Re: AMBER: make serial failure for xleap

From: Francesco Pietra <>
Date: Sat, 30 Jun 2007 01:39:32 -0700 (PDT)

Thanks to all. I have installed the debian package xorg-dev, run "make clean"
and again "make", which exited with Error 2.

Remembering that I was instructed to configure as:

"./configure -static ifort_x86_64"

I imagined what happened. I deleted previous errors.log and run "make >&
errors.log", which is in attachment (renamed "errors").

It seems to me that such warning as "Using 'gethostname' in statically linked
applications requires at runtime the shared libraries from glibc version used
for linking" means that the command line for ./configure as above indicated is
not appropriate, though I don't know exactly why. I known that intel comprises
the static libraries, don't know for gcc.

I would be most indebted for suggestion what to do. I understand that the xleap
issue could be ignored - without much loss - through a modification of the
Makefile,though it is disturbing to continue when something is not correct.

I have been told that running first a serial compilation is on the good reason
that certain parts of amber9 are not compiled if running a parallel compilation
only. Then, I expected that "make install" has to be run after a successful
serial "make". I am confused about that, because it is not specifid to command
"make install" before moving to a parallel compilation.

Were not for the last problem (is it is a problem at all) I would skip the
serial compilation, trying a non-static parallel compilation immediately, with
ifort C and C++ from intel.

All that under the understanding that I am a beginner in compilation and I
apologize for any trouble I am trying to tranfer to Those who know.


francesco pietra

--- "M. L. Dodson" <> wrote:

> Francesco Pietra wrote:
> > ere is provided errors.log and gcc -v (sent again because with previous
> email
> > the attachment did not show up)
> >
> >
> >
> > $ make clean (configure was from "./configure -static ifort_x86_64")
> >
> > $ make >& errors.log
> >
> >
> > Attached is the errors.log. Hope that by renaming "errors" gnome mail will
> > really attach
> >
> > Although various warnings appear at the first instance of
> >
> > gcc -c -D_FILE OFFSET_BITS=64
> >
> > errors begin at
> >
> > WcActCB for X11/IntrinsicP.h and X11/ShellP.h
> >
> As Professor Case suggested, the compile is not picking up key X header
> files. Make sure you have the X _development_ package installed, not
> just the packages needed to _run_ X. If you do have them installed,
> locate the missing header files and edit the gcc command lines in
> config.h to be sure those directories are included (via -I directives).
> Be sure you get the 64-bit versions (if they differ from the 32-bit,
> although they should not, IIRC). Since xleap is the only code dependent
> on X, how you plan to compile for parallel is completely independent of
> how you compile xleap. Compiling xleap with gcc instead of an Intel
> compiler is perfectly OK. I might even be able to make a good case for
> it being desirable to compile it with gcc (less complicated).
> As for the details of your X installation, OpenGL, etc, that is likely a
> diversion. If you can display anything in X, even just the graphical
> login prompt, you can run a properly compiled xleap.
> Bud Dodson
> --
> M. L. Dodson
> Email: mldodson-at-houston-dot-rr-dot-com
> Phone: eight_three_two-five_63-386_one
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Received on Sun Jul 01 2007 - 06:07:42 PDT
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