[petsc-users] Configure/make with "--download-hdf5" or "--with-hdf5-dir=" crashes

[Åsmund Ervik]

On 01. sep. 2014 13:52, Matthew Knepley wrote:
> On Mon, Sep 1, 2014 at 6:18 AM, Åsmund Ervik <asmund.ervik at ntnu.no> wrote:
> 
>>
>>
>> On 01. sep. 2014 12:51, Matthew Knepley wrote:
>>> On Mon, Sep 1, 2014 at 3:22 AM, Åsmund Ervik <asmund.ervik at ntnu.no>
>> wrote:
>>>
>>>>
>>>> Subsequently I installed HDF5 v. 1.8.12 using my OS package manager and
>>>> then tried to configure with "--with-hdf5
>>>> --with-hdf5-dir=/path/to/system/hdf5" using PETSc 3.5.1. This time both
>>>> configure and make were successful, but "make test" fails with loads of
>>>> undefined references to PETSc HDF5 stuff (see below). configure.log and
>>>> make.log attached also for this case (error-with-hdf5.tar.gz)
>>>>
>>>
>>> It did not build src/sys/classes/viewer/impls/hdf5/, clearly from the
>> log.
>>> However, it
>>> should have. We have been trying to understand why Make behaves in a bad
>> way
>>> after configuration failure. It should go away with make clean and
>> another
>>> make.
>>
>> Thanks Matt, make clean and then make did result in make test passing
>> all tests.
>>
>> However, I am still unable to use HDF5 functionality. When I compile and
>> run e.g. vec/vec/examples/tutorials/ex10.c it works fine with binary
>> output, but with HDF5 I get the error message below.
>>
>> I'm guessing this is some incompatibility between the various MPI, HDF5
>> and PETSc versions, i.e. that the HDF5 from my OS is not using the same
>> MPI as PETSc. Is it simple to edit something in PETSc and have
>> "./configure --download-hdf5" get the most recent HDF5 library which
>> compiles on my machine?
>>
> 
> Yes, I cannot reproduce, so it must be something like that. Can you
> reconfigure
> using the --download version?

No, I am not able to, that is why I switched to "--with-hdf5-dir=". Like
I said in the first email, the version of HDF5 (1.8.10) that ships with
PETSc 3.5.1 does not compile on my machine. This is apparently a known
bug that was fixed upstream, cf.

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777

This is the reason why I asked whether I can somehow tell
"--download-hdf5" to download a more recent version. 1.8.11 should do it.

Åsmund

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