AMBER Archive (2006)

Subject: Re: AMBER: Xleap crash

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Tue Feb 14 2006 - 11:53:37 CST

On 2/14/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Tue, Feb 14, 2006, Scott Pendley wrote:
> >
> > I have installed amber8 on my work computer (dual athlon, RHEL 4).
> > Installation has been working great with one exception, xleap. I
> compiled
> > xleap without any problems and can run the program in text mode
> only. When
> > I try to edit a molecule, it immediately crashes and records a
> segmentation
> > fault. This problem seems to be independant of the unit to be editted.
>
> Can you give us some more information about your environment:

Dual processor Athlon 64 bit. Other programs seem to work: sander, ptraj,
anal, etc.

What arguments did you supply to the configure script?

./configure -athlon -static ifort

What are the values of CC and CFLAGS in $AMBERHOME/src/config.h?

CC = gcc
CFLAGS = -O2 $(AMBERBUILDFLAGS)

What does "gcc --version" report?

 version 3.4.4

What does "uname -a" report?

Linux cytosine.pharm.utah.edu 2.6.9-22.0.1.EL #1 Tue Oct 18 18:29:22 EDT
2005 x86_64 x86_64 x86_64 GNU/Linux

I was thinking this was likely a problem with the XConfiguation since that
seems to be the only problem I find.

I use the following variables in $AMBERHOME/src/leap/src/leap/Makefile
XLIB64 = /usr/X11R6/lib64
XALEAP_LIB = ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a \
    ../Xmu/libXmu.a -L$(XLIB64) -lXt -lXext -lSM -lICE -lX11 -lm -ldl
-lpthread

This problem seems to be pretty specific to particular compile/link
> environments. While you are waiting for a resolution(!?!), you might try
> to compile a static version on some one else's computer (if that is
> possible),
> and see if you can move it to your system.
>
> ...regards...dac
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