Not to beat the dead horse any more, but I'm assuming that this patch is in
reference to the error I get in xleap when I try to load it (correct me if
I'm wrong here)?
setenv AMBERHOME /usr/local/apps/amber9
echo $AMBERHOME
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
X11 connection rejected because of wrong authentication.
X connection to localhost:14.0 broken (explicit kill or server shutdown).
I've received this error while using both Cygwin and Linux platforms. If
there is a bug in loading the graphical interface, how do I go about
applying the patch? It wasn't clear from the previous email
correspondences.
Thanks,
Lili
On 15/11/2007, M. L. Dodson <activesitedynamics.comcast.net> wrote:
>
> Xuebin Qiao wrote:
> > >If I may make a suggestion, rather than hack the configure script,
> > >why not limit the fix to the makefile in the patch? Something along
> > >the line of:
> >
> > It is unwise to hack in makefile using non-portable features. Put all
> > ugly things into a single place would be more decent design.
> >
>
> Yes, /bin/sh certainly has more, and more portable, features to
> implement this "ugly thing". :-)
>
> The only thing is that linking to libXau and libXdmcp should
> probably occur right before -lm -lpthread, as linking to the libs
> earlier on the command line probably causes the dependencies on
> libXau and libXdmcp. If this is so the link command line would
> probably have to be set up in the configure script, not in the
> makefile. I.e., it should be in config.h after configuration.
>
> Maybe we should take this off list as most people could probably
> care less.
>
> > >The only corner case I can think of that this might miss is a
> > >partial or messed up X installation.
> >
> > maybe yes or maybe not, function dlsym is used when programmer need to
> > load certain dynamic library by hand, and it resides in libc.so. So I
> > guess add -lc may be ok, though some other unresolved symbols may appear
> > too. :-) If only this symbol missed, it would has nothing to with X, but
> > may due to a unsuccessful partial upgrading to the OS.
> >
> > qxb
>
> Correct. I was not even considering libc, only corner cases
> having to do with the need or no need to link to libXau and
> libXdmcp. It would be a fairly strange contemporary c compiler to
> not be able to link to its libc in some automatic fashion, though,
> would it not?
>
> Bud Dodson
>
> >
> > On Nov 15, 2007 2:51 AM, M. L. Dodson <activesitedynamics.comcast.net
> > <mailto:activesitedynamics.comcast.net>> wrote:
> >
> > I sent this out last week, but it never appeared on the list.
> > So here we go again.
> >
> > Bud Dodson
> >
> > -------- Original Message --------
> > Subject: Re: AMBER: xleap patch for xorg-7.3 ??
> > Date: Fri, 09 Nov 2007 10:39:15 -0600
> > From: M. L. Dodson <activesitedynamics.comcast.net
> > <mailto:activesitedynamics.comcast.net>>
> > Reply-To: activesitedynamics.comcast.net
> > <mailto:activesitedynamics.comcast.net>
> > To: amber.scripps.edu <mailto:amber.scripps.edu>
> >
> > Xuebin Qiao wrote:
> > > Hi,
> > >
> > > The Xorg7 has been designed to a new modularized architecture
> > instead of
> > > the old monolithic source tree. So it may break many old
> packages,
> > > especially for those are linked with hand-coded linker options.
> > >
> > > qxb
> > >
> > > On Nov 9, 2007 10:03 AM, David A. Case <case.scripps.edu
> > <mailto:case.scripps.edu>
> > > <mailto:case.scripps.edu <mailto:case.scripps.edu>>> wrote:
> > >
> > > On Thu, Nov 08, 2007, M. L. Dodson wrote:
> > > >
> > > > I found the following patch to be necessary for
> successfully
> > > > linking xaLeap with xorg-7.3
> > > >
> > >
> > > > --- leap/src/leap/Makefile.orig 2007-10-03 09:59:
> > > 50.000000000 -0500
> > > > +++ leap/src/leap/Makefile 2007-11-08
> > 12:08:59.000000000 -0600
> > > > .. -114,7 +114,7 ..
> > > > # XlcDL.o(.text+0xe2): undefined reference to `dlsym'
> > > > #
> > > > XALEAP_LIB = ../Xraw/libXaw.a ../Wc/libWcLeap.a
> > ../Xpm/libXpm.a \
> > > > - ../Xmu/libXmu.a $(XLIBS) -lXt -lXext -lSM -lICE
> > -lX11 $(LM)
> > > -lpthread
> > > > + ../Xmu/libXmu.a $(XLIBS) -lXt -lXext -lSM -lICE
> > -lX11 -lXau
> > > -lXdmcp $(LM) -lpthread
> > > >
> > > > OBJ = $(OA) $(OG) $(OO) $(OL)
> > > >
> > >
> > > Thanks for the report. But some more information might help:
> > >
> > > What is the error when you don't have -lXau -lXdmcp
> specified?
> > Do you
> > > undertstand why xorg-7.3 needs these but not other
> > X-implementations?
> > >
> >
> > Unresolved symbols in the link. No, although it may have
> > something to do with factoring the functionality of X,
> > contemporaneously at least, with the build factorization qxb
> > described above.
> >
> > > (extra credit:) how standard are libXau and libXdmcp? They
> > seem to
> > > be present
> > > on IRIX, Cygwin and Linuces, but I don't know about AIX or
> MacOS
> > > (for example).
> > >
> >
> > I can speak only for recent FreeBSD X installs and MacOS 10.4.10
> > (my laptop). On the mac, xdpyinfo says it is XFree86 4.4.0, and
> > it is at least two years since I installed it (several OS minor
> > version upgrades since then). I.e., it predates the xorg split
> > from XFree86, I think. Both libs present on these OS types.
> >
> > > These "standard X" libraries are ancient...why would xorg
> move
> > > things around
> > > in a way almost guaranteed to break old programs?
> > >
> >
> > The ABI is probably still intact, but the implementations may now
> > call functions in the new libs. This may be associated with the
> > functionality factorization I implied above.
> >
> > > I'm happy to make the above patch if it is safe for all
> machines.
> > > Otherwise,
> > > we'll have to add code to the configure script to
> > special-case this
> > > out.
> > >
> > > ...dac
> > >
> >
> > If I may make a suggestion, rather than hack the configure script,
> > why not limit the fix to the makefile in the patch? Something along
> > the line of:
> >
> > XALEAP_LIB = ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a \
> > ../Xmu/libXmu.a $(XLIBS) -lXt -lXext -lSM -lICE -lX11
> > <test for the existence of the libs>
> > if (libs present)
> > XALEAP_LIB += -lXau -lXdmcp $(LM) -lpthread
> > else
> > XALEAP_LIB += $(LM) -lpthread
> >
> > My SysV make-foo is not up to this test (I'm a Berkeley make kind
> > of guy), but this should be possible, at least for gmake, I would
> > think.
> >
> > The only corner case I can think of that this might miss is a
> > partial or messed up X installation. It may give a misleading
> > error message in that case.
> >
> > Bud Dodson
> >
>
>
> --
> M. L. Dodson
> Business Email: activesitedynamics-at-comcast-dot-net
> Personal Email: mldodson-at-comcast-dot-net
> Phone: eight_three_two-56_three-386_one
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Received on Sun Nov 18 2007 - 06:07:35 PST
