[yt-users] IOError in h5py

[Patrick Rieser]

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 <mailto: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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