AMBER Archive (2007)

Subject: Fwd: Re: AMBER: make serial failure for xleap

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Jun 30 2007 - 08:00:31 CDT

My guess below was correct.

$ rm configure

$ rm config.log

$ /.configure ifort_x86_64

$ make

ended with "Installation of Amber 9 is complete" and now I understand that
"make install" occurs within. I can see the installed files under /exe,
including sander, leap, and xleap. Now I can try parallel installation.

Cheers

francesco

--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Sat, 30 Jun 2007 01:39:32 -0700 (PDT)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: Re: AMBER: make serial failure for xleap
> To: amber_at_scripps.edu
>
> 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.
>
> Thanks
>
> francesco pietra
>
>
> --- "M. L. Dodson" <mldodson_at_houston.rr.com> 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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>
>
>
>
>
>
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