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[netCDF #LEF-356666]: compiling parallel NetCDF problems



> Hi Ed
> 
> I still have problems ...
> 
> Tried with netcdf-4.1.3-rc1-ed2011051617 and
> netcdf-4.1.3-rc1-snapshot2011052320 but get the same error:
> 
> make[3]: Entering directory
> `/data/kb/compile/netcdf-4.1.3-rc1-snapshot2011052320/fortran'
> /bin/bash ../libtool --tag=FC   --mode=link mpif90  -g  -version-number
> 5:1:0  -L/opt/hdf5-par/lib -o libnetcdff.la -rpath
> /opt/netcdf-4.1.3-rc1-snapshot2011052320_IFORT-par/lib fort-attio.lo
> fort-control.lo fort-dim.lo fort-genatt.lo fort-geninq.lo fort-genvar.lo
> fort-lib.lo fort-misc.lo fort-v2compat.lo fort-vario.lo fort-var1io.lo
> fort-varaio.lo fort-varmio.lo fort-varsio.lo fort-nc4.lo
> ../liblib/libnetcdf.la ../f90/libnetcdff90.la -lm -lhdf5_hl -lhdf5 -lz
> -lm
> libtool: link: mpif90 -shared   .libs/fort-attio.o .libs/fort-control.o
> .libs/fort-dim.o .libs/fort-genatt.o .libs/fort-geninq.o
> .libs/fort-genvar.o .libs/fort-lib.o .libs/fort-misc.o
> .libs/fort-v2compat.o .libs/fort-vario.o .libs/fort-var1io.o
> .libs/fort-varaio.o .libs/fort-varmio.o .libs/fort-varsio.o
> .libs/fort-nc4.o   --whole-archive ../f90/.libs/libnetcdff90.a
> --no-whole-archive  -rpath
> /data/kb/compile/netcdf-4.1.3-rc1-snapshot2011052320/liblib/.libs -rpath
> /opt/netcdf-4.1.3-rc1-snapshot2011052320_IFORT-par/lib
> -L/opt/hdf5-par/lib ../liblib/.libs/libnetcdf.so -L/usr/lib
> /usr/lib/libcurl-gnutls.so /opt/hdf5-1.8.6-par/lib/libhdf5_hl.a
> /opt/hdf5-1.8.6-par/lib/libhdf5.a -lz -L/opt/mpich2-1.3.2p1-romio/lib
> -L/data/opt/intel/composerxe-2011.2.137/compiler/lib/ia32
> -L/data/opt/intel/composerxe-2011.2.137/mkl/lib/ia32
> -L/usr/lib/gcc/i686-linux-gnu/4.4.5/
> -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../../../lib/ -L/lib/../lib/
> -L/usr/lib/../lib/
> -L/data/opt/intel/composerxe-2011.2.137/compiler/lib/ia32/
> -L/data/opt/intel/composerxe-2011.2.137/mkl/lib/ia32/
> -L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../../ -L/lib/ -L/usr/lib/
> -L/usr/lib/i686-linux-gnu -lmpichf90 -lmpich
> /opt/mpich2-1.3.2p1-romio/lib/libopa.a
> /opt/mpich2-1.3.2p1-romio/lib/libmpl.a -lrt -lpthread -lifport -lifcore
> -limf -lsvml -lm -lipgo_pic -lintlc -lgcc_s -lirc_s -ldl -lc    -soname
> libnetcdff.so.5 -o .libs/libnetcdff.so.5.1.0
> ifort: command line warning #10006: ignoring unknown option
> '-fwhole-archive'
> ifort: command line warning #10006: ignoring unknown option
> '-fno-whole-archive'
> ifort: command line warning #10156: ignoring option '-r'; no argument
> required
> ifort: command line warning #10156: ignoring option '-r'; no argument
> required
> ifort: error #10236: File not found:
> '/opt/netcdf-4.1.3-rc1-snapshot2011052320_IFORT-par/lib'
> ifort: command line warning #10156: ignoring option '-s'; no argument
> required
> ifort: error #10236: File not found:  'libnetcdff.so.5'
> 
> The error seems to be associated with the fact that it looks in the
> install directory -
> /opt/netcdf-4.1.3-rc1-snapshot2011052320_IFORT-par/lib - during
> compilation.
> 
> Karsten
> 
> 
> 
> On Mon, May 23, 2011 at 03:33:07 -0600, Unidata netCDF Support wrote:
> > > Morning (at least here)
> > >
> > > Still not there ....
> > >
> > > hdf_ver=1.8.6
> > > netcdf_ver=4.1.3-rc1-ed2011051617
> > > FC=mpif90 CC=mpicc LIBS=-lm  ./configure 
> > > --prefix=/opt/netcdf-${netcdf_ver}_IFORT-par --enable-dap 
> > > --enable-netcdf4 --enable-ncgen4 --with-hdf5=/opt/hdf5-par/ 
> > > -enable-parallel-tests
> > >
> > > make[2]: Entering directory
> > > `/data/kb/compile/netcdf-4.1.3-rc1-ed2011051617/libsrc4'
> > > /bin/bash ../libtool  --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H
> > > -I. -I.. -I../fortran  -I../include -I../oc     -g -O2 -MT
> > > libnetcdf4_la-nc4file.lo -MD -MP -MF .deps/libnetcdf4_la-nc4file.Tpo -c
> > > -o libnetcdf4_la-nc4file.lo `test -f 'nc4file.c' || echo './'`nc4file.c
> > > libtool: compile:  mpicc -DHAVE_CONFIG_H -I. -I.. -I../fortran
> > > -I../include -I../oc -g -O2 -MT libnetcdf4_la-nc4file.lo -MD -MP -MF
> > > .deps/libnetcdf4_la-nc4file.Tpo -c nc4file.c  -fPIC -DPIC -o
> > > .libs/libnetcdf4_la-nc4file.o
> > > nc4file.c: In function 'nc4_create_file':
> > > nc4file.c:272: error: 'H5F_LIBVER_18' undeclared (first use in this
> > > function)
> > > nc4file.c:272: error: (Each undeclared identifier is reported only once
> > > nc4file.c:272: error: for each function it appears in.)
> > > make[2]: *** [libnetcdf4_la-nc4file.lo] Error 1
> > >
> > > Karsten

OK, Karsten, we can get through this!

Firstly, no need to try with more than one daily snapshot. When in doubt, get 
the latest one.

Please send me your config.log and the full output of make check.

Thanks,

Ed

Ticket Details
===================
Ticket ID: LEF-356666
Department: Support netCDF
Priority: High
Status: Open


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