangamesh
>>
>>    On Tue, May 13, 2008 at 9:01 AM, Melvin Koh <Melvin.Koh at sun.com
>>    <mailto:Melvin.Koh at sun.com>> wrote:
>>
>>        I'm not sure why you get the problem. How often does it happen?
>>        Is the job completed successfully? You should have some output
>>        files in the sleeper project folder if the job runs without error.
>>
>>        Sangamesh B wrote:
>>
>>            Thanks for the response,
>>
>>            I'm facing one more problem with GEP.
>>
>>            After submitting a job( say sleeper.sh) "Sun TCP New Project
>>            Status" window appears. But it is blank, instead containing
>>            the job-submission info.
>>            Sometimes it works properly showing "Your job $JOB_ID
>>            submitted". I checked submitting sleeper script thru qsub.
>>            It works. Restarting the portal-server/system didn't solve
>>            the problem.
>>
>>            In the user's home dir, the folder
>>            "Sleeper.sh12052008173737" gets created with no files in it.
>>
>>            May I know what's causing this?
>>
>>            Shall I reinstall/redo the GEP config?
>>
>>            Thanks,
>>            Sangamesh
>>
>>            On 5/12/08, *Melvin Koh* <Melvin.Koh at sun.com
>>            <mailto:Melvin.Koh at sun.com> <mailto:Melvin.Koh at sun.com
>>
>>            <mailto:Melvin.Koh at sun.com>>> wrote:
>>
>>               Sangamesh,
>>
>>               The form can be modified. It is the file
>>               "<GEP_dir>/apps/A1064135261085/.suntcp-form". The form is
>>            basically
>>               constructed using HTML and Javascript, so just add a new
>> HTML
>>               textbox as appropriate. GEP will pass the form values to the
>>               "fasta.sh" submit script located in the same directory.
>>            You will
>>               also need to modify this script to handle the newly added
>>            input
>>               parameter.
>>
>>               For adding a new applications to GEP, we have a simple
>>            tutorial:
>>
>> http://apstc.sun.com.sg/research/projects/gep/download/addnewapp.pdf
>>
>>
>>               Sangamesh B wrote:
>>
>>                   Hi gepusers,
>>
>>                      I installed Bio Cluster Grid 1.5 on RHEL 3 AS U4.
>>
>>                   A sample sleeper program executes fine. So BCG is
>>            configured fine.
>>
>>                   I'm facing probelm with Fasta program. It requires
>>            two input
>>                   files( i.e one sequence file and a library file), but
>>            the fasta
>>                   job submission window has a provision for only one
>>            input file.
>>                   Where to mention the other input?
>>
>>                   Is there a procedure to add one more text box?
>>
>>                   Is there document for adding new application?
>>
>>                   Thanks in advance,
>>                   Sangamesh
>>
>>
>>
>
> --
> -----------------------------------------
> Melvin Koh Chee Kian
> Grid Solution Architect
> APSTC and Global Systems Practice
> Sun Microsystems Inc.
> Website: http://apstc.sun.com.sg/
> -----------------------------------------
>



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