[yt-users] IOError in h5py

[Matthew Turk]

Hi Patrick,

This could also be related to a critical bug fix identified not too
long ago.  One tricky thing about HDF5 is that once in a while
depending on the order of operations, errors can accumulate without
being flushed.  What may have happened is that the file was left open
at a different juncture and then never closed; this could result in a
non-intuitive error message.  What we identified  was that the
GridDataFormat frontend was in fact leaving the files open, which then
left the handle around and caused non-intuitive errors later on during
the process.  Could you send the output of:

yt instinfo

This will help us determine how the error is occurring.

Best,

Matt

On Mon, Jan 7, 2013 at 11:02 AM, Patrick Rieser
<patrick.rieser at uibk.ac.at> wrote:
> In iyt I can load a snapshot just fine.
>
> It could be a problem using the Sun Grid Engine then. Here is my python
> submit script if you need it (it sources the yt environment, does some
> things on the data set and then submits a yt job for a subset):
> http://paste.yt-project.org/show/3045/
>
>
> h5ls output seems ok:
> bflags                   Dataset {2633, 1}
> block\ size              Dataset {2633, 3}
> bounding\ box            Dataset {2633, 3, 2}
> coordinates              Dataset {2633, 3}
> dens                     Dataset {2633, 16, 16, 16}
> gid                      Dataset {2633, 15}
> integer\ runtime\ parameters Dataset {46}
> integer\ scalars         Dataset {14}
> logical\ runtime\ parameters Dataset {53}
> logical\ scalars         Dataset {2}
> magp                     Dataset {2633, 16, 16, 16}
> magx                     Dataset {2633, 16, 16, 16}
> magy                     Dataset {2633, 16, 16, 16}
> magz                     Dataset {2633, 16, 16, 16}
> node\ type               Dataset {2633}
> pden                     Dataset {2633, 16, 16, 16}
> pres                     Dataset {2633, 16, 16, 16}
> processor\ number        Dataset {2633}
> real\ runtime\ parameters Dataset {76}
> real\ scalars            Dataset {15}
> refine\ level            Dataset {2633}
> sim\ info                Dataset {1}
> string\ runtime\ parameters Dataset {78}
> string\ scalars          Dataset {1}
> temp                     Dataset {2633, 16, 16, 16}
> unknown\ names           Dataset {11, 1}
> velx                     Dataset {2633, 16, 16, 16}
> vely                     Dataset {2633, 16, 16, 16}
> velz                     Dataset {2633, 16, 16, 16}
> which\ child             Dataset {2633}
>
>
> Could the problem be caused by a defunct snapshot that got mixed in?
>
>
> Best wishes,
> Patrick
>
>
> Am 2013-01-07 16:54, schrieb j s oishi:
>
> Hi Patrick,
>
> What happens if you do
>
> $ h5ls <filename>
>
> where <filename> is the file you're trying to open? This looks like it could
> be an error outside of yt.
>
> Also, can you load() any other snapshots?
>
> Jeff
>
>
> On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser at uibk.ac.at>
> wrote:
>>
>> I stumbled over some error in yt while executing a script that used to
>> work on an older version of yt. Here is the traceback:
>>
>>   File "start_SGE.py", line 28, in <module>
>>   File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58,
>> in get_snapshots
>>   File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43,
>> in get_redshift
>>   File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py",
>> line 71, in load
>>   File
>> "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py",
>> line 218, in __init__
>>   File
>> "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py",
>> line 165, in __init__
>>   File
>> "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py",
>> line 57, in make_fid
>>   File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626)
>> IOError: unable to open file (File accessability: Unable to open file)
>> Exception AttributeError: "'NoneType' object has no attribute 'close'" in
>> ignored
>>
>>
>> I'd be very thankful if somebody got any idea how to fix this!
>>
>> Best wishes,
>> Patrick
>>
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>
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