What are your system specs?
On Sat, Oct 2, 2010 at 6:53 PM, Seibold, Stephen <Seibold79.stmary.edu>wrote:
> 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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>
>
> _______________________________________________
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>
>
--
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 - 19:00:03 PDT
