[ITK-dev] HDF5 TransformIO broken with System HDF5

[Bradley Lowekamp]

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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