Hello,
On Wed, May 19, 2010 at 11:34 PM, Steve Henderson <toma0052.gmail.com>wrote:
> Hello,
> I am trying to install Ambertools 1.4 under cygwin. I have been
> following the installation described here:
>
> <http://ambermd.org/mswindows.html>
>
> When running ./configure -cygwin gnu I get the warning message:
>
> Warning: the X11 libraries are not in the usual location !
> To search for them try the command: locate libXt
> On new Fedora OS's install the libXt-devel libXext-devel
> libX11-devel libICE-devel libSM-devel packages.
> On old Fedora OS's install the xorg-x11-devel package.
> On RedHat OS's install the XFree86-devel package.
> On Ubuntu OS's install the xorg-dev package.
> For the moment Amber will be configured not to build XLEaP.
>
This is due to the fact that you did not select X11 when you installed
Cygwin. xleap requires the X environment to run, so when configure can't
find it, it prevents it from compiling (since it's missing required headers
and libraries). This should not cause problems during compilation.
>
> Everything else checks out okay, but if I proceed to make install, the
> process terminates with:
>
> mkdir .libs/libnetcdff.lax/libnetcdff90.a
> (cd .libs/libnetcdff.lax/libnetcdff90.a && ar x
>
> /home/mtomas/Amber_Tools/amber11/AmberTools/src/netcdf/src/fortran/../f90/.libs/libnetcdff90.a)
> libtool: link: ERROR: object name conflicts:
>
> .libs/libnetcdff.lax/libnetcdff90.a//home/mtomas/Amber_Tools/amber11/AmberTools/src/netcdf/src/fortran/../f90/.libs/libnetcdff90.a
> make[2]: *** [libnetcdff.la] Error 1
> make[2]: Leaving directory
> `/home/mtomas/Amber_Tools/amber11/AmberTools/src/netcdf/src/fortran'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory
> `/home/mtomas/Amber_Tools/amber11/AmberTools/src/netcdf/src'
> make: *** [../netcdf/lib/libnetcdf.a] Error 2
>
This is a different error. It is, for some reason, having trouble building
NETCDF (the binary trajectory format used for amber trajectories). Whenever
I've had problems during the compilation, it's never happened with netcdf
(but I'm too impatient to attempt a build on cygwin ;) ).
A good guide to this is
http://ambermd.org/mswindows.html which has
instructions on what packages to install cygwin with in order to
successfully build amber on windows. There is no note on that website about
incompatibilities with netcdf, so I'm guessing that you're missing one of
the packages listed in the "installing cygwin" section. Make sure you
install all of these cygwin packages and retry.
Good luck!
Jason
> I am assuming that these two errors are related, but I'm not sure. Can
> anyone shed light on what may be wrong with my system?
>
> Thank you,
> Mike
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed May 19 2010 - 21:30:04 PDT
