[yt-users] strange errors

[Geoffrey So]

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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