[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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