[MITgcm-support] Recommended NetCDF libraries

[Jonny Williams]

Many thanks to all of those who gave me some very useful hints as to how to
proceed with this problem!

I no know that this problem concerned the C++ API, as detailed at this
link...

http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg07894.html

After recompiling the NetCDF (version 3.6.2) libraries with --disable-cxx,
the mitgcmuv executable was produced successfuly.

I will let you know if I encounter any problems at run time.

Many thanks again.

Jonny

On 14 April 2015 at 13:11, Roland Young <Roland.Young at physics.ox.ac.uk>
wrote:

> Hi Jonny,
>
> I had this exact error and was able to fix it. It was a little while ago
> so the fix may not be quite as I remember.
>
> Anyway, I started to get those "undefined reference to `nf_create_” type
> errors immediately after NetCDF v4 had been installed on my system. v4 and
> pre-v4 use differently formatted include files as far as I can tell, and
> the C preprocessor was trying to use the wrong one. The C preprocessor
> searches several default directories for include files. In my case it
> searches /usr/local/include first followed by some others, including
> /usr/include. Now the NetCDF file you need (netcdf.inc), which defines
> those variables you list, was in /usr/include but the new version (with the
> same filename, but wrong declarations) had been put in /usr/local/include,
> so cpp was finding and using that first.
>
> You can force a particular folder to the top of the list of default
> folders that CPP searches by adding the following flag to CPP:
>
> -isystem <folder>
>
> (you can force cpp to search custom folders first with another option but
> if the folder you add is already in the default list cpp will ignore that
> option)
>
> To get this to work in the MITgcm compilation, I had to add the following
> line to my MITgcm/tools/build_options/ machine file:
>
> INC_OVERWRITE=“-isystem /usr/include”
>
> to get the right directory, and then I had to edit genmake2 and
> xmakedepend to get the compilation scripts to recognise and use this
> option. Running diff on my new and original files I get the output below,
> which you should be able to apply to your scripts with the patch command.
> These basically just pass my overwrite option through the scripts correctly
> to make sure they are added to the cpp calls in the Makefile.
>
> I expect there is a simpler way to do this but it seemed to work for me.
>
> What is weird is that I’ve run this on other machines which only have v4
> NetCDF libraries and it seems to work fine - if it ain’t broke, don’t look
> too closely…
>
> Let me know if it works.
>
> Best wishes,
>
> Roland
>
>
>
> --- genmake2.orig       2015-03-10 12:37:08.610641646 +0000
> +++ genmake2    2015-03-10 14:30:43.581113027 +0000
> @@ -1278,6 +1278,7 @@
> GSL=
> DEVEL=
> HAVE_TEST_L=
> +INC_OVERWRITE=
>
> # set this to "t" to enable lapack test
> CHECK_FOR_LAPACK=f
> @@ -2955,7 +2956,7 @@
>
> depend:
>         @\$(MAKE) -f \$(MAKEFILE) links
> -       \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES)
> \$(CPPINCLUDES) \$(F77_SRC_FILES)
> +       \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS $INC_OVERWRITE \$(DEFINES)
> \$(INCLUDES) \$(CPPINCLUDES) \$(F77_SRC_FILES)
>         \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
>         -rm -f makedepend.out
>
> @@ -3053,7 +3054,7 @@
> ## %.o : %.F
>
> # C preprocessing and replacing the _d in constants:
> -CPPCMD = cat \$< | ${CPP} \$(DEFINES) \$(INCLUDES) | ${S64}
> +CPPCMD = cat \$< | ${CPP} $INC_OVERWRITE \$(DEFINES) \$(INCLUDES) | ${S64}
>
> .F.$FS:
>         \$(CPPCMD)  > \$@
> @@ -3319,7 +3320,7 @@
>
> .PHONY: adDepend
> adDepend: \$(ALL_LINKED_FILES) \$(addsuffix _mod.h,
> \$(CB2M_F90_SRC_NAMES)) \$(addsuffix _mod.FF90, \$(CB2M_F90_SRC_NAMES))
> \$(F77_SRC_FILES:.F=_cb2m.FF90)
> -       \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS \$(DEFINES) \$(INCLUDES)
> \$(F77_SRC_FILES)
> +       \$(MAKEDEPEND) -f \$(MAKEFILE) -o .$FS $INC_OVERWRITE \$(DEFINES)
> \$(F77_SRC_FILES)
>         \$(TOOLSDIR)/f90mkdepend >> \$(MAKEFILE)
>         -rm -f makedepend.out
>
>
>
>
> --- xmakedepend.orig    2015-03-10 12:58:49.774383594 +0000
> +++ xmakedepend 2015-03-10 13:27:14.303975347 +0000
> @@ -142,6 +142,11 @@
>                             shift
>                             ;;
>
> +         -isystem)
> +             echo $n "-isystem $2 $c" >> $ARGS
> +             shift
> +             ;;
> +
>                         -*)
>                             echo "Unknown option '$1' ignored" 1>&2
>                             ;;
>
>
>
>
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
>



-- 
Dr Jonny Williams
School of Geographical Sciences
Cabot Institute
University of Bristol
BS8 1SS

+44 (0)117 3318352
jonny.williams at bristol.ac.uk
http://www.bristol.ac.uk/geography/people/jonny-h-williams
<http://bit.ly/jonnywilliams>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20150414/501b1f49/attachment-0001.htm>