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[netCDF #AMX-724559]: error: Can't find or link to the hdf5 library.

Hello,

I am not certain why this is happening; I wonder if there is another `libhdf5` 
installed in the system on the default path, perhaps.  I wonder if you might be 
able to update your version of netcdf to a more recent version? The most recent 
release is v4.9.0, available here: https://github.com/Unidata/netcdf-c/releases 
.  It is possible that there is an issue with the `configure` script (4.6.0) 
and a modern linux environment.  As it stands, it appears that the issue is 
related to something in the autotools-based build system and not the netCDF 
library itself.  Can you provide the libhdf5.settings file generated, when you 
installed libhdf5?  That will also provide some additional information we can 
use to try to figure this out.

Thank you!

-Ward  


> Dear Unidata netCDF Support group:
> 
> 
> I am trying to install ncview.
> 
> 
> Fist step: Install zlib
> tar -xzvf zlib-1.2.8.tar.gz
> cd zlib-1.2.8
> ./congfigure --prefix=$DIR/netcdf_ncview
> make
> make check
> make install
> 
> 
> Next :Install HDF5
> tar -xzvf hdf5-1.10.4.tar.gz
> cd hdf5-1.10.4
> ./configure --prefix=$DIR/netcdf_ncview CPPFLAGS=-I$DIR/netcdf_view/include 
> LDFLAGS=-L$DIR/netcdf_view/lib  --with-zlib=$DIR/netcdf_view
> make
> make check
> make install
> 
> 
> Next:install Netcdf-c
> ./configure --prefix=$DIR/netcdf_ncview CPPFLAGS=-I$DIR/netcdf_view/include 
> LDFLAGS=-L$DIR/netcdf_view/lib  --with-hdf5=$DIR/netcdf_view
> 
> 
> It reported as follow:
> checking for library containing deflate... -lz
> checking for floor in -lm... yes
> checking for dlfcn.h... (cached) yes
> checking for dlopen in -ldl... yes
> checking for library containing H5Fflush... no
> configure: error: Can't find or link to the hdf5 library. Use 
> --disable-netcdf-4, or see config.log for errors.
> 
> 
> I'm not sure why this is happening.
> I also checked the hdf5_examples: run-all-ex.sh. There no error.
> 
> 
> Whats more,when i first check nm libhdf5.so |fgrep H5Fflush and nm 
> libhdf5_hl.so | fgrep H5Fflush, it even not exesisted.
> Then reinstalled hdf5 and rechecked nm libhdf5.so |fgrep H5Fflush and nm 
> libhdf5_hl.so | fgrep H5Fflush.
> It reported that under the command nm libhdf5.so |fgrep H5Fflush :  
> 00000000001094f0 T H5Fflush
> No report appeared under the command(nm libhdf5_hl.so | fgrep H5Fflush).
> 
> 
> And i already installed netcdf (--disable-netcdf4) for CMAQ at $DIR/netcdf,  
> also installed hdf5 at that path. I'm not sure that would affect new 
> installation of HDF5 at a new directory. Because i seemed see that (libtool: 
> warning: relinking 'libhdf5_hl.la' )
> 
> 
> 
> 
> Tip:
> export CC=icc
> export CXX=icc
> export FC=ifort
> export CPP='icpc -E'
> export CXXCPP='icc -E'
> export CPPFLAGS='-fPIC'
> 
> 
> 
> 
> Thanks in advance.
> -Yu Liu
> 
> 
> | |
> ??
> |
> |
> address@hidden
> |
> ???????????


Ticket Details
===================
Ticket ID: AMX-724559
Department: Support netCDF
Priority: Normal
Status: Closed
===================
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