HDF5 Problem

[Barry McInnes (NOAA Affiliate)]

We were almost out of version issues, until the latest selfupdate yesterday

The problem is that the netcdf-C library 
(/opt/local/lib/libnetcdf.dylib) is now trying to dynamically link to 
the HDF5 1.10 library in /opt/local/lib.  It should instead be linking 
to the HDF5 1.8.x library in /opt/local/lib/hdf5-18/lib
The port info for netcdf states the dependency is hdf5-18 ?
mac56:~/fortran/simple-examples/nc-ex 14> port info netcdf
netcdf @4.4.1_2 (science)
Variants:             clang33, clang34, clang35, clang36, clang37, 
clang38, clang39, [+]dap, debug, dragonegg33, dragonegg34, gcc44, gcc45, 
gcc46, gcc47, gcc48, gcc49, gcc5, gcc6, gcc7, hdf4, llvm,
                       mpich, mpich_devel, [+]netcdf4, openmpi, 
openmpi_devel, universal

Description:          NetCDF (network Common Data Form) is a set of 
software libraries and machine-independent data formats that support the 
creation, access, and sharing of array-oriented scientific
                       data.
Homepage:             http://www.unidata.ucar.edu/software/netcdf/

Build Dependencies:   cmake
Library Dependencies: hdf5-18, curl
Platforms:            darwin
License:              Permissive
Maintainers:          takeshi at macports.org, openmaintainer at macports.org
mac56:
On 10/18/16 07:48, Adam Dershowitz wrote:
>
>
>> On Oct 13, 2016, at 11:32 AM, Ryan Schmidt <ryandesign at macports.org 
>> <mailto:ryandesign at macports.org>> wrote:
>>
>>>
>>> On Oct 13, 2016, at 10:14 AM, Adam Dershowitz <dersh at alum.mit.edu 
>>> <mailto:dersh at alum.mit.edu>> wrote:
>>>
>>> I just updated hdf5 and hdf5-18:
>>>
>>> hdf5                           1.10.0_1 < 1.10.0-patch1_0
>>> hdf5-18                        1.8.16_6 < 1.8.17_0
>>>
>>> Now when I try to use pandas to open an HDF5 file I get this error:
>>>
>>> Warning! ***HDF5 library version mismatched error***
>>> The HDF5 header files used to compile this application do not match
>>> the version used by the HDF5 library to which this application is 
>>> linked.
>>> Data corruption or segmentation faults may occur if the application 
>>> continues.
>>> This can happen when an application was compiled by one version of 
>>> HDF5 but
>>> linked with a different version of static or shared HDF5 library.
>>> You should recompile the application or check your shared library 
>>> related
>>> settings such as 'LD_LIBRARY_PATH'.
>>> You can, at your own risk, disable this warning by setting the 
>>> environment
>>> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
>>> Setting it to 2 or higher will suppress the warning messages totally.
>>> Headers are 1.8.16, library is 1.8.17
>>
>> Sounds like whatever library generated that error (you mentioned 
>> py27-pandas and py27-tables but I don't know) is being possibly 
>> overzealous in its hdf5 version checking. Sounds like we should 
>> increase the revision of whichever port is triggering this error, and 
>> add a comment to the hdf5 port to remind us to do that every time the 
>> version of hdf5 is increased.
>>
>> It looks to me like py27-tables is the one that depends on hdf5-18, 
>> so that's the one that probably needs to be rebuilt. py27-pandas only 
>> depends on py27-tables and other python modules.
>>
>>
>>> I tried uninstalling and reinstalling pandas and py27-tables, but 
>>> that didn’t help.
>>
>> If you received a binary from our server, it would be a binary built 
>> with the old version of hdf5. We need to increase that port's 
>> revision to cause it to rebuild with the new version of hdf5.
>>
>> You can try rebuilding from source on your system to identify the 
>> problem.
>>
>> sudo port -ns upgrade --force py27-tables
>>
>> If that works, let us know so we can increase its revision.
>
> Yes, forcing the rebuild of py27-tables seems to fix the problem.
> Although, it was slightly more complicated because that rebuild 
> complained that py27-tables can’t be built with hdf5 active, so i had 
> to force deactivate that, then it built fine, and reactivated hdf5 after.
>
>
>>
>>
>> Looking a little further, I see that the "HDF5 library version 
>> mismatched error" actually comes from the hdf5-18 (and hdf5) source 
>> code. This makes me think that *any* port that uses hdf5-18 (or hdf5) 
>> will encounter this problem, and they should all be revbumped any 
>> time the version of hdf5-18 (or hdf5) is increased. This is a pain 
>> and the developers of hdf5 should be contacted to explain this to 
>> them, so that they can weigh in on why they are inflicting this pain 
>> on us and what they can do to mitigate it in subsequent versions of 
>> their software.
>>
>>
>>> So, I’m not sure where the bug actually is, what to do about it, or 
>>> what port to file a bug report against.
>>> Any suggestions? 
>
>
>
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-- 

Barry McInnes
325 Broadway
Boulder CO 80304
(303)4976231
barry.j.mcinnes at noaa.gov

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