Does this happen with other trajectories for other systems on your computer?
On Mon, Oct 4, 2010 at 7:18 PM, Seibold, Stephen <Seibold79.stmary.edu>wrote:
>
> Hello
> I am using Red Hat Linux version release 5 (enterprise), x86_64. Other
> AMBER personal have been able, with similar systems, to run MY trajectories
> (i.e. ptraj distance measurements) without problems. So, it must be
> something specific to my personal set up. I just don't know what would cause
> this.
>
> Ptraj AmberTools 4.1 will read my trajectory files fine. It is only when it
> goes to print out data to a file that I get this "segmentation" fault.
>
> I hope this information helps.
>
> Thanks Steve
>
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Sat 10/2/2010 8:56 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Segmentation fault
>
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> 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 Mon Oct 04 2010 - 19:00:05 PDT
