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[netCDF #JZT-105309]: neCDF 4.3.0 installation issue - Can't find or link to the hdf5 library

Hi Peter or Brian,

> In the meantime, I did try the build with HDF5.1.8.9, and managed to get 
> through the netcdf-4.3.0 installation.
> I have an installed binary on /usr/local/netcdf4.3-intel/nc430_hdf5_189sz.
> When the script proceeds with netcdf-fortran-4.2, it then fails.

From these errors in config.log, it appears the environment is not set up 
correctly for 
running icc:

  configure:3796: checking whether the C compiler works
  configure:3818: /opt/intel/composer_xe_2013.0.079/bin/intel64/icc -O3 -xHost 
-ip -no-prec-div -static-intel 
-L/usr/local/netcdf4.3-intel/hdf5_189sz/lib conftest.c -lnetcdf -lhdf5_hl 
-lhdf5 -lz -lcurl >&5
  icc: warning #10237: -lcilkrts linked in dynamically, static library not 
  ld: warning: libimf.so, needed by 
/usr/local/netcdf4.3-intel/nc430_hdf5_189sz/lib/libnetcdf.so, not found (try 
using -rpath or -rpath-link)
  ld: warning: libsvml.so, needed by 
/usr/local/netcdf4.3-intel/nc430_hdf5_189sz/lib/libnetcdf.so, not found (try 
using -rpath or -rpath-link)
  ld: warning: libirng.so, needed by 
/usr/local/netcdf4.3-intel/nc430_hdf5_189sz/lib/libnetcdf.so, not found (try 
using -rpath or -rpath-link)
  ld: warning: libintlc.so.5, needed by 
/usr/local/netcdf4.3-intel/nc430_hdf5_189sz/lib/libnetcdf.so, not found (try 
using -rpath or -rpath-link)
  ld: a.out: hidden symbol `__intel_cpu_indicator_init' in 
/opt/intel/composer_xe_2013.0.079/compiler/lib/intel64/libirc.a(cpu_disp.o) is 
referenced by DSO
  ld: final link failed: Nonrepresentable section on output
  configure:3822: $? = 1
  configure:3860: result: no

All those libraries libimf, libsvml, libirng, and libintlc are supposed to be 
for icc.

Have you run

  source /opt/intel/bin/iccvars.sh intel64

before compiling with icc in this shell?


> configure: error: C compiler cannot create executables
> See `config.log' for more details
> make: *** No rule to make target `check'.  Stop.
> I have attached the script, make.log and config.log on netcdf-fortran-4.2.
> Much appreciated if you can look into this too.
> By the way, I need to be away for few days.  I might need to ask my colleague 
> Brian Coan to liaise with you on this.
> You can reach us on address@hidden
> Thanks.
> Regards,
> Peter
> ________________________________________
> From: Unidata netCDF Support address@hidden
> Sent: 21 June 2013 22:13
> To: Chiu, Peter (STFC,RAL,RALSP)
> Cc: address@hidden
> Subject: [netCDF #JZT-105309]: neCDF 4.3.0 installation issue - Can't find or 
> link to the hdf5 library
> Oops, sorry, I just noticed the error you are seeing in h5dump was caused
> by a last minute "simplification" I made to the script I included which was
> actually a mistake.  The line for building HDF5-1.8.11 should be corrected
> from
> ./configure --prefix=${H5DIR} --with-szlib=${SZDIR} && make check install
> to
> ./configure --prefix=${H5DIR} --with-szlib=${SZDIR} && make all check install
> because otherwise the utilities like h5dump don't get built before they're
> needed in some of the tests.
> I'm testing again with that fix and it looks like things are OK.
> Sorry!
> --Russ
> > Peter,
> >
> > > Looks like not my luck day.
> > >
> > > I have tried downloaded the HDF5 1.8.11, but unfortunately the hdf5 wont 
> > > build with the Intel compilers.
> > > It failed on some H5dump tests. I have attached the logs.
> >
> > The configure for HDF5-1.8.11 worked fine.
> >
> > I can't see what H5dump test failed in the files you attached, which seem to
> > be for the netCDF-4.3.0 build rather than the HDF5-1.8.11 build.  If you 
> > still
> > have the log or details for that failure, could you send them?
> >
> > I also can't see the details of what went wrong in the netCDF-4.3.0 test, 
> > for
> > which the apps3-build-netcdf-hdf5.1811.log just reports one failure in 
> > nc_test
> > and says
> >
> > See nc_test/test-suite.log
> >
> > If you've still got that, could you send it?  It's possible it is a bug in a
> > test rather than the library code.
> >
> > --Russ
> >
> > > I am retrying this with HDF5 1.8.9.
> > >
> > > Peter
> > >
> --
> Scanned by iCritical.

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu

Ticket Details
Ticket ID: JZT-105309
Department: Support netCDF
Priority: Normal
Status: Closed

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