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

[John ZuHone]

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