[yt-users] IOError in h5py

[Patrick Rieser]

Here you go:

yt module located at:
     /home/patrick/Programme/yt-x86_64/src/yt-hg
The supplemental repositories are located at:
     /home/patrick/Programme/yt-x86_64/src/yt-supplemental

The current version of the code is:

---
9d5b945ee428+ (yt) tip
---

This installation CAN be automatically updated.
Updated successfully.


Best wishes,
Patrick

Am 2013-01-07 17:04, schrieb 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
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>>
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