Hi Alan,
Others have seen problems with gcc 5.2 - it's just too 'new' right now. I'd suggest installing Mac Ports and gcc / gfortran 4.9 - I've had no issues with this and compiled just now using OSX 10.11.1. See Jason's extremely useful guide here:
http://jswails.wikidot.com/mac-os-x
All the best
Ross
> On Oct 26, 2015, at 16:03, Alan <alanwilter.gmail.com> wrote:
>
> So I am trying to get AT15 compiled.
>
> I use Fink with MacOS 10.11.1.
>
> I’ve installed Fink gcc 5.2 (the only option I have, since 4.2 is Mac OS
> system and it not cross built with gfortran).
>
> I’ve changed AmberTools/src/configure2 so to use gfortran-fsf-5, g++-fsf-5
> and gcc-fsf-5.
>
> All starts fine but at
>
> hecking NetCDF...
> Using bundled NetCDF library.
> NetCDF must be rebuilt.
> Configuring NetCDF C interface (may be time-consuming)...
> Compiling the NetCDF C interface (may be time-consuming)...
> Configuring NetCDF Fortran interface (may be time-consuming)...
> Compiling the NetCDF Fortran interface (may be time-consuming)...
> Error: Could not compile with NetCDF Fortran interface.
> Compile error follows:
> Undefined symbols for architecture x86_64:
> …
> ___netcdf_MOD_nf90_sync in libnetcdff.a(netcdf.o)
> ld: symbol(s) not found for architecture x86_64
> collect2: error: ld returned 1 exit status
>
> Error: NetCDF build failed.
> Configure failed due to the errors above!
>
> Who had successfully built AT15 on 10.11.1 with Fink gcc?
>
> Any suggestion would be very welcome.
>
> Thanks,
>
> Alan
>
> PS. I have Amber11 and I will try to get it working too, but let me get
> AT15 first.
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 26 2015 - 16:30:04 PDT
