[ITK-dev] HDF5 TransformIO broken with System HDF5

[Matt McCormick]

Hi Brad,

Not at the moment, but it is still on the radar.  More time will be
available after the ITK RC's start.

Thanks,
Matt

On Tue, Jun 17, 2014 at 9:14 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Matt,
>
> Have you had a change to look into this issue further?
>
> Thanks,
> Brad
>
> On May 9, 2014, at 8:14 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>
>> Matt,
>>
>> SimpleITK's super build passes CMAKE variable with the prefix "ITK_" to the ITK external project so customizing the ITK in the superbuild is easy. Here is the build script for the system build for the dashboard:
>>
>> http://open.cdash.org/viewNotes.php?buildid=3322976
>>
>> Brad
>>
>> On May 9, 2014, at 12:33 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>
>>> Yes [1], but it looks like ITK was not configured correctly?  I will
>>> try turning on the Review module...
>>>
>>> [1] http://open.cdash.org/buildSummary.php?buildid=3320996
>>>
>>> On Thu, May 8, 2014 at 9:14 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>> Great,
>>>>
>>>> Hopefully it's finished by now :)
>>>>
>>>> Brad
>>>>
>>>> On May 7, 2014, at 5:46 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>>>
>>>>> Thanks, Brad.
>>>>>
>>>>> Debug build with those packages on Ubuntu 12.04:
>>>>>
>>>>> http://open.cdash.org/buildSummary.php?buildid=3320987
>>>>>
>>>>> Starting SimpleITK Debug build...
>>>>>
>>>>> On Wed, May 7, 2014 at 1:39 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>>>> Matt on Ubuntu 12 I have the following installed:
>>>>>>
>>>>>> libhdf5-serial-1.8.4                            install
>>>>>> libhdf5-serial-dev                              install
>>>>>>
>>>>>> And on RHEL I have:
>>>>>>
>>>>>> hdf5-devel-1.8.5.patch1-7.el6.x86_64
>>>>>> hdf5-1.8.5.patch1-7.el6.x86_64
>>>>>>
>>>>>> Brad
>>>>>>
>>>>>> On May 7, 2014, at 1:31 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>>>>>
>>>>>>> Hi Brad,
>>>>>>>
>>>>>>> On Ubuntu 12.04, there appears to be a number of HDF5 "-dev" packages:
>>>>>>>
>>>>>>> libhdf5-lam-dev
>>>>>>> libhdf5-mpi-dev
>>>>>>> libhdf5-mpich-dev
>>>>>>> libhdf5-openmpi-dev
>>>>>>> libhdf5-serial-dev
>>>>>>>
>>>>>>> Which one are you using?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Matt
>>>>>>>
>>>>>>> On Wed, May 7, 2014 at 1:23 PM, Matt McCormick
>>>>>>> <matt.mccormick at kitware.com> wrote:
>>>>>>>> Hi Brad,
>>>>>>>>
>>>>>>>> It looks like our code coverage for the HDF TransformIO is pretty good
>>>>>>>> [1], but I do not see a dashboard submission for those platforms that
>>>>>>>> use a system HDF5.  I will set one up on faraway.kitware and try to
>>>>>>>> reproduce the SimpleITK test failure.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Matt
>>>>>>>>
>>>>>>>> [1] http://lorensen.github.io/VTKCodeCoverage/ITK/IO/TransformHDF5/src/index.html
>>>>>>>>
>>>>>>>> On Wed, May 7, 2014 at 8:59 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> I wrote some SimpleITK tests to write out HDF5 transforms. They are failing when using ITK built with system HDF5. Specifically with RHEL5 and Ubuntu 12.04. I believe this is a critical issue as it's how ITK is being built for Linux distributions.
>>>>>>>>>
>>>>>>>>> Looking through my ITK nightly build testing directory I didn't see any hdf5 files which leads me to believe this IO transform format may not be well tested.
>>>>>>>>>
>>>>>>>>> I would greatly appreciate some assistance on this issue.
>>>>>>>>>
>>>>>>>>> Here is my related SimpleITK issue.
>>>>>>>>> https://issues.itk.org/jira/browse/SIMPLEITK-535
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Brad
>>>>>>>>>
>>>>>>
>>>>
>>
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