[yt-users] pHOP child halos

[Britton Smith]

Hi Brian,

It looks like this installation of yt is using h5py 1.2, which I believe has
a bug that causes issues when using the same variable name to open multiple
hdf5 files in sequence.  If this is the case, then the only solution is to
upgrade the hdf5 version being used to version 1.3 or higher.  Stephen will
know better than I if this is the issue.  Stephen, can you confirm this?

Britton

On Mon, Jul 4, 2011 at 5:56 PM, Brian Crosby <crosby.bd at gmail.com> wrote:

> Hi everyone,
>
> I'm using Nautilus to run pHOP on a 1024^3 dataset and have encountered a
> strange problem.  All of the halos are found and written to the SQL database
> successfully, but then when pHOP attempts to go back and identify the
> parent/child relationships, it hangs and gives message:
>
> Traceback (most recent call last):
>  File "halofinding.py", line 14, in <module>
>    MergerTree(restart_files=files,
> database='/gpfs/medusa/oshea/PopIII_1024/halos1024.db',
> halo_finder_function=parallelHF)
>  File
> "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/analysis_modules/halo_merger_tree/merger_tree.py",
> line 201, in __init__
>    last = self._compute_child_fraction(pair[0], pair[1], last)
>  File
> "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/analysis_modules/halo_merger_tree/merger_tree.py",
> line 489, in _compute_child_fraction
>    for group in h5fp:
>  File
> "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/h5py-1.2.0-py2.7-linux-x86_64.egg/h5py/highlevel.py",
> line 300, in __iter__
>    return self.id.__iter__()
>  File
> "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/h5py-1.2.0-py2.7-linux-x86_64.egg/h5py/_sync.py",
> line 94, in wrap
>    return func(*args, **kwds)
>  File "h5g.pyx", line 449, in h5py.h5g.GroupID.__iter__ (h5py/h5g.c:3441)
>  File "h5g.pyx", line 103, in h5py.h5g.GroupIter.__init__ (h5py/h5g.c:1235)
>  File
> "/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/lib/python2.7/site-packages/h5py-1.2.0-py2.7-linux-x86_64.egg/h5py/_sync.py",
> line 88, in wrap
>    return func(*args, **kwds)
>  File "h5g.pyx", line 316, in h5py.h5g.GroupID.get_num_objs
> (h5py/h5g.c:2469)
> h5py._stub.ValueError: Invalid group id (Invalid arguments to routine: Bad
> value)
>
> Does anyone have an idea what might be going wrong here, or how I should go
> about fixing it?
>
> Thanks,
> Brian
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