Re: [AMBER] amber11 Installation Test Failures

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 20 Mar 2011 07:36:09 -0700

amber11/src/netcdf is just a symbolic link to amber11/AmberTools/src/netcdf,
so it doesn't matter which one you edit, it'll change them both (since one
is really just a pointer to another). There is only one netcdf copy bundled
with amber.

Hope this helps,
Jason

On Sat, Mar 19, 2011 at 11:39 PM, David Cantu <cantudav.gmail.com> wrote:

> Dr Huynh,
>
> Ok, I found the config.h file that you are talking about.
>
> Question:
>
> Is it the file in: /amber11/AmberTools/src/netcdf/src/
> or in: /amber11/src/netcdf/src/
>
> ?
>
> Thanks,
>
> David
>
> On Sat, Mar 19, 2011 at 7:30 PM, Tru Huynh <tru.pasteur.fr> wrote:
>
> > On Tue, Mar 15, 2011 at 09:08:04PM -0500, David Cantu wrote:
> > > By the way, this is the error that came out during the "make serial"
> > > command:
> > >
> > > ../netcdf/lib/libnetcdf.a(netcdf.o): In function
> > > `__netcdf_MOD_nf90_rename_var':
> > > netcdf.f90:(.text+0x1b73): undefined reference to `nf_rename_var_'
> > > collect2: ld returned 1 exit status
> > > make[1]: *** [sander] Error 1
> > > make[1]: Leaving directory
> > > `/working002b/chem_eng3/dcantu/amber11/src/sander'
> > > make: *** [serial] Error 2
> > >
> > > Thanks,
> > >
> > I don't recall the reason, but I had to fix the netcdf/config.h to make
> it
> > built
> > with the gcc44 compilers (after patching the configure script).
> >
> >
> > [tru.sillage src]$ diff -uNr config.h-automatic config.h
> > --- config.h-automatic 2010-11-02 14:45:37.000000000 +0100
> > +++ config.h 2010-11-02 21:06:10.000000000 +0100
> > .@ -198,10 +198,10 @@
> > /* #undef const */
> >
> > /* Turned on by netCDF configure. */
> > -#define f2cFortran 1
> > +/* #undef f2cFortran */
> >
> > /* Turned on by netCDF configure. */
> > -/* #undef gFortran */
> > +#define gFortran 1
> >
> > /* Define to `long' if <sys/types.h> does not define. */
> > /* #undef off_t */
> >
> > my 2 cents
> >
> > Tru
> > --
> > Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/
> > mailto:tru.pasteur.fr | tel/fax +33 1 45 68 87 37/19
> > Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> 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 Sun Mar 20 2011 - 08:00:03 PDT
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