Re: [netcdfgroup] HD5 library error

• To: Mahmood Naderan <mahmood.nt@xxxxxxxxx>
• Subject: Re: [netcdfgroup] HD5 library error
• From: Dominikus Heinzeller <climbfuji@xxxxxxxxx>
• Date: Thu, 21 Jul 2016 15:33:03 +0200

Hi Mahmood,

firstly there would be a type in your call to configure: "--with-hd5=“ would 
have to be "--with-hdf5=“, but in netcdf-4.4.1 there is no option --with-hdf5 
according to ./configure --help.

What I usually do is:

LD_LIBRARY_PATH=“/export/apps/computer/hdf5-1.8.17-linux-centos6-x86_64-gcc447-shared/lib:$LD_LIBRARY_PATH”
 \
LIBS="-lhdf5 -lhdf5_hl -lsz -lz" \
./configure \
…

It’s weird because it should be in your path already, but …

Cheers

Dom


> On 21/07/2016, at 3:17 PM, Mahmood Naderan <mahmood.nt@xxxxxxxxx> wrote:
> 
> Hi,
> There are several pages about this error
> 
> configure: error: Can't find or link to the hdf5 library. Use 
> --disable-netcdf-4, or see config.log for errors.
> 
> 
> However, I am sure that hd5 library is OK. I downloaded the package and gave 
> the path to the configure script.
> 
> root@cluster:~# cd /export/apps/computer/netcdf-4.4.1
> root@cluster:netcdf-4.4.1# ls 
> ../hdf5-1.8.17-linux-centos6-x86_64-gcc447-shared/
> bin  COPYING  include  lib  README  RELEASE.txt  share
> root@cluster:netcdf-4.4.1# ls 
> ../hdf5-1.8.17-linux-centos6-x86_64-gcc447-shared/lib
> libhdf5.a              libhdf5_fortran.so.10.0.3  libhdf5hl_fortran.so.10     
>  libhdf5.so.10.2.0
> libhdf5_cpp.a          libhdf5_hl.a               libhdf5hl_fortran.so.10.0.3 
>  libsz.so
> libhdf5_cpp.so         libhdf5_hl_cpp.a           libhdf5_hl.so               
>  libsz.so.2
> libhdf5_cpp.so.12      libhdf5_hl_cpp.so          libhdf5_hl.so.10            
>  libsz.so.2.0.0
> libhdf5_cpp.so.12.0.0  libhdf5_hl_cpp.so.11       libhdf5_hl.so.10.1.0        
>  libz.so
> libhdf5_fortran.a      libhdf5_hl_cpp.so.11.1.0   libhdf5.settings            
>  libz.so.1
> libhdf5_fortran.so     libhdf5hl_fortran.a        libhdf5.so                  
>  libz.so.1.2.5
> libhdf5_fortran.so.10  libhdf5hl_fortran.so       libhdf5.so.10
> 
> root@cluster:netcdf-4.4.1# echo $LD_LIBRARY_PATH
> /export/apps/computer/hdf5-1.8.17-linux-centos6-x86_64-gcc447-shared/lib
> root@cluster:netcdf-4.4.1# ./configure 
> --with-hd5=/export/apps/computer/hdf5-1.8.17-linux-centos6-x86_64-gcc447-shared
> ...
> ...
> 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 really don't understand why it is still giving me the error.
> Thanks for any suggestion.
> 
> 
> Regards,
> Mahmood
> 
> 
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• References:
  • [netcdfgroup] HD5 library error
    • From: Mahmood Naderan