[yt-users] IOError in h5py
Patrick Rieser
patrick.rieser at uibk.ac.at
Mon Jan 7 08:38:08 PST 2013
Thanks a lot, it seems to be working now!
By the way, I did only change the fields.py in frontends/flash to
include some more stuff.
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
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
More information about the yt-users
mailing list