[yt-users] IOError in h5py
Matthew Turk
matthewturk at gmail.com
Mon Jan 7 08:42:21 PST 2013
Hi Patrick,
On Mon, Jan 7, 2013 at 11:38 AM, Patrick Rieser
<patrick.rieser at uibk.ac.at> wrote:
> Thanks a lot, it seems to be working now!
Awesome, I'm glad to hear it!
>
> By the way, I did only change the fields.py in frontends/flash to include
> some more stuff.
If you think these are of general use, please feel free to submit a
pull request. The "yt bootstrap_dev" command will get you bitbucket
and hg usernames. You can then do this by forking on BitBucket:
https://bitbucket.org/yt_analysis/yt/fork
then pushing to your new repository:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg
hg commit
hg push https://bitbucket.org/your_username/yt
and issuing a pull request:
https://bitbucket.org/your_username/yt/pull-request/new
But if you'd rather not, of course that's okay too. :)
Best,
Matt
>
>
> Best wishes,
> Patrick
>
>
> Am 2013-01-07 17:19, schrieb Matthew Turk:
>
>> Hi Patrick,
>>
>> Ah, interesting -- this is before the fix to the GDF frontend. A
>> couple things -- it looks like you've made some changes to the source
>> code (the + at the end of the hash indicates this.) If this isn't a
>> big deal, or you don't need those changes, I'd recommend you update to
>> the latest version manually:
>>
>> cd /home/patrick/Programme/yt-x86_64/src/yt-hg
>> hg pull
>> hg up -C
>> python2.7 setup.py build_ext -i
>>
>> If you want to retain those changes, you can be a bit safer about it:
>>
>> cd /home/patrick/Programme/yt-x86_64/src/yt-hg
>> hg diff > backup.patch
>> hg pull
>> hg up
>> python2.7 setup.py build_ext -i
>>
>> This will prompt you to merge your changes into the tip of the
>> development repository. If the merge fails, you can use the contents
>> of "backup.patch" to restore your changes later.
>>
>> Can you try updating and see if that fixes the issue?
>>
>> -Matt
>>
>> On Mon, Jan 7, 2013 at 11:16 AM, Patrick Rieser
>> <patrick.rieser at uibk.ac.at> wrote:
>>>
>>> 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
>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
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