AMBER Archive (2004)

Subject: Re: RE: AMBER: New problem on our 64bit box: xleap Segmentation fault

From: xhu1_at_memphis.edu
Date: Mon Nov 22 2004 - 16:37:03 CST

Thank you Ross! There are 32bit X11 libraries in our box and I checked
the "Imakefile" of leap. leap should be linked against these libraries,
not 64bit ones. But anyway, I just used the second method you
suggested: copy executable xleap and xaLeap from a 32bit box, and it
works! Thanks again.

All the best

Shawn

 
----- Original Message -----
From: "Ross Walker" <ross_at_rosswalker.co.uk>
Date: Monday, November 22, 2004 3:29 pm
Subject: RE: AMBER: New problem on our 64bit box: xleap Segmentation fault

> Chances are xleap is not 64 bit clean - you are elcome to try and
> fix it
> but I don't recommend it.
>
> It works on PURE 64 bit machines like Itaniums as all integers and
> pointersare 64 bit but the new Xeons are a hybrid 64 / 32 bit
> system and so you are
> probably compiling most of the code as 32 bit but linking against
> 64 bit
> libraries - a bad idea. Just stick to pure 32 bit on these machines
> unlessyou have any real reason for needing 64 bit integers.
>
> Ideally you should try and get hold of the 32bit versions of the X11
> libraries - an RPM should be available. Install these in
> /usr/X11R6/lib and
> then compile leap and link it against these libraries and not the
> 64 bit
> ones. Alternatively you could try compiling leap on a pure 32 bit
> machine as
> static and then copying the executables over to your machine.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of xhu1_at_memphis.edu
> > Sent: 22 November 2004 13:04
> > To: amber_at_scripps.edu
> > Subject: AMBER: New problem on our 64bit box: xleap
> > Segmentation fault
> >
> > As I mentioned in my previous email: after modifying the
> > "Imakefile" at
> > /usr/loca> completely
> > and tests were passed. But still there is a problem(although I
> don't> think it's very important): whenever I start xleap, it's
> core dumped.
> >
> > ********************************************
> > peptide 17% xleap
> > -I: Adding /usr/loca> -I: Adding /usr/loca> -I: Adding /usr/loca>
> -I: Adding /usr/loca> Segmentation fault
> >
> > ************************************************
> >
> > tleap is fine.
> >
> > Does anyone have a clue to solve this? I realized that Jiten had the
> > same problem before. Do you find a solution? Thank you very much
> >
> > Again, have a great thanksgiving!
> >
> > Shawn
> >
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