[yt-users] Problem with yt and h5py

Brian O'Shea bwoshea at gmail.com
Sun Apr 18 11:16:24 PDT 2010


Hi everybody,

A quick followup:  at Sam Skillman's suggestion, I removed the .harrays and
.yt files that were already existing in the DD0050 directory.  After
removing these, everything worked fine.

Thanks for the quick turnaround!

--Brian

On Sun, Apr 18, 2010 at 2:05 PM, Brian O'Shea <bwoshea at gmail.com> wrote:

> Dear yt-users,
>
> I'm having a strange problem with yt (svn trunk, r1693).  If I run this
> script:
>
> from yt.mods import *
> fn = "DD0050/DD0050"
> pf = load(fn)
> dd = pf.h.all_data()
>
> I get the following error:
>
> yt         INFO       2010-04-18 13:41:48,183 Getting the binary hierarchy
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/OutputTypes.py", line
> 150, in _get_hierarchy
>     self.__hierarchy = self._hierarchy_class(self,
> data_style=self.data_style)
>   File
> "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line
> 374, in __init__
>     AMRHierarchy.__init__(self, pf, data_style)
>   File
> "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line
> 55, in __init__
>     self._parse_hierarchy()
>   File
> "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line
> 435, in _parse_hierarchy
>     if self._parse_binary_hierarchy(): return
>   File
> "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line
> 506, in _parse_binary_hierarchy
>     self.grid_dimensions[:] = f["/ActiveDimensions"][:]
>   File
> "/mnt/home/oshea/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg/h5py/highlevel.py",
> line 961, in __getitem__
>     basetype = self.id.dtype
>   File "h5d.pyx", line 109, in h5py.h5d.DatasetID.dtype.__get__
> (h5py/h5d.c:1423)
>   File "h5t.pyx", line 364, in h5py.h5t.TypeID.dtype.__get__
> (h5py/h5t.c:2919)
>   File "h5t.pyx", line 367, in h5py.h5t.TypeID.py_dtype (h5py/h5t.c:2976)
> TypeError: No NumPy equivalent for TypeIntegerID exists
>
> I installed this version of yt on MSU's supercomputer using the install
> script at http://svn.enzotools.org/yt/trunk/doc/install_script.sh (the
> supercomputer uses gcc v4.1.2), and as far as I can tell everything
> relevant, including hdf5 and h5py, installed successfully.  The same simple
> set of commands works fine on my laptop with the same dataset.  I'm pointing
> my LD_LIBRARY_PATH environmental variable to the correct directory, so I
> don't think it's that.  Any ideas about what's going on here?
>
> Some more system details:  The output of uname -a for this system is is
> "Linux dev-amd09 2.6.16.60-0.21-smp #1 SMP Tue May 6 12:41:02 UTC 2008
> x86_64 x86_64 x86_64 GNU/Linux".  The system uses gcc v4.1.2 and I'm
> installing yt _without_ wxPython.
>
> Thanks,
> Brian
>
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