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

[tazkera haque]

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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