[yt-users] strange errors

[Geoffrey So]

I've verified that there's nothing wrong with the HDF5 files themselves,
because I can restart the script at the DD of failure and it would continue
without problem, until it dies again with similar error.  I've encountered
corrupted files before, and it would be just the same error, except I
cannot restart because it fails at the same spot again every time, this
isn't one of those times though.

From
G.S.

On Tue, Jul 3, 2012 at 10:32 AM, Britton Smith <brittonsmith at gmail.com>wrote:

> Hi Geoffrey,
>
> This could also be due simply to a single corrupt hdf5 file.  I have seen
> these errors before where a file did not get fully written.  You might want
> to verify that all of the files associated with that dataset are readable.
>
> Britton
>
>
> On Tue, Jul 3, 2012 at 1:28 PM, Geoffrey So <gsiisg at gmail.com> wrote:
>
>> Already submitted the ticket yesterday just haven't heard back.
>> Yeah I didn't think it was OOM, just wanted to confirm it with the
>> experts, thanks!
>>
>> From
>> G.S.
>>
>> On Tue, Jul 3, 2012 at 3:22 AM, Matthew Turk <matthewturk at gmail.com>wrote:
>>
>>> Hi Geoffrey,
>>>
>>> If you're using a script that iterates with an individual python
>>> instance (i.e., calling "python my_script.py") for each data dump,
>>> then I don't think it's an OOM unless somehow multiple instances are
>>> running simultaneously.
>>>
>>> I'm not sure what to suggest other than talking to the help desk at
>>> the particular supercomputer center.
>>>
>>> -Matt
>>>
>>> On Tue, Jul 3, 2012 at 5:32 AM, Geoffrey So <gsiisg at gmail.com> wrote:
>>> > I am trying to make projections and slices in the same script and an
>>> > iterating over several DD datasets, but after a while I get this error
>>> > pasted below, it seems that there's some hdf5 error where h5py cannot
>>> open a
>>> > file.  I've made sure the file exists and the script continues to run
>>> if I
>>> > change the DD#### to continue where it failed.  I've already modified
>>> the
>>> > script so that each DD is using a new python instace intead of
>>> iterating
>>> > through the files with one python call.  I tried this in queue and
>>> > interactive and get the same error, sometimes after many DD, but
>>> sometimes
>>> > after only 1 or 2.  Is this indicative of memory issue?   If it is,
>>> I'm not
>>> > getting the OOM messages even in interactive node.  Has anyone
>>> encountered
>>> > this before?  I've stuck in import gc at the top and gc.collect() at
>>> the end
>>> > of the script, too, but doesn't help.
>>> >
>>> > From
>>> > G.S.
>>> >
>>> > Traceback (most recent call last):
>>> >   File "moviesGrey.py", line 35, in <module>
>>> >     proj = pf.h.proj(0, field, weight_field=field)
>>> >   File
>>> >
>>> "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
>>> > line 2001, in __init__
>>> >     if self._okay_to_serialize and self.serialize:
>>> > self._serialize(node_name=self._node_name)
>>> >   File
>>> >
>>> "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
>>> > line 970, in _serialize
>>> >     self._store_fields(self._key_fields, node_name, force)
>>> >   File
>>> >
>>> "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",
>>> > line 947, in _store_fields
>>> >     passthrough = True)
>>> >   File
>>> >
>>> "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
>>> > line 241, in in_order
>>> >     f2(*args, **kwargs)
>>> >   File
>>> >
>>> "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_objects/hierarchy.py",
>>> > line 278, in _reload_data_file
>>> >     self._data_file = h5py.File(self.__data_filename, self._data_mode)
>>> >   File
>>> > "/home/ux455076/dev-yt/lib/python2.7/site-packages/h5py/_hl/files.py",
>>> line
>>> > 150, in __init__
>>> >     fid = make_fid(name, mode, fapl)
>>> >   File
>>> > "/home/ux455076/dev-yt/lib/python2.7/site-packages/h5py/_hl/files.py",
>>> line
>>> > 45, in make_fid
>>> >     fid = h5f.open(name, h5f.ACC_RDONLY, fapl=plist)
>>> >   File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1618)
>>> > IOError: unable to open file (File accessability: Unable to open file)
>>> > Exception AttributeError: "'EnzoHierarchy' object has no attribute
>>> > '_data_file'" in <bound method EnzoHierarchy.__del__ of
>>> > <yt.frontends.enzo.data_structures.EnzoHierarchy object at 0x32a4d10>>
>>> > ignored
>>> >
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