AMBER Archive (2008)

Subject: RE: AMBER: empty output

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Jul 12 2008 - 11:54:01 CDT

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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