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

tazkera haque h.tazkera at gmail.com
Tue Oct 18 14:22:09 PDT 2016 

Hi Suoqing,

I ran the code in the interactive mode and it returned me the same error as
it was with submitting the job script. What happens is that It checks
through all the files and instead of producing the output files or images,
it returns me the error.

Best

On Tue, Oct 18, 2016 at 4:48 PM, Suoqing Ji <suoqing at physics.ucsb.edu>
wrote:

> Hi Tazkera,
>
> I have the access to Stampede but I can not reproduce your error either
> (using a slightly different script though).
>
> apparently jobs can only be submitted through the $WORK folder on Stampede
>>>>
>>>
> Btw, I believe you could submit job from both work and scratch directory
> on Stampede.
>
> Could you run your code in interactive mode, by
>
> srun -p normal -t 0:30:00 -n 16 -A _your_project_code_ --pty /bin/bash -l
>
> and then enter
>
> python abundance.py
>
> and see what’s going on?
>
> Best wishes,
> --
> Suoqing JI
> Ph.D Candidate
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing
>
> On Oct 18, 2016, at 1:20 PM, tazkera haque <h.tazkera at gmail.com> wrote:
>
> 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
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> yt-users mailing list
>>>>>>> yt-users at lists.spacepope.org
>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20161018/c4648b6b/attachment.html>

More information about the yt-users mailing list