[netCDF #CWH-106634]: Error in Test

Phil,

> I did build HDF5 and zlib from source, and configured with the 
> --with-zlib=.....
> The HDF5 library (libhdf5.a) contains the filters: shuffle,fletcher32,nbit, 
> scaleoffset.

None of those are from zlib. They are independent filters, some of which can be 
used with zlib (for example shuffle).

> However, these are defined as internal. Here is the relevant part of the 
> HDF5/settings:
>         "With Deprecated Public Symbols: yes
>          I/O filters (external):
>          I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset"

OK, that means HDF5 was not built with zlib, even though you specified
--with-zlib=...  

You used

  
--with-zlib=/work/00046/tg457095/software/NewPism/HDF5/ZHOPE/include,/work/00046/tg457095/software/NewPism/HDF5/ZHOPE/lib

to specify the include/ and lib/ install locations for zlib.  You might
instead try the CPPFLAGS and LDFLAGS method, which is also documented to
work.

ZDIR=/work/00046/tg457095/software/NewPism/HDF5/ZHOPE
CPPFLAGS="-I${ZDIR}/include"
LDFLAGS="-L${ZDIR}/lib"

You might also check the HDF5 build output to see any error
messages in the config.log about finding zlib, check the 
permissions of the zlib install directories, and check the 
32-bit vs 64-bit architectures of the libraries ...

--Russ

> So HDF5 got at least some filters from zlib (I assume), but if it needs to 
> specify an external filter and it doesn't then I obviously made a mistake 
> somewhere.
> 
> Here is the configure script for HDF5 1.8.14 that I used (all on the same 
> line. I don't do well with line breaks!":
> 
> FC=/work/00046/tg457095/software/NewPism/MVAPICH2/MVAHOPE/bin/mpif90 
> CC=/work/00046/tg457095/software/NewPism/MVAPICH2/MVAHOPE/bin/mpicc 
> CXX=/work/00046/tg457095/software/NewPism/MVAPICH2/MVAHOPE/bin/mpic++  
> ./configure --disable-shared --enable-fortran --enable-cxx 
> --enable-unsupported 
> --with-zlib=/work/00046/tg457095/software/NewPism/HDF5/ZHOPE/include,/work/00046/tg457095/software/NewPism/HDF5/ZHOPE/lib
>  --prefix=/work/00046/tg457095/software/NewPism/HDF5/HHOPE


> Any thoughts would be greatly appreciated!
> Phil
> 
> 
> From: Unidata netCDF Support <address@hidden>
> To: address@hidden
> Cc: address@hidden
> Sent: Tuesday, December 23, 2014 5:36 PM
> Subject: [netCDF #CWH-106634]: Error in Test
> 
> Hi Phil,
> 
> >  I have installed netcdf-4.3.2, and, for the most part, it seems to be 
> > fine. In the h5_test directory, it bombs on 1 of the 27 tests. Various 
> > error reports are provided below. It looks like it is having trouble with 
> > some filter functions. I have installed zlib, but not any other filter 
> > libraries. Any help would be most appreciated!
> 
> It's not enough to have zlib installed, you also need to have built the
> HDF5 libraries with zlib. That happens by default if you build from source
> with zlib installed somewhere standard, where the HDF5 build system will
> look, but if not, you need to run the configure script with the option
>   --with-zlib=DIR
> where DIR is the directory where it's installed.
> 
> If you didn't build HDF5 from source, you can tell whether it was built
> with zlib by looking at the lib/libhdf5.settings file where HDF5 was
> installed.  Under "Features" in that file, you should see:
>         I/O filters (external): deflate(zlib)
> If you don't see that, you need to get an HDF5 library built with zlib,
> or build it again from source.
> 
> > Thanks,
> > Phil
> 
> You're welcome, I hope this helps.
> 
> --Russ
> 
> >     Checking HDF5 deflate, fletcher32, shuffle filter setting and 
> > getting...Sorry! Unexpected     result, tst_h_vars.c, line: 305
> > I have the following from the error stack:
> > #000: H5Z.c line 1710 in H5Z_get_filter_info(): Filter not defined
> >     major: Data filters
> >     minor: Bad value
> >   #001: H5Z.c line 1254 in H5Z_find(): required filter is not registered
> >     major: Data filters
> >     minor: Object not found
> >   #002: H5Z.c line 1254 in H5Z_find(): required filter is not registered
> >     major: Data filters
> >     minor: Object not found
> > Sorry! Unexpected result, tst_h_vars.c, line: 309
> >
> > High level make check output.
> > # TOTAL: 27
> > # PASS:  26
> > # SKIP:  0
> > # XFAIL: 0
> > # FAIL:  1
> > # XPASS: 0
> > # ERROR: 0
> > ============================================================================
> > See h5_test/test-suite.log
> > Please report to address@hidden
> > ============================================================================
> > make[2]: *** [test-suite.log] Error 1
> > make[2]: Leaving directory 
> > `/work/00046/tg457095/software/NewPism/NET4/netcdf-4.3.2/h5_test'
> > make[1]: *** [check-TESTS] Error 2
> > make[1]: Leaving directory 
> > `/work/00046/tg457095/software/NewPism/NET4/netcdf-4.3.2/h5_test'
> > make: *** [check-am] Error 2
> > login2.stampede(142)$
> >
> >
> >
> >
> Russ Rew                                        UCAR Unidata Program
> address@hidden                      http://www.unidata.ucar.edu
> 
> 
> 
> Ticket Details
> ===================
> Ticket ID: CWH-106634
> Department: Support netCDF
> Priority: Normal
> Status: Closed
> 
> 
> 
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: CWH-106634
Department: Support netCDF
Priority: Normal
Status: Closed