[yt-dev] Opening, closing, re-opening HDF5 files

[Matthew Turk]

Hi John,

I tracked this down.  The GDF frontend's _is_valid routine was leaving
a dangling HDF5 handle open; this was showing up in the load() call.
I've issued a PR I'd like you to test.  It also includes a check on
the _particle_handle during the finalizer for FLASHStaticOutput.

https://bitbucket.org/yt_analysis/yt/pull-request/368/fixing-hdf5-dangling-handles-for-flash-gdf/diff

-Matt

On Mon, Dec 10, 2012 at 7:27 PM, John ZuHone <jzuhone at gmail.com> wrote:
> Hi all,
>
> I've got a problem I'm trying to solve regarding HDF5, and I've found it's specifically related to yt.
>
> This sequence works:
>
> f = h5py.open(filename, "r")
>
> do stuff with f
>
> f.close()
>
> f = h5py.open(filename, "r+")
>
> However, this sequence does not:
>
> pf = load(filename)
>
> do stuff with the pf
>
> pf._handle.close()
>
> del pf
>
> f = h5py.open(filename, "r+")
>
> It results in this:
>
> ---------------------------------------------------------------------------
> NameError                                 Traceback (most recent call last)
> <ipython-input-8-186261e4952a> in <module>()
> ----> 1 f = h5py.File("desktop_stuff/GasSloshing/GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150", "r+")
>
> NameError: name 'h5py' is not defined
>
> In [9]: import h5py
>
> In [10]: f = h5py.File("desktop_stuff/GasSloshing/GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150", "r+")
> ---------------------------------------------------------------------------
> IOError                                   Traceback (most recent call last)
> <ipython-input-10-186261e4952a> in <module>()
> ----> 1 f = h5py.File("desktop_stuff/GasSloshing/GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150", "r+")
>
> /Users/jzuhone/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.pyc in __init__(self, name, mode, driver, libver, **kwds)
>     148                 pass
>     149             fapl = make_fapl(driver,libver,**kwds)
> --> 150             fid = make_fid(name, mode, fapl)
>     151         Group.__init__(self, fid)
>     152         self._shared.lcpl = make_lcpl()
>
> /Users/jzuhone/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.pyc in make_fid(name, mode, plist)
>      45         fid = h5f.open(name, h5f.ACC_RDONLY, fapl=plist)
>      46     elif mode == 'r+':
> ---> 47         fid = h5f.open(name, h5f.ACC_RDWR, fapl=plist)
>      48     elif mode == 'w-':
>      49         fid = h5f.create(name, h5f.ACC_EXCL, fapl=plist)
>
> /Users/jzuhone/yt-x86_64/lib/python2.7/site-packages/h5py/h5f.so in h5py.h5f.open (h5py/h5f.c:1618)()
>
> IOError: unable to open file (File accessability: Unable to open file)
>
> Anyone have any ideas?
>
> Best,
>
> John Z
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