[Users] SimulationTools/h5mma: Unable to communicate with closed link

[Bernard Kelly]

Hi Barry (and Ian). Thanks for your responses.

Barry, I tried the notebook you sent, and it fails in the same way
(i.e. the bare ImportHDF5 command fails).

Ian, the HDF5 file *could* be corrupt, but I've read it into VisIt and
used it with no issues.

As you suggested, I tried running h5mma on its own from a Terminal command line:

> ./h5mma
Create link:

... so it's expecting a "link", whatever it means by that. A target?

Beany

On 12 April 2016 at 12:17, Barry Wardell <barry.wardell at gmail.com> wrote:
> Hi Beany,
>
> This suggests that there is a problem with the h5mma reader for HDF5 data.
> Can you try running the attached notebook in a fresh Mathematica kernel,
> changing the path to point to your own home directory? You should be able to
> reproduce the output that is in the notebook.
>
> I have just run this on my Mac with Mathematica 10.4.0, OS X 10.11.4,
> SimulationTools 1.0.0 and h5mma 1.2.0 and it worked fine, so this should
> tell us if the problem is with h5mma, or elsewhere.
>
> Regards,
> Barry
>
> On Tue, Apr 12, 2016 at 4:41 PM, Bernard Kelly <physicsbeany at gmail.com>
> wrote:
>>
>> BTW, I'm running Mathematica 10.4.0 on OS X 10.11.4 ("El Capitan")
>>
>> B
>>
>> On 12 April 2016 at 11:30, Bernard Kelly <physicsbeany at gmail.com> wrote:
>> > Hi. Today's silly question:
>> >
>> > I'm trying to use SimulationTools to work with some Carpet HDF5 data.
>> > I've loaded SimulationTools & h5mma with no apparent issues, but this
>> > line fails:
>> >
>> >> ToDataRegion[ ImportHDF5[  "<full path to mydata.h5", {"Datasets",
>> >> "mydataset"}]]
>> >
>> > ... with the error message:
>> >
>> > LinkObject::linkd: Unable to communicate with closed link
>> >
>> > LinkObject['/Users/bjkelly1/Library/Mathematica/Applications/h5mma/MacOSX-x86-64/h5mma',397,6].
>> >>>
>> >
>> > I can verify that the executable is where that error message says it
>> > is, and it's world-runnable. Any ideas why it's not working?
>> >
>> > thanks
>> >
>> > Beany
>> >
>> > P.S. I've never used SimulationTools or h5mma before. I followed the
>> > simple installation instructions from
>> >
>> > http://simulationtools.org/Documentation/English/Tutorials/Introduction.html
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