Re: [netcdfgroup] Error Building netCDF with Parallel I/O and pnetcdf and Parallel HDF5

• To: "Capehart, William J" <William.Capehart@xxxxxxxxx>
• Subject: Re: [netcdfgroup] Error Building netCDF with Parallel I/O and pnetcdf and Parallel HDF5
• From: Nick Papior Andersen <nickpapior@xxxxxxxxx>
• Date: Mon, 14 Jul 2014 14:50:22 +0200

I suspect you mean the latest hdf version 1.8.13? No?

In that case hdf5 have removed the functions that you find errors on.
See these release notes for hdf5:
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
You should change the calls H5Pset_fapl_mpiposix to H5Pset_fapl_mpio (in
file libsrc4/nc4file.c).

DISCLAIMER: I do not know if this breaks anything. My test with
netcdf-fortran does complete without errors.

Else, revert to the 1.8.12 version. That one works :)



2014-07-13 23:55 GMT+02:00 Capehart, William J <William.Capehart@xxxxxxxxx>:

> I am having difficulty building netCDF 4.3.2 on a new Fedora 20 machine
> (64 bit) with a PGI 14.6 compiler with 3.0.1 MPI that comes WITH the PGI
> compiler. This is the only version of HDF5, Parallel NetCDF, NetCDF and
> the rest of the usual /usr/local suspects such as PGI,  szip and libz that
> are on the rig.  (This is a totally fresh install of Fedora on a clean
> slate).
>
> The resulting error is:
>
> mpicc -DHAVE_CONFIG_H -I. -I..  -I../include   -DpgiFortran
> -I/usr/local/include   -Msignextend  -c -o ncgentab.o ncgentab.c
> PGC-W-0114-More than one type specified
> (/usr/local/pgi/linux86-64/14.6/include-gcc48/sys/types.h: 152)
> PGC-W-0143-Useless typedef declaration (no declarators present)
> (/usr/local/pgi/linux86-64/14.6/include-gcc48/sys/types.h: 152)
> PGC-W-0136-Function ncglex has non-prototype declaration in scope
> (lex.ncg.c: 1066)
> PGC/x86-64 Linux 14.6-0: compilation completed with warnings
> /bin/sh ../libtool  --tag=CC   --mode=link mpicc  -Msignextend
> -L/usr/local/lib -o ncgen3 main.o load.o escapes.o getfill.o init.o
> genlib.o ncgentab.o ../liblib/libnetcdf.la  -lpnetcdf -lm
> -L/usr/local/lib -ldl -lhdf5_hl -lhdf5 -lz -lsz -lm
> libtool: link: mpicc -Msignextend -o ncgen3 main.o load.o escapes.o
> getfill.o init.o genlib.o ncgentab.o  -L/usr/local/lib
> ../liblib/.libs/libnetcdf.a -lpnetcdf /usr/local/lib/libhdf5_hl.a
> /usr/local/lib/libhdf5.a -ldl -lz /usr/local/lib/libsz.so -lm
> ../liblib/.libs/libnetcdf.a(libnetcdf4_la-nc4file.o): In function
> `nc4_create_file':
> /usr/local/netcdf-4.3.2/libsrc4/./nc4file.c:314: undefined reference to
> `H5Pset_fapl_mpiposix'
> ../liblib/.libs/libnetcdf.a(libnetcdf4_la-nc4file.o): In function
> `nc4_open_file':
> /usr/local/netcdf-4.3.2/libsrc4/./nc4file.c:2174: undefined reference to
> `H5Pset_fapl_mpiposix'
> make[2]: *** [ncgen3] Error 2
> make[2]: Leaving directory `/usr/local/netcdf-4.3.2/ncgen3'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/usr/local/netcdf-4.3.2'
> make: *** [all] Error 2
>
>
> I am doing this with
>
> Fedora 20
> PGI 14.6 (MPI 3.0.1 that comes with the PGI build, not compiled separately)
> HDF5 1.18.14
> ANL¹s Parallel netcdf 1.5.0
> And the 4.3.2 edition of NetCDF (haven¹t gotten to the Fortran or C++
> libraries yet).
>
> Ideas?
>
> Thanks Much,
> ================================================================
> Bill Capehart <William.Capehart@xxxxxxxxx>   Associate Professor
> Atmospheric & Environmental Sciences         Program Coordinator
> 213 Mineral Industries Building                 Hydrometeorology
> South Dakota School of Mines and Technology     Skype: wcapehart
> 501 East Saint Joseph Street                 Ph: +1-605-394-1994
> Rapid City, SD 57701-3995                Mobile: +1-605-484-5692
> =================== http://capehart.sdsmt.edu ==================
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-- 
Kind regards Nick

• References:
  • [netcdfgroup] Error Building netCDF with Parallel I/O and pnetcdf and Parallel HDF5
    • From: Capehart, William J