apparently jobs can only be submitted through the $WORK folder on Stampede
On Oct 18, 2016, at 1:20 PM, tazkera haque <h.tazkera@gmail.com> wrote:I typed$ 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 loadedm: built for host and native MIC$ module avail h5pyreturns blank, if that helps_______________________________________________On Tue, Oct 18, 2016 at 4:08 PM, Nathan Goldbaum <nathan12343@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?-NathanOn Tue, Oct 18, 2016 at 3:05 PM, tazkera haque <h.tazkera@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.ThanksOn Tue, Oct 18, 2016 at 2:34 AM, tazkera haque <h.tazkera@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 thoughOn 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 thereOn 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 thenOn 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 = 28.1847530806yt : [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 = 0.0Executin lessg abundance.pyTraceback (most recent call last):File "abundance2.py", line 304, in <module>main(chkFilenames_own)File "abundance2.py", line 59, in mainpf = yt.load(filenames[n])File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/s ite-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/s ite-packages/yt/frontends/flas h/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/s ite-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/s ite-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: 1TACC: 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 advanceBestTazkera_________________
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