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[netCDF #IDJ-549001]: Problem installing netcdf-4.1.3 with hdf5



Hi Alejandro,

> Such as you told me i rebuilt HDF5 with --with-zlib= option, and then
> rebuilt the netCDF.
> 
> But i got a new issue here.
> 
> I typed:
> 
> export CC=icc
> export CXX=icpc
> export F77=ifort
> export FC=ifort
> export CPP='icc -E'
> export CXXCPP='icpc -E'
> export F90=ifort
> CPPFLAGS=-I/hdf5/local/include LDFLAGS=-L/hdf5/local/lib ./configure
> 
> And configure looks like ends good (attached config.log)
> 
> So i try:
> 
> make check install 2>&1 | tee make.log
> 
> it shows
> 
> ===================
> All 26 tests passed
> ===================
> 
> Great! This solved the problem and "make check install" continues till a
> new error (attached make.log):
> 
> ld: warning: libimf.so, needed by ../liblib/.libs/libnetcdf.so, not found
> (try using -rpath or -rpath-link)
> ld: warning: libsvml.so, needed by ../liblib/.libs/libnetcdf.so, not found
> (try using -rpath or -rpath-link)
> ld: warning: libintlc.so.5, needed by ../liblib/.libs/libnetcdf.so, not
> found (try using -rpath or -rpath-link)
> ld: .libs/nctest: hidden symbol `__intel_cpu_indicator_init' in
> /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libirc.a(cpu_disp.o)
> is referenced by DSO
> ld: final link failed: Nonrepresentable section on output
> make[2]: *** [nctest] Error 1
> make[2]: Leaving directory `/netcdf-4.1.3/nctest'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/netcdf-4.1.3/nctest'
> make: *** [check-recursive] Error 1
> 
> Then i dont know what is the matter right now.

Those libraries are not related to netCDF.  They provide runtime
support needed by the Intel compilers.  It may be that you need to set
a LD_LIBRARY_PATH environment variable to tell ld where to find these
Intel libraries, or that may be done by shell scripts you have to run
to configure the environment when using the Intel compilers.  For
example, see this previous response to a similar user support
question:

  http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg10723.html

There may also be some help in this Intel guide for using their compilers
to build netCDF libraries:

  
http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-netcdf-with-the-intel-compilers

--Russ

> 2012/12/28 Unidata netCDF Support <address@hidden>
> 
> > Hi Alejandro,
> >
> > > I'm trying to buid netcdf-4.1.3.
> > >
> > > I am using hdf5-1.8.9 wich had be donne with zlib-1.2.7 and szip-2.1.
> > >
> > > I type
> > > cd netcdf-4.1.3/
> > > export CC=icc
> > > export CXX=icpc
> > > export F77=ifort
> > > export FC=ifort
> > > export CPP='icc -E'
> > > export CXXCPP='icpc -E'
> > > export F90=ifort
> > >
> > > CPPFLAGS=-I/hdf5/local/include LDFLAGS=-L/hdf5/local/lib ./configure
> > >
> > > And configure ends good (attached config.log)
> > >
> > > So i continued with:
> > > make check install 2>&1 | tee make.log
> > >
> > > After some minutes i got:
> > > ...
> > > ================================================
> > > 1 of 26 tests failed
> > > Please report to address@hidden
> > > ================================================
> > > make[2]: *** [check-TESTS] Error 1
> > > make[2]: Leaving directory `/netcdf-4.1.3/h5_test'
> > > make[1]: *** [check-am] Error 2
> > > make[1]: Leaving directory `/netcdf-4.1.3/h5_test'
> > > make: *** [check-recursive] Error 1
> > >
> > > (attached make.log)
> > >
> > > Looking for the error in make.log i found:
> > >
> > > PASS: tst_h_atts4
> > > HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
> > > #000: H5Z.c line 1376 in H5Zget_filter_info(): Filter not defined
> > > major: Invalid arguments to routine
> > > minor: Bad value
> > > #001: H5Z.c line 1019 in H5Z_find(): required filter is not registered
> > > major: Data filters
> > > minor: Object not found
> > >
> > > *** Checking HDF5 variable functions.
> > > *** Checking HDF5 boolean variables...ok.
> > > *** Checking HDF5 variable with unlimited dimension...ok.
> > > *** Checking HDF5 deflate filter setting and getting...Sorry! Unexpected
> > > result, tst_h_vars.c, line: 230
> > > FAIL: tst_h_vars
> >
> > This indicates the HDF5 library can't find zlib.  When you build HDF5, you
> > need to configure it with the --with-zlib= option to tell it where to find
> > the zlib library.  The value of that option should point to a directory
> > above
> > the lib and include directories that contain the libz library and header
> > file.
> >
> > Then rebuild the netCDF library and this problem should go away.  I hope
> > this helps ...
> >
> > --Russ
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: IDJ-549001
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: IDJ-549001
Department: Support netCDF
Priority: Normal
Status: Closed


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