Hi Jason
Thanks for your response.
It occurs no matter how many frames. Just 2 or 1 cause the fault. It is certainly the size of the system though because I used a much smaller protein without any problem. Other people have taken my trajectories of my large system and using the new toolset have had no problems; so, it must be some peculiarity with my computer system. What is strange is that on a separate account (same computer) I have the old toolset from amber8 and on this account the trajectories run fine. It is just the new toolset that is not working with my protein system. Amber 11 (sander) has no problem running the system and writing out the trajectories; but, ptraj just will not do distance measurements with them.
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Sat 10/2/2010 5:40 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Segmentation fault
Hello,
If it was a missing libraries issue, you'd get an error that said so, I
believe. A segfault is indicative of a memory violation, so it's unlikely
to be that (though of course someone may prove me wrong). How many frames
are you trying to calculate a distance for? Can you reduce the number of
frames, to say 1 or 2, and see if you still get the segfault?
(I don't remember how the thread started, so I'm sorry if this is
redundant/useless).
Good luck!
Jason
On Sat, Oct 2, 2010 at 5:33 PM, Seibold, Stephen <Seibold79.stmary.edu>wrote:
>
> Hi AMBER
> I re-compiled AmberToolset with gcc 4.1.0 ( I was using 4.4.0) and ran all
> the tests. It passed them all. However, again, when I try to run ptraj using
> distances, I get "Segmentation fault". Again, rdparm reads the trajectory
> files without any problem.
>
> I was worried about memory and so, I made sure I was set at "unlimited" on
> my memory stack...I don't know it this was useless or not, but I tried.
>
> Could it be that my AmberTools is pointing to the wrong libraries??? Could
> someone please tell me how to check this??
>
>
> Thanks for your help. Responses have been very consistent with AMBER and I
> am truly grateful.
>
> Cheers, Steve
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Oct 02 2010 - 16:00:05 PDT
