Will do.<div><br></div><div>From</div><div>G.S.<br><br><div class="gmail_quote">On Tue, Jul 3, 2012 at 11:09 AM, Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Geoffrey,<br>
<br>
Yeah, seems weird. But without knowing more about how you are<br>
launching your script or what it does, I think we might be out of<br>
ideas. If you hear back and it's definitely funny business with<br>
yt/Python/etc, write back and let us know.<br>
<br>
-Matt<br>
<div class="HOEnZb"><div class="h5"><br>
On Tue, Jul 3, 2012 at 2:05 PM, Geoffrey So <<a href="mailto:gsiisg@gmail.com">gsiisg@gmail.com</a>> wrote:<br>
> I've verified that there's nothing wrong with the HDF5 files themselves,<br>
> because I can restart the script at the DD of failure and it would continue<br>
> without problem, until it dies again with similar error. I've encountered<br>
> corrupted files before, and it would be just the same error, except I cannot<br>
> restart because it fails at the same spot again every time, this isn't one<br>
> of those times though.<br>
><br>
> From<br>
> G.S.<br>
><br>
><br>
> On Tue, Jul 3, 2012 at 10:32 AM, Britton Smith <<a href="mailto:brittonsmith@gmail.com">brittonsmith@gmail.com</a>><br>
> wrote:<br>
>><br>
>> Hi Geoffrey,<br>
>><br>
>> This could also be due simply to a single corrupt hdf5 file. I have seen<br>
>> these errors before where a file did not get fully written. You might want<br>
>> to verify that all of the files associated with that dataset are readable.<br>
>><br>
>> Britton<br>
>><br>
>><br>
>> On Tue, Jul 3, 2012 at 1:28 PM, Geoffrey So <<a href="mailto:gsiisg@gmail.com">gsiisg@gmail.com</a>> wrote:<br>
>>><br>
>>> Already submitted the ticket yesterday just haven't heard back.<br>
>>> Yeah I didn't think it was OOM, just wanted to confirm it with the<br>
>>> experts, thanks!<br>
>>><br>
>>> From<br>
>>> G.S.<br>
>>><br>
>>> On Tue, Jul 3, 2012 at 3:22 AM, Matthew Turk <<a href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>><br>
>>> wrote:<br>
>>>><br>
>>>> Hi Geoffrey,<br>
>>>><br>
>>>> If you're using a script that iterates with an individual python<br>
>>>> instance (i.e., calling "python my_script.py") for each data dump,<br>
>>>> then I don't think it's an OOM unless somehow multiple instances are<br>
>>>> running simultaneously.<br>
>>>><br>
>>>> I'm not sure what to suggest other than talking to the help desk at<br>
>>>> the particular supercomputer center.<br>
>>>><br>
>>>> -Matt<br>
>>>><br>
>>>> On Tue, Jul 3, 2012 at 5:32 AM, Geoffrey So <<a href="mailto:gsiisg@gmail.com">gsiisg@gmail.com</a>> wrote:<br>
>>>> > I am trying to make projections and slices in the same script and an<br>
>>>> > iterating over several DD datasets, but after a while I get this error<br>
>>>> > pasted below, it seems that there's some hdf5 error where h5py cannot<br>
>>>> > open a<br>
>>>> > file. I've made sure the file exists and the script continues to run<br>
>>>> > if I<br>
>>>> > change the DD#### to continue where it failed. I've already modified<br>
>>>> > the<br>
>>>> > script so that each DD is using a new python instace intead of<br>
>>>> > iterating<br>
>>>> > through the files with one python call. I tried this in queue and<br>
>>>> > interactive and get the same error, sometimes after many DD, but<br>
>>>> > sometimes<br>
>>>> > after only 1 or 2. Is this indicative of memory issue? If it is,<br>
>>>> > I'm not<br>
>>>> > getting the OOM messages even in interactive node. Has anyone<br>
>>>> > encountered<br>
>>>> > this before? I've stuck in import gc at the top and gc.collect() at<br>
>>>> > the end<br>
>>>> > of the script, too, but doesn't help.<br>
>>>> ><br>
>>>> > From<br>
>>>> > G.S.<br>
>>>> ><br>
>>>> > Traceback (most recent call last):<br>
>>>> > File "moviesGrey.py", line 35, in <module><br>
>>>> > proj = pf.h.proj(0, field, weight_field=field)<br>
>>>> > File<br>
>>>> ><br>
>>>> > "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",<br>
>>>> > line 2001, in __init__<br>
>>>> > if self._okay_to_serialize and self.serialize:<br>
>>>> > self._serialize(node_name=self._node_name)<br>
>>>> > File<br>
>>>> ><br>
>>>> > "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",<br>
>>>> > line 970, in _serialize<br>
>>>> > self._store_fields(self._key_fields, node_name, force)<br>
>>>> > File<br>
>>>> ><br>
>>>> > "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_objects/data_containers.py",<br>
>>>> > line 947, in _store_fields<br>
>>>> > passthrough = True)<br>
>>>> > File<br>
>>>> ><br>
>>>> > "/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",<br>
>>>> > line 241, in in_order<br>
>>>> > f2(*args, **kwargs)<br>
>>>> > File<br>
>>>> ><br>
>>>> > "/home/ux455076/dev-yt/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_objects/hierarchy.py",<br>
>>>> > line 278, in _reload_data_file<br>
>>>> > self._data_file = h5py.File(self.__data_filename, self._data_mode)<br>
>>>> > File<br>
>>>> > "/home/ux455076/dev-yt/lib/python2.7/site-packages/h5py/_hl/files.py",<br>
>>>> > line<br>
>>>> > 150, in __init__<br>
>>>> > fid = make_fid(name, mode, fapl)<br>
>>>> > File<br>
>>>> > "/home/ux455076/dev-yt/lib/python2.7/site-packages/h5py/_hl/files.py",<br>
>>>> > line<br>
>>>> > 45, in make_fid<br>
>>>> > fid = h5f.open(name, h5f.ACC_RDONLY, fapl=plist)<br>
>>>> > File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1618)<br>
>>>> > IOError: unable to open file (File accessability: Unable to open file)<br>
>>>> > Exception AttributeError: "'EnzoHierarchy' object has no attribute<br>
>>>> > '_data_file'" in <bound method EnzoHierarchy.__del__ of<br>
>>>> > <yt.frontends.enzo.data_structures.EnzoHierarchy object at 0x32a4d10>><br>
>>>> > ignored<br>
>>>> ><br>
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</div></div></blockquote></div><br></div>