<div dir="ltr"><div>I typed </div><div><br></div><div>$ module avail HDF5</div><div><br></div><div>------------------------------------------------- /opt/apps/intel15/mvapich2_2_1/modulefiles --------------------------------------------------</div><div> phdf5/1.8.16</div><div><br></div><div>-------------------------------------------------------- /opt/apps/intel15/modulefiles --------------------------------------------------------</div><div> hdf5/1.8.16 (m,L)</div><div><br></div><div> Where:</div><div> L: Module is loaded</div><div> m: built for host and native MIC</div><div><br></div><div>$ module avail h5py</div><div>returns blank, if that helps</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 18, 2016 at 4:08 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Tazkera,<div><br></div><div>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><br></div><div>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><br></div><div>Can you share exactly which h5py and HDF5 library versions you're using?</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>-Nathan</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 18, 2016 at 3:05 PM, tazkera haque <span dir="ltr"><<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">HI Nathan, <div><br></div><div>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><br></div><div>Thanks</div></div><div class="m_-3081621645219472836HOEnZb"><div class="m_-3081621645219472836h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 18, 2016 at 2:34 AM, tazkera haque <span dir="ltr"><<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">HI Nathan, <div><br></div><div>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><div class="gmail_quote">On Tue, Oct 18, 2016 at 1:22 AM, tazkera haque <span dir="ltr"><<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Nathan, <div><br></div><div>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><div class="gmail_quote">On Tue, Oct 18, 2016 at 12:54 AM, tazkera haque <span dir="ltr"><<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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><div class="gmail_quote"><div><div class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912h5">On Tue, Oct 18, 2016 at 12:50 AM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><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"><span></span></font></span><div><span class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912m_-4374703221355933864HOEnZb"><font color="#888888"><div><br></div></font></span><div><span class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912m_-4374703221355933864HOEnZb"><font color="#888888">Nathan</font></span><div><div class="m_-3081621645219472836m_5274618939355493361m_2549907504023929652m_3485652829179782912m_-4374703221355933864h5"><br><br>On Monday, October 17, 2016, tazkera haque <<a href="mailto:h.tazkera@gmail.com" target="_blank">h.tazkera@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">HI people, <div><br></div><div>I am using yt 3.3.1 and submitting my SLURM script to stampede.</div><div>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><br></div><div><div><b>yt : [INFO ] 2016-10-17 23:22:24,295 Parameters: current_time = 28.1847530806</b></div><div><b>yt : [INFO ] 2016-10-17 23:22:24,295 Parameters: domain_dimensions = [128 128 128]</b></div><div><b>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><b>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><b>yt : [INFO ] 2016-10-17 23:22:24,296 Parameters: cosmological_simulation = 0.0</b></div><div><b>Executin lessg abundance.py</b></div><div><b>Traceback (most recent call last):</b></div><div><b> File "abundance2.py", line 304, in <module></b></div><div><b> main(chkFilenames_own)</b></div><div><b> File "abundance2.py", line 59, in main</b></div><div><b> pf = yt.load(filenames[n])</b></div><div><b> File "/work/03858/thaque56/sw/yt-ne<wbr>w-3.3/yt-conda/lib/python2.7/s<wbr>ite-packages/yt/convenience.py<wbr>", line 79, in load</b></div><div><b> if c._is_valid(*args, **kwargs): candidates.append(n)</b></div><div><b> File "/work/03858/thaque56/sw/yt-ne<wbr>w-3.3/yt-conda/lib/python2.7/s<wbr>ite-packages/yt/frontends/flas<wbr>h/data_structures.py", line 478, in _is_valid</b></div><div><b> if "bounding box" not in fileh["/"].keys() \</b></div><div><b> File "/work/03858/thaque56/sw/yt-ne<wbr>w-3.3/yt-conda/lib/python2.7/s<wbr>ite-packages/h5py/_hl/base.py"<wbr>, line 368, in keys</b></div><div><b> return list(self)</b></div><div><b> File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrappe<wbr>r (/home/ilan/minonda/conda-bld/<wbr>work/h5py/_objects.c:2696)</b></div><div><b> File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrappe<wbr>r (/home/ilan/minonda/conda-bld/<wbr>work/h5py/_objects.c:2654)</b></div><div><b> File "/work/03858/thaque56/sw/yt-ne<wbr>w-3.3/yt-conda/lib/python2.7/s<wbr>ite-packages/h5py/_hl/group.py<wbr>", line 303, in __len__</b></div><div><b> return self.id.get_num_objs()</b></div><div><b> File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrappe<wbr>r (/home/ilan/minonda/conda-bld/<wbr>work/h5py/_objects.c:2696)</b></div><div><b> File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrappe<wbr>r (/home/ilan/minonda/conda-bld/<wbr>work/h5py/_objects.c:2654)</b></div><div><b> File "h5py/h5g.pyx", line 321, in h5py.h5g.GroupID.get_num_objs (/home/ilan/minonda/conda-bld/<wbr>work/h5py/h5g.c:4194)</b></div><div><b>RuntimeError: Can't determine (Bad symbol table node signature)</b></div><div><b>[c560-102.stampede.tacc.utexas<wbr>.edu:mpispawn_0][child_handler<wbr>] MPI process (rank: 0, pid: 22137) exited with status 1</b></div><div><b>TACC: MPI job exited with code: 1</b></div><div><b><br></b></div><div><b>TACC: Shutdown complete. Exiting.</b></div></div><div><br></div><div>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><br></div><div>Best</div><div>Tazkera</div></div>
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