Re: HDF5 Problem

[Adam Dershowitz]

> On Oct 13, 2016, at 11:32 AM, Ryan Schmidt  wrote:
> 
>> 
>> On Oct 13, 2016, at 10:14 AM, Adam Dershowitz  wrote:
>> 
>> I just updated hdf5 and hdf5-18:
>> 
>> hdf5   1.10.0_1 < 1.10.0-patch1_0   
>> hdf5-181.8.16_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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Re: 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:  take...@macports.org, openmaintai...@macports.org
mac56:
On 10/18/16 07:48, Adam Dershowitz wrote:



On Oct 13, 2016, at 11:32 AM, Ryan Schmidt > wrote:




On Oct 13, 2016, at 10:14 AM, Adam Dershowitz > wrote:


I just updated hdf5 and hdf5-18:

hdf5   1.10.0_1 < 1.10.0-patch1_0
hdf5-181.8.16_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.mcin...@noaa.gov

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