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

[tazkera haque]

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
>>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
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>>>
>>>
>>
>
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