<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Tazkera,<div class=""><br class=""></div><div class="">I have the access to Stampede but I can not reproduce your error either (using a slightly different script though).</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div class="m_-3081621645219472836HOEnZb"><div class="m_-3081621645219472836h5"><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div dir="ltr" class=""><div class="">apparently jobs can only be submitted through the $WORK folder on Stampede</div></div></blockquote></div></div></div></div></blockquote></div></div></div></div></blockquote></div></div></blockquote></div><div class=""><br class=""></div><div class="">Btw, I believe you could submit job from both work and scratch directory on Stampede.</div><div class=""><br class=""></div><div class="">Could you run your code in interactive mode, by</div><div class=""><br class=""></div><div class="">srun -p normal -t 0:30:00 -n 16 -A _your_project_code_ --pty /bin/bash -l</div><div class=""><br class=""></div><div class="">and then enter</div><div class=""><br class=""></div><div class="">python abundance.py</div><div class=""><br class=""></div><div class="">and see what’s going on?</div><div class=""><br class=""><div class="">
<div class=""><div class="">Best wishes,</div><div class="">--</div><div class="">Suoqing JI</div><div class="">Ph.D Candidate</div><div class="">Department of Physics</div><div class="">University of California, Santa Barbara</div><div class=""><a href="http://web.physics.ucsb.edu/~suoqing" class="">http://web.physics.ucsb.edu/~suoqing</a></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Oct 18, 2016, at 1:20 PM, tazkera haque <<a href="mailto:h.tazkera@gmail.com" class="">h.tazkera@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">I typed </div><div class=""><br class=""></div><div class="">$ module avail HDF5</div><div class=""><br class=""></div><div class="">------------------------------------------------- /opt/apps/intel15/mvapich2_2_1/modulefiles --------------------------------------------------</div><div class=""> phdf5/1.8.16</div><div class=""><br class=""></div><div class="">-------------------------------------------------------- /opt/apps/intel15/modulefiles --------------------------------------------------------</div><div class=""> hdf5/1.8.16 (m,L)</div><div class=""><br class=""></div><div class=""> Where:</div><div class=""> L: Module is loaded</div><div class=""> m: built for host and native MIC</div><div class=""><br class=""></div><div class="">$ module avail h5py</div><div class="">returns blank, if that helps</div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Oct 18, 2016 at 4:08 PM, Nathan Goldbaum <span dir="ltr" class=""><<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi Tazkera,<div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Can you share exactly which h5py and HDF5 library versions you're using?</div><span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">-Nathan</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Oct 18, 2016 at 3:05 PM, tazkera haque <span dir="ltr" class=""><<a href="mailto:h.tazkera@gmail.com" target="_blank" class="">h.tazkera@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">HI Nathan, <div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Thanks</div></div><div class="m_-3081621645219472836HOEnZb"><div class="m_-3081621645219472836h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Oct 18, 2016 at 2:34 AM, tazkera haque <span dir="ltr" class=""><<a href="mailto:h.tazkera@gmail.com" target="_blank" class="">h.tazkera@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">HI Nathan, <div class=""><br class=""></div><div class="">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</div></div><div class="m_-3081621645219472836m_5274618939355493361HOEnZb"><div class="m_-3081621645219472836m_5274618939355493361h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Oct 18, 2016 at 1:22 AM, tazkera haque <span dir="ltr" class=""><<a href="mailto:h.tazkera@gmail.com" target="_blank" class="">h.tazkera@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi Nathan, <div class=""><br class=""></div><div class="">I tried with one file in my ipython notebook, it seems to work there</div></div><div class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652HOEnZb"><div class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Oct 18, 2016 at 12:54 AM, tazkera haque <span dir="ltr" class=""><<a href="mailto:h.tazkera@gmail.com" target="_blank" class="">h.tazkera@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">yes it's being run in parallel, I didn't check with one core yet, I will let you know what happens then</div><div class="gmail_extra"><br class=""><div class="gmail_quote"><div class=""><div class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912h5">On Tue, Oct 18, 2016 at 12:50 AM, Nathan Goldbaum <span dir="ltr" class=""><<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>></span> wrote:<br class=""></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class=""><div class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912h5">Is the script being run in parallel? If so, does it crash if you run it on only one core?<span class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912m_-4374703221355933864HOEnZb"><font color="#888888" class=""><span class=""></span></font></span><div class=""><span class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912m_-4374703221355933864HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div></font></span><div class=""><span class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912m_-4374703221355933864HOEnZb"><font color="#888888" class="">Nathan</font></span><div class=""><div class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912m_-4374703221355933864h5"><br class=""><br class="">On Monday, October 17, 2016, tazkera haque <<a href="mailto:h.tazkera@gmail.com" target="_blank" class="">h.tazkera@gmail.com</a>> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">HI people, <div class=""><br class=""></div><div class="">I am using yt 3.3.1 and submitting my SLURM script to stampede.</div><div class="">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:</div><div class=""><br class=""></div><div class=""><div class=""><b class="">yt : [INFO ] 2016-10-17 23:22:24,295 Parameters: current_time = 28.1847530806</b></div><div class=""><b class="">yt : [INFO ] 2016-10-17 23:22:24,295 Parameters: domain_dimensions = [128 128 128]</b></div><div class=""><b class="">yt : [INFO ] 2016-10-17 23:22:24,296 Parameters: domain_left_edge = [ -2.80000000e+10 -2.80000000e+10 -2.80000000e+10]</b></div><div class=""><b class="">yt : [INFO ] 2016-10-17 23:22:24,296 Parameters: domain_right_edge = [ 2.80000000e+10 2.80000000e+10 2.80000000e+10]</b></div><div class=""><b class="">yt : [INFO ] 2016-10-17 23:22:24,296 Parameters: cosmological_simulation = 0.0</b></div><div class=""><b class="">Executin lessg abundance.py</b></div><div class=""><b class="">Traceback (most recent call last):</b></div><div class=""><b class=""> File "abundance2.py", line 304, in <module></b></div><div class=""><b class=""> main(chkFilenames_own)</b></div><div class=""><b class=""> File "abundance2.py", line 59, in main</b></div><div class=""><b class=""> pf = yt.load(filenames[n])</b></div><div class=""><b class=""> File "/work/03858/thaque56/sw/yt-ne<wbr class="">w-3.3/yt-conda/lib/python2.7/s<wbr class="">ite-packages/yt/convenience.py<wbr class="">", line 79, in load</b></div><div class=""><b class=""> if c._is_valid(*args, **kwargs): candidates.append(n)</b></div><div class=""><b class=""> File "/work/03858/thaque56/sw/yt-ne<wbr class="">w-3.3/yt-conda/lib/python2.7/s<wbr class="">ite-packages/yt/frontends/flas<wbr class="">h/data_structures.py", line 478, in _is_valid</b></div><div class=""><b class=""> if "bounding box" not in fileh["/"].keys() \</b></div><div class=""><b class=""> File "/work/03858/thaque56/sw/yt-ne<wbr class="">w-3.3/yt-conda/lib/python2.7/s<wbr class="">ite-packages/h5py/_hl/base.py"<wbr class="">, line 368, in keys</b></div><div class=""><b class=""> return list(self)</b></div><div class=""><b class=""> File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrappe<wbr class="">r (/home/ilan/minonda/conda-bld/<wbr class="">work/h5py/_objects.c:2696)</b></div><div class=""><b class=""> File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrappe<wbr class="">r (/home/ilan/minonda/conda-bld/<wbr class="">work/h5py/_objects.c:2654)</b></div><div class=""><b class=""> File "/work/03858/thaque56/sw/yt-ne<wbr class="">w-3.3/yt-conda/lib/python2.7/s<wbr class="">ite-packages/h5py/_hl/group.py<wbr class="">", line 303, in __len__</b></div><div class=""><b class=""> return self.id.get_num_objs()</b></div><div class=""><b class=""> File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrappe<wbr class="">r (/home/ilan/minonda/conda-bld/<wbr class="">work/h5py/_objects.c:2696)</b></div><div class=""><b class=""> File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrappe<wbr class="">r (/home/ilan/minonda/conda-bld/<wbr class="">work/h5py/_objects.c:2654)</b></div><div class=""><b class=""> File "h5py/h5g.pyx", line 321, in h5py.h5g.GroupID.get_num_objs (/home/ilan/minonda/conda-bld/<wbr class="">work/h5py/h5g.c:4194)</b></div><div class=""><b class="">RuntimeError: Can't determine (Bad symbol table node signature)</b></div><div class=""><b class="">[c560-102.stampede.tacc.utexas<wbr class="">.edu:mpispawn_0][child_handler<wbr class="">] MPI process (rank: 0, pid: 22137) exited with status 1</b></div><div class=""><b class="">TACC: MPI job exited with code: 1</b></div><div class=""><b class=""><br class=""></b></div><div class=""><b class="">TACC: Shutdown complete. Exiting.</b></div></div><div class=""><br class=""></div><div class="">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</div><div class=""><br class=""></div><div class="">Best</div><div class="">Tazkera</div></div>
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