[yt-users] error while trying to find abundances through checkpoint files

[tazkera haque]

HI Nathan,

Sorry to bother you again, but the problem seems to prevail even working
from $WORK directory. I got the same error msg this morning again with a
different script. Do you see anything wrong with the script I attached ? I
have used it for a long time now without any sort of error.

Thanks

On Tue, Oct 18, 2016 at 2:34 AM, tazkera haque <h.tazkera at gmail.com> wrote:

> HI Nathan,
>
> I figured out what was going wrong, I submitted my job script from the
> $SCRATCH folder. apparently jobs can only be submitted through the $WORK
> folder on Stampede. thanks for your prompt response though
>
> On Tue, Oct 18, 2016 at 1:22 AM, tazkera haque <h.tazkera at gmail.com>
> wrote:
>
>> Hi Nathan,
>>
>> I tried with one file in my ipython notebook, it seems to work there
>>
>> On Tue, Oct 18, 2016 at 12:54 AM, tazkera haque <h.tazkera at gmail.com>
>> wrote:
>>
>>> yes it's being run in parallel, I didn't check with one core yet, I will
>>> let you know what happens then
>>>
>>> On Tue, Oct 18, 2016 at 12:50 AM, Nathan Goldbaum <nathan12343 at gmail.com
>>> > wrote:
>>>
>>>> Is the script being run in parallel? If so, does it crash if you run it
>>>> on only one core?
>>>>
>>>> Nathan
>>>>
>>>>
>>>> On Monday, October 17, 2016, tazkera haque <h.tazkera at gmail.com> wrote:
>>>>
>>>>> HI people,
>>>>>
>>>>> I am using yt 3.3.1 and submitting my SLURM script to stampede.
>>>>> I was using this script to find abundances of C, O etc through
>>>>> checkpoint files in FLASH. while my script worked fine with old yt (3.1) ,
>>>>> suddenly it crashed today and returned me the following error:
>>>>>
>>>>> *yt : [INFO     ] 2016-10-17 23:22:24,295 Parameters: current_time
>>>>>          = 28.1847530806*
>>>>> *yt : [INFO     ] 2016-10-17 23:22:24,295 Parameters:
>>>>> domain_dimensions         = [128 128 128]*
>>>>> *yt : [INFO     ] 2016-10-17 23:22:24,296 Parameters: domain_left_edge
>>>>>          = [ -2.80000000e+10  -2.80000000e+10  -2.80000000e+10]*
>>>>> *yt : [INFO     ] 2016-10-17 23:22:24,296 Parameters:
>>>>> domain_right_edge         = [  2.80000000e+10   2.80000000e+10
>>>>> 2.80000000e+10]*
>>>>> *yt : [INFO     ] 2016-10-17 23:22:24,296 Parameters:
>>>>> cosmological_simulation   = 0.0*
>>>>> *Executin lessg abundance.py*
>>>>> *Traceback (most recent call last):*
>>>>> *  File "abundance2.py", line 304, in <module>*
>>>>> *    main(chkFilenames_own)*
>>>>> *  File "abundance2.py", line 59, in main*
>>>>> *    pf = yt.load(filenames[n])*
>>>>> *  File
>>>>> "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/yt/convenience.py",
>>>>> line 79, in load*
>>>>> *    if c._is_valid(*args, **kwargs): candidates.append(n)*
>>>>> *  File
>>>>> "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/yt/frontends/flash/data_structures.py",
>>>>> line 478, in _is_valid*
>>>>> *    if "bounding box" not in fileh["/"].keys() \*
>>>>> *  File
>>>>> "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/h5py/_hl/base.py",
>>>>> line 368, in keys*
>>>>> *    return list(self)*
>>>>> *  File "h5py/_objects.pyx", line 54, in
>>>>> h5py._objects.with_phil.wrapper
>>>>> (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2696)*
>>>>> *  File "h5py/_objects.pyx", line 55, in
>>>>> h5py._objects.with_phil.wrapper
>>>>> (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2654)*
>>>>> *  File
>>>>> "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/h5py/_hl/group.py",
>>>>> line 303, in __len__*
>>>>> *    return self.id.get_num_objs()*
>>>>> *  File "h5py/_objects.pyx", line 54, in
>>>>> h5py._objects.with_phil.wrapper
>>>>> (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2696)*
>>>>> *  File "h5py/_objects.pyx", line 55, in
>>>>> h5py._objects.with_phil.wrapper
>>>>> (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2654)*
>>>>> *  File "h5py/h5g.pyx", line 321, in h5py.h5g.GroupID.get_num_objs
>>>>> (/home/ilan/minonda/conda-bld/work/h5py/h5g.c:4194)*
>>>>> *RuntimeError: Can't determine (Bad symbol table node signature)*
>>>>> *[c560-102.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI
>>>>> process (rank: 0, pid: 22137) exited with status 1*
>>>>> *TACC: MPI job exited with code: 1*
>>>>>
>>>>> *TACC: Shutdown complete. Exiting.*
>>>>>
>>>>> I was wondering if there is something wrong with my code or the new
>>>>> yt. I am also attaching my code here to look at. Thanks in advance
>>>>>
>>>>> Best
>>>>> Tazkera
>>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>
>>
>
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