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

[Nathan Goldbaum]

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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