AMBER Archive (2008)

Subject: RE: AMBER: empty output

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Tue Jul 15 2008 - 12:31:50 CDT

Hi Ross
Thanks for your help, it was a problem related to specifying stack size.
Regards
Boutheina
> Hi Boutheina,
>
> I am assuming all the test cases pass in both serial an parallel and you
> can
> run your job in serial find. If that is the case then the problem you see
> is
> likely an issue with the submission script, job scheduler rather than
> amber.
> I would start by taking a look at the load leveler logs for this run, is
> what you see below the only error?
>
> What does your job submission script look like? Are all the paths correct
> etc?
>
> Often when running in parallel simple error messages (like the executable
> not existing in the path specified etc) can get lost so you need to check
> this carefully.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of Boutheina Kerkeni
>> Sent: Saturday, July 12, 2008 8:30 AM
>> To: amber_at_scripps.edu
>> Subject: AMBER: empty output
>>
>> Hi
>>
>> I submitted a minimization job, but as soon as it is submitted it
>> stops with an empty output.
>> The error file contains the following:
>>
>>
>> ATTENTION: 0031-408 16 tasks allocated by LoadLeveler, continuing...
>> ERROR: 0031-250 task 0: Terminated
>> ERROR: 0031-250 task 2: Terminated
>> ERROR: 0031-250 task 3: Terminated
>> ERROR: 0031-250 task 5: Terminated
>> ERROR: 0031-250 task 8: Terminated
>> ERROR: 0031-250 task 9: Terminated
>> ERROR: 0031-250 task 10: Terminated
>> ERROR: 0031-250 task 11: Terminated
>> ERROR: 0031-250 task 12: Terminated
>> ERROR: 0031-250 task 13: Terminated
>> ERROR: 0031-250 task 14: Terminated
>> ERROR: 0031-250 task 15: Terminated
>> ERROR: 0031-250 task 1: Terminated
>> ERROR: 0031-250 task 4: Terminated
>> ERROR: 0031-250 task 6: Terminated
>> ERROR: 0031-250 task 7: Terminated
>>
>>
>> Any idea to what is this due to?
>> Thanks
>>
>> B
>>
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