On Tue, Jun 11, 2013 at 4:25 PM, Matthew Wampole <
Matthew.Wampole.jefferson.edu> wrote:
> Hi Dan,
>
> I've attached a log of libnetcdf.a from the command you gave. Everything
> looks to be in order for libnetcdf.a that is contained in amber12.
> Branching from your idea, I searched my computer for other copies of
> libnetcdf.a and found one in my usr/lib directory installed with the
> libnetcdf developer kit. That version of libnetcdf.a does not contain nf90
> routines so I'm wondering if AMBER could be using the Synaptic installed
> version instead of the one built by AMBER.
>
> I removed the developer kit of libnetcdf from my Ubuntu machine and was
> able to install like normal without removing the bintraj functionality.
> I've had the developer kit installed for a while for other programs and
> this is the first time this has occurred, curious but it provided a
> temporary fix.
>
This actually makes a lot of sense now. It was definitely pulling the
libnetcdf.a file from /usr/lib (maybe it was pulling libnetcdf.so -- do you
have the shared objects installed, too?) More recent versions of NetCDF
actually bundle the Fortran and C symbols in separate libraries. The
Fortran symbols are found in libnetcdff.a (and/or libnetcdff.so). (In
fact, there may be a separate Fortran NetCDF package, depending on your
particular system and package manager).
You can actually skip the Amber NetCDF build altogether with the
--with-netcdf flag to configure and just use the existing NetCDF on the
system.
I don't know that I would necessarily suggest this route, though
(especially now that you seem to have fixed it).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 11 2013 - 14:00:03 PDT
