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

Ian Hinder ian.hinder at aei.mpg.de
Tue Apr 12 11:32:24 CDT 2016

On 12 Apr 2016, at 17:41, Bernard Kelly <physicsbeany at gmail.com> wrote:

> BTW, I'm running Mathematica 10.4.0 on OS X 10.11.4 ("El Capitan")

Hi Beany,

This could indicate that h5mma has crashed, or possibly that it could never run it in the first place.  Can you try running the h5mma executable from a terminal? It should give some output, rather than segfault.  

Can you do an h5dump on the HDF5 file to check it is OK?  If the file is corrupt, it's possible that the HDF5 library is segfaulting. You can also try reading it with the built-in Mathematica HDF5 reader.  Just replace ImportHDF5 with Import.  We found the built-in reader to be extremely flakey with complicated and large HDF5 files, but in simple cases it is probably fine.  

> 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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Ian Hinder

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