AMBER Archive (2004)

Subject: Re: AMBER: segmentation fault in Leap

From: David E. Konerding (dekonerding_at_lbl.gov)
Date: Thu Jan 22 2004 - 09:22:47 CST

Ioana Cozmuta wrote:

>On Wed, 21 Jan 2004, Bill Ross wrote:
>
>
>
>>>Placed Cl- in foo at (34.61, -13.78, 49.32).
>>>Segmentation fault (core dumped)
>>>
>>>Does anyone have any idea what may be wrong in this case? Could it be that
>>>there is a memory problem?
>>>
>>>
>>There is. As a workaround you could try adding Cl-'s one-by-one
>>explicitly.
>>
>>
>
>I am not sure how I could trace this down. I'm running tleap on one
>processor, but it does not seem to be eating up memory (swap memory does
>not change). I've also tried to run tleap in a pbs job asking for 1Gb of
>memory and still I get a segmentation fault.
>I've also tried to add Ions one by one but it does not seem to matter.
>What seems strange is that the charge calculation over the grid is
>completed and only after the ion is placed the segmentation fault happens.
>
>I also remember working some while ago with larger files than the present
>one and never got a segmentation fault.
>
>I know this sound very imprecies but I'm looking for help to find a
>starting point to try and trace this down.
>
>Thanks,
>Ioana
>
>

Run the program under valgrind
http://freshmeat.net/projects/valgrind/

it's very effective for identifying the cause of seg faults at run time.

Dave

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