[ITK-dev] HDF5 TransformIO broken with System HDF5

Matt McCormick matt.mccormick at kitware.com
Tue Jun 17 10:19:14 EDT 2014


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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