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

> Hello Russ,
> 
> Well, I have just tried your suggestion tonight, but still no joy.
> 
> I have included
> source /opt/intel/bin/iccvars.sh intel64
> 
> source /opt/intel/bin/ifortvars.sh intel64
> 
> but get similar errors...
> 
> Here are the config.log, the make script and the make log.

The error messages you're getting, that the icc compiler fails to
build a trivial C program when "-lnetcdf" is included because of
missing internal Intel libraries, still don't seem to have anything
to do with netCDF.

You may be overspecifying things in your environment variables, according
to the Intel instructions for building an earlier version of netCDF
libraries:

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

There, they recommend just using

  export CC=icc
  export CXX=icpc

instead of the full paths to the compilers, which should be found 
anyway after running

  source <compiler_install_dir>/bin/compilervars.sh intel64

(They also imply the above is sufficient, and that you shouldn't need to
 source other files.)

I'm still not sure why you're using "--disable-shared".  Insisting on
making only a static library may have something to do with the problem you're
seeing.

If the above doesn't resolve the problem, I suggest asking Intel support for
help explaining what causes these compiler errors and warnings that appear in
the config.log:

icc: warning #10237: -lcilkrts linked in dynamically, static library not 
available
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

By the way, it has nothing to do with this problem, but your script has a 
mistake
(commented out) for the hdf5 build.  You should change

  #./configure --prefix=${H5DIR} --with-szlib=${SZDIR} --enable-fortran 
--enable-cxx
  #make check install

to

  #./configure --prefix=${H5DIR} --with-szlib=${SZDIR} --enable-fortran 
--enable-cxx
  #make all check install

as explained in a previous response.  That would have permitted you to use 
HDF5-1.8.11
instead of HDF5-1.8.9.  But I don't think that has any relevance to the problem 
you're
seeing now.

If you find a solution to the icc problem, please let us know ...

--Russ

> From: Unidata netCDF Support [address@hidden]
> Sent: 23 June 2013 22:46
> To: Chiu, Peter (STFC,RAL,RALSP)
> Cc: address@hidden; SDDCS
> Subject: [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 
> -I/usr/local/netcdf4.3-intel/nc430_hdf5_189sz/include 
> -I/usr/local/netcdf4.3-intel/hdf5_189sz/include 
> -L/usr/local/netcdf4.3-intel/nc430_hdf5_189sz/lib 
> -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 
> available
> 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: $? = 1
> configure:3860: result: no
> 
> All those libraries libimf, libsvml, libirng, and libintlc are supposed to be 
> installed
> for icc.
> 
> Have you run
> 
> source /opt/intel/bin/iccvars.sh intel64
> 
> before compiling with icc in this shell?
> 
> --Russ
> 
> > configure: error: C compiler cannot create executables
> > See `config.log' for more details
> > make: *** No rule to make target `check'.  Stop.
> >
> > I have attached the script, make.log and config.log on netcdf-fortran-4.2 .
> >
> > Much appreciated if you can look into this too.
> >
> > By the way, I need to be away for few days.  I might need to ask my 
> > colleague Brian Coan to liaise with you on this.
> > You can reach us on address@hidden.
> >
> > Thanks.
> > Regards,
> > Peter
> >
> >
> > ________________________________________
> > From: Unidata netCDF Support [address@hidden]
> > Sent: 21 June 2013 22:13
> > To: Chiu, Peter (STFC,RAL,RALSP)
> > Cc: address@hidden
> > Subject: [netCDF #JZT-105309]: neCDF 4.3.0 installation issue - Can't find 
> > or link to the hdf5 library
> >
> > Oops, sorry, I just noticed the error you are seeing in h5dump was caused
> > by a last minute "simplification" I made to the script I included which was
> > actually a mistake.  The line for building HDF5-1.8.11 should be corrected
> > from
> >
> > ./configure --prefix=${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
> 
> 
> --
> 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