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

tazkera haque h.tazkera at gmail.com
Tue Oct 18 13:20:09 PDT 2016 

I typed

$ module avail HDF5

-------------------------------------------------
/opt/apps/intel15/mvapich2_2_1/modulefiles
--------------------------------------------------
   phdf5/1.8.16

--------------------------------------------------------
/opt/apps/intel15/modulefiles
--------------------------------------------------------
   hdf5/1.8.16 (m,L)

  Where:
   L:  Module is loaded
   m:  built for host and native MIC

$ module avail h5py
returns blank, if that helps


On Tue, Oct 18, 2016 at 4:08 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> Hi Tazkera,
>
> When I tried googling your error message last night, I found that it's
> associated with more than one MPI process trying to access an HDF5 file at
> the same time, presumably using a serial version of the HDF5 library.
>
> I just did a quick test and I'm unable to reproduce here on my laptop.
> Unfortunately I don't have access to stampede so can't reproduce there.
>
> Can you share exactly which h5py and HDF5 library versions you're using?
>
> -Nathan
>
> On Tue, Oct 18, 2016 at 3:05 PM, tazkera haque <h.tazkera at gmail.com>
> wrote:
>
>> HI Nathan,
>>
>> Sorry to bother you again, but the problem seems to prevail even working
>> from $WORK directory. I got the same error msg this morning again with a
>> different script. Do you see anything wrong with the script I attached ? I
>> have used it for a long time now without any sort of error.
>>
>> Thanks
>>
>> On Tue, Oct 18, 2016 at 2:34 AM, tazkera haque <h.tazkera at gmail.com>
>> wrote:
>>
>>> 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
>>>>>>>
>>>>>>
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>>>>>>
>>>>>
>>>>
>>>
>>
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