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@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@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@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@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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