[yt-users] strange errors

[Britton Smith]

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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