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

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• Subject: [netcdfgroup] Error Building netCDF with Parallel I/O and pnetcdf and Parallel HDF5
• From: "Capehart, William J" <William.Capehart@xxxxxxxxx>
• Date: Sun, 13 Jul 2014 21:55:32 +0000

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