[ITK-dev] HDF5 TransformIO broken with System HDF5

[Bradley Lowekamp]

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
>>>>> 
>>