Did you run the AT15_Amber11.py script before trying to build Amber11?
This error is fixed by that script. Furthermore, the configure script
should say something about running that script before building amber.
HTH,
Jason
On Tue, May 24, 2011 at 8:03 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Hi,
>
> Thanks for the reply.
> My NetCDF configure did succeed,
> with $AMBERHOME/AmberTools/src/netcdf_config.log exactly like you wrote,
> without error messages.
> I also have
> NETCDF=netcdf.mod
> NETCDFLIB=$(LIBDIR)/libnetcdf.a
>
> in my $AMBERHOME/AmberTools/src/config.h, followed by:
> PNETCDF=no
> PNETCDFLIB=
>
> I know I shouldn't have to do any extra linking or copying, but I just
> wanted to try and see if it helped (as I didn't have any indications of
> something else having gone wrong).
> I will try and install both AmberTools 1.5 and AMBER 11 again, in a clean
> directory.
>
> Thanks,
> Marc
>
> On 24 May 2011 12:53, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi, it sounds like your netcdf might not have configured properly. My
> > comments are below:
> >
> > On Tue, May 24, 2011 at 6:11 AM, Marc van der Kamp
> > <marcvanderkamp.gmail.com> wrote:
> > > When doing 'make serial', I first got the following error:
> > >
> > > cp ../../AmberTools/src/netcdf/include/*.mod .
> > > cp: cannot stat `../../AmberTools/src/netcdf/include/*.mod': No such
> file
> > or
> > > directory
> > > make[1]: *** [netcdf.mod] Error 1
> > >
> > > It turned out that $AMBERHOME/AmberTools/src/netcdf/include didn't
> exist,
> >
> > When you ran "$AMBERHOME/AmberTools/src/configure" did you get a
> > message that "NetCDF configure succeeded"? Check near the end of
> > $AMBERHOME/AmberTools/src/netcdf_config.log for any error messages. It
> > should look something like:
> >
> > ...
> > config.status: creating f90/Makefile
> > config.status: creating examples/Makefile
> > config.status: creating examples/C/Makefile
> > config.status: creating examples/CDL/Makefile
> > config.status: creating examples/CXX/Makefile
> > config.status: creating examples/F90/Makefile
> > config.status: creating examples/F77/Makefile
> > config.status: creating config.h
> > config.status: creating fortran/nfconfig1.inc
> > config.status: executing depfiles commands
> > ...
> >
> > Also, check your $AMBERHOME/AmberTools/src/config.h file. You should
> > have two lines in it that read:
> >
> > NETCDF=netcdf.mod
> > NETCDFLIB=$(LIBDIR)/libnetcdf.a
> >
> > > So I did 'make clean', and then made
> > > the $AMBERHOME/AmberTools/src/netcdf/include directory with simlinks to
> > > the $AMBERHOME/AmberTools/include/*mod files.
> >
> > You shouldn't have to do any extra linking or copying. At this point I
> > would start with a clean directory, apply the bugfixes, the run
> > configure and check all the output before attempting to make.
> >
> > -Dan
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 24 2011 - 06:00:02 PDT
