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

[tazkera haque]

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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