[Insight-developers] CSI-ITK: HDF5 intermittent failures

[Luis Ibanez]

Hi Kent,

Valgrind is still reporting uninitialized variables in HDF5

http://www.cdash.org/CDash/viewDynamicAnalysisFile.php?id=2406474

They seem to be related to the process of closing a file:

==19114==    at 0x4E3DC40: __write_nocancel (syscall-template.S:82)
==19114==    by 0x7AC5BC: H5FD_sec2_write (H5FDsec2.c:799)
==19114==    by 0x7A12B9: H5FD_write (H5FDint.c:184)
==19114==    by 0x785D23: H5F_accum_flush (H5Faccum.c:1000)
==19114==    by 0x77E524: H5F_flush (H5F.c:1703)
==19114==    by 0x77BCAE: H5F_dest (H5F.c:1005)
==19114==    by 0x77EE75: H5F_try_close (H5F.c:1929)
==19114==    by 0x77E7CE: H5F_close (H5F.c:1774)
==19114==    by 0xA17067: H5I_dec_ref (H5I.c:1406)
==19114==    by 0xA171C8: H5I_dec_app_ref (H5I.c:1449)
==19114==    by 0x77F24D: H5Fclose (H5F.c:1990)
==19114==    by 0x7153C0: H5::H5File::close() (H5File.cpp:770)


They seem to be worth investigating...


    Luis


----------------------------
On Wed, Jun 8, 2011 at 9:44 AM, Williams, Norman K
<norman-k-williams at uiowa.edu> wrote:
> There are a lot of builds that fail, and they all (save one) have
> something in common.  The test writes a file, but then cannot read it --
> either it fails to open or it fails to read the first dataset.
>
>
> I verified that the tests do in fact close the file they've created.
>
> I also notice that for many systems that fail, very similar systems
> succeed.
>
> I can add a test that attempts to read a known-good image, and see if that
> fails as well.
>
> I've been loading up VMs in virtual boxes that are, where possible1 as
> close as possible to the failing systems.  So far no failures.
>
> As I've said before, if someone can give me an account on any of the
> machines with failures I'll gladly investigate.
>
> On 6/8/11 6:47 AM, "Brad King" <brad.king at kitware.com> wrote:
>
>>On 06/07/2011 10:51 AM, Brad King wrote:
>>> On 06/04/2011 12:02 PM, Bill Lorensen wrote:
>>>> Looks like an uninitialized variable somewhere? valgrind does not
>>>> catch them all... Maybe you should run cppcheck on the HDF5 thirdparty
>>>> code.
>>>
>>> At Kent's request I've updated the HDF5 snapshot to version 1.8.7 from
>>> upstream.  I manually built and tested it on Linux with GCC and Windows
>>> with MinGW and VS 9 tools.  We should all keep an eye out for new
>>> warnings.
>>>
>>> The commit range of the changes is "e1f9e848..b76ce0bd".
>>
>>Well, there are quite a few places that the HDF5 tests now fail:
>>
>>http://www.cdash.org/CDash/testSummary.php?project=2&name=itkHDF5ImageIOTe
>>st&date=2011-06-07
>>http://www.cdash.org/CDash/testSummary.php?project=2&name=itkHDF5ImageIOSt
>>reamingReadWriteTest&date=2011-06-07
>>
>>However, they pass on all the Kitware machines and on all my own builds
>>(except itkHDF5ImageIOTest on factory.kitware fails for an unrelated
>> reason).
>>
>>Can anyone with a machine where it fails investigate, please?
>>
>>Thanks,
>>-Brad
>
>
>
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