Hi Geoffrey,<br><br>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.<br>
<br>Britton<br><br><div class="gmail_quote">On Tue, Jul 3, 2012 at 1:28 PM, Geoffrey So <span dir="ltr"><<a href="mailto:gsiisg@gmail.com" target="_blank">gsiisg@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>Already submitted the ticket yesterday just haven't heard back.</div><div>Yeah I didn't think it was OOM, just wanted to confirm it with the experts, thanks!</div><div> </div><div>From</div><span class="HOEnZb"><font color="#888888"><div>
G.S.<br><br></div></font></span><div class="HOEnZb"><div class="h5">
<div class="gmail_quote">On Tue, Jul 3, 2012 at 3:22 AM, Matthew Turk <span dir="ltr"><<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>></span> wrote:<br><blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
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>
<div><div><br>
On Tue, Jul 3, 2012 at 5:32 AM, Geoffrey So <<a href="mailto:gsiisg@gmail.com" target="_blank">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 open a<br>
> file. I've made sure the file exists and the script continues to run if I<br>
> change the DD#### to continue where it failed. I've already modified the<br>
> script so that each DD is using a new python instace intead of 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 sometimes<br>
> after only 1 or 2. Is this indicative of memory issue? If it is, I'm not<br>
> getting the OOM messages even in interactive node. Has anyone encountered<br>
> this before? I've stuck in import gc at the top and gc.collect() at 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>
> "/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>
> "/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>
> "/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>
> "/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>
> "/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", 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", 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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