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

tazkera haque h.tazkera at gmail.com
Mon Oct 17 22:22:27 PDT 2016


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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