I forgot to mention that on
$ cd $AMBERHOME/test
$ make test serial
PASSED was indicated for every module (it was mostly so fast that some
-non-passed may have gone undetected). On rethinking, the last line is now of
my concern:
make: *** No rule to make target 'serial'. Stop
I overlooked that message when I emailed below. Now I believe better to delay
parallel compilation until I get clarification. I could cot solve my doubts
throug internet. The last "PASSED" before that "make" line, was about "elsize"
Thanks
francesco
--- Francesco Pietra <chiendarret.yahoo.com> wrote:
> Date: Sat, 30 Jun 2007 06:00:31 -0700 (PDT)
> From: Francesco Pietra <chiendarret.yahoo.com>
> Subject: Fwd: Re: AMBER: make serial failure for xleap
> To: Amber <amber.scripps.edu>
>
> 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.yahoo.com> wrote:
>
> > Date: Sat, 30 Jun 2007 01:39:32 -0700 (PDT)
> > From: Francesco Pietra <chiendarret.yahoo.com>
> > Subject: Re: AMBER: make serial failure for xleap
> > To: amber.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.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
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
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> > >
> >
> >
> >
> >
> >
> >
>
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Received on Sun Jul 01 2007 - 06:07:51 PDT
