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[netCDF #TQJ-415567]: problem configuring netCDF 4.1.2 on bluefire

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  • Subject: [netCDF #TQJ-415567]: problem configuring netCDF 4.1.2 on bluefire
  • Date: Fri, 22 Apr 2011 13:08:53 -0600
> Hi,
> 
> I'm trying to install netCDF 4.1.2 on bluefire, configuring as follows:
> 
> ./configure --enable-netcdf-4 --enable-cxx-4 --with-udunits --with-libcf
> --with-hdf5=/contrib/hdf5-1.8.6_seq --with-zlib=/contrib/zlib/
> --with-szlib=/contrib/szip/ --prefix=/contrib/netcdf-4.1.2_seq
> 
> And it fails with the following error:
> 
> Can't find or link to the hdf5 library. Configure with --with-hdf5, or
> use       --disable-netcdf-4, or see config.log for errors
> 
> In fact, hdf5 is fine - but yes, compiled with szlib, i.e. configured with
> 
> ./configure --disable-shared --enable-cxx --enable-fortran
> --enable-gpfs --with-zlib=/contrib/zlib/ --with-szlib=/contrib/szip/
> --prefix=/contrib/hdf5-1.8.6_seq
> 
> The real problem is there are two missing linking switches. The
> configure script is running:
> 
> xlc_r -o conftest  -qarch=auto -qtune=auto -qcache=auto
> -I/contrib/zlib//include -I/contrib/hdf5-1.8.6_seq/include
> -I/contrib/szip//include  -L/contrib/zlib//lib
> -L/contrib/hdf5-1.8.6_seq/lib -L/contrib/szip//lib conftest.c -lhdf5  -lz
> 
> which leads to
> 
> ld: 0711-317 ERROR: Undefined symbol: .ceil
> ld: 0711-317 ERROR: Undefined symbol: .SZ_encoder_enabled
> ld: 0711-317 ERROR: Undefined symbol: .SZ_BufftoBuffDecompress
> ld: 0711-317 ERROR: Undefined symbol: .SZ_BufftoBuffCompress
> ld: 0711-317 ERROR: Undefined symbol: .pow
> ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
> information.
> 
> whereas it should also have -lsz (to resolve SZ_encoder_enabled,
> SZ_BufftoBuffDecompress and SZ_BufftoBuffCompress) and -lm (to resolve
> ceil and pow).
> 
> As a workaround, I added "-L/contrib/szip//lib -lm -lsz" to LDFLAGS, and
> it works (at least until now - I haven't completed the installation
> yet), but this looks like overkill (it's linking everything to lsz,
> which might not required). Is there a better way to workaround this issue?
> 
> Regards,
> Davide Del Vento,
> NCAR Computational & Information Services Laboratory
> Consulting Services Software Engineer
> http://www.cisl.ucar.edu/hss/csg/
> SEA Chair http://sea.ucar.edu/
> office: Mesa Lab, Room 55G
> phone:  (303) 497-1233
> 
> 

Thanks Davide, this bug will be fixed in the next netCDF release.

Ticket Details
===================
Ticket ID: TQJ-415567
Department: Support netCDF
Priority: Normal
Status: Closed