<div dir="ltr"><div>NCL has been pretty robust when handling HDF5 files.</div><div>-------------------------------<br></div><div>Maybe examine the file via h5dump which, I think, is distributed with the HDF5 libraries.<br></div><div><br></div><div><a href="https://www.systutorials.com/docs/linux/man/1-h5dump/"><b>https://www.systutorials.com/docs/linux/man/1-h5dump/</b></a></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 7, 2021 at 8:37 AM Rick Brownrigg via ncl-talk <<a href="mailto:ncl-talk@mailman.ucar.edu">ncl-talk@mailman.ucar.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi,</div><div><br></div><div>I can see from the stack trace that the SEGV occurs in NCL code, shortly aftering being called from the HDF5 library. The NCL function was evidently handed a bogus address (but something that was not NULL). What I can't tell is if there's a bug in NCL, or a bug in the HDF% library, or possibly a corrupt HDF5 file.</div><div><br></div><div>Are you seeing this behavior regularly, or with a specific file(s)? Are the HDF5 files from the same data product? I was unable to duplicate the behavior with the HDF5 file you sent with your original posting. <br></div><div><br></div><div>I'm not sure what to advise at this point.</div><div><br></div><div>Rick<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Sep 5, 2021 at 2:44 AM Geeta Geeta <<a href="mailto:geetag54@yahoo.com" target="_blank">geetag54@yahoo.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:Helvetica Neue,Helvetica,Arial,sans-serif;font-size:13px"><div><div dir="ltr"><div dir="ltr"><div dir="ltr">sir, extremely sorry for sending the info without activating the environment. I am sending the output once again. <br></div><div dir="ltr"><br></div><div dir="ltr">(base) geeta@geetax230:~/restore/geeta/HEM_IMSRA_DATA$ conda activate ncl_stable</div>(ncl_stable) geeta@geetax230:~/restore/geeta/HEM_IMSRA_DATA$ gdb ncl core<br>GNU gdb (Ubuntu 9.2-0ubuntu1~20.04) 9.2<br>Copyright (C) 2020 Free Software Foundation, Inc.<br>License GPLv3+: GNU GPL version 3 or later <<a href="http://gnu.org/licenses/gpl.html" target="_blank">http://gnu.org/licenses/gpl.html</a>><br>This is free software: you are free to change and redistribute it.<br>There is NO WARRANTY, to the extent permitted by law.<br>Type "show copying" and "show warranty" for details.<br>This GDB was configured as "x86_64-linux-gnu".<br>Type "show configuration" for configuration details.<br>For bug reporting instructions, please see:<br><<a href="http://www.gnu.org/software/gdb/bugs/" target="_blank">http://www.gnu.org/software/gdb/bugs/</a>>.<br>Find the GDB manual and other documentation resources online at:<br> <<a href="http://www.gnu.org/software/gdb/documentation/" target="_blank">http://www.gnu.org/software/gdb/documentation/</a>>.<br><br>For help, type "help".<br>Type "apropos word" to search for commands related to "word"...<br>Reading symbols from ncl...<br>[New LWP 34114]<br>[New LWP 34116]<br>[New LWP 34117]<br>[New LWP 34115]<br>[Thread debugging using libthread_db enabled]<br>Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".<br>Core was generated by `ncl -x hem_rgrid.ncl'.<br>Program terminated with signal SIGSEGV, Segmentation fault.<br>#0 0x000055e2de11ac45 in NrmStringToQuark ()<br>[Current thread is 1 (Thread 0x7f72d8aaab40 (LWP 34114))]<br>(gdb) bt<br>#0 0x000055e2de11ac45 in NrmStringToQuark ()<br>#1 0x000055e2dde5315f in _addH5address ()<br>#2 0x000055e2dde5851a in _searchH5byName ()<br>#3 0x00007f72e206b38e in H5G_visit_cb () from /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103<br>#4 0x00007f72e2072ddd in H5G__node_iterate () from /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103<br>#5 0x00007f72e1fa2a17 in H5B__iterate_helper () from /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103<br>#6 0x00007f72e1fa3f98 in H5B_iterate () from /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103<br>#7 0x00007f72e207906d in H5G__stab_iterate () from /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103<br>#8 0x00007f72e2075aac in H5G__obj_iterate () from /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103<br>#9 0x00007f72e206cf95 in H5G_visit () from /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103<br>#10 0x00007f72e20a76bf in H5Lvisit_by_name () from /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103<br>#11 0x000055e2dde5a966 in H5OpenFile ()<br>#12 0x000055e2dddf0a86 in _NclAdvancedFileCreate ()<br>#13 0x000055e2dddd47a5 in _NclOpenFile ()<br>#14 0x000055e2ddecc936 in _NclIAddFile ()<br>#15 0x000055e2ddea4da5 in CallINTRINSIC_FUNC_CALL ()<br>#16 0x000055e2ddeaf37d in _NclExecute ()<br>#17 0x000055e2ddd835fb in yyparse ()<br>#18 0x000055e2ddd78020 in NclDriver ()<br>#19 0x00007f72df8740b3 in __libc_start_main (main=0x55e2ddd746d0 <main>, argc=3, argv=0x7ffc63c11c08, init=<optimized out>, <br> fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7ffc63c11bf8) at ../csu/libc-start.c:308<br>#20 0x000055e2ddd74701 in _start ()<br>(gdb) <br><br><br></div><div><br></div></div><div><br></div><div>Geeta.</div></div>
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On Monday, 30 August, 2021, 09:41:00 pm IST, Geeta Geeta <<a href="mailto:geetag54@yahoo.com" target="_blank">geetag54@yahoo.com</a>> wrote:
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<div><div id="gmail-m_-2190494404464614471gmail-m_277708533336914142yiv1968575678"><div><div style="font-family:Helvetica Neue,Helvetica,Arial,sans-serif;font-size:13px"><div id="gmail-m_-2190494404464614471gmail-m_277708533336914142yiv1968575678ydp28c1a638yiv4253755034"><div dir="ltr">
<br clear="none"><div dir="ltr">sir, while using addfile, it gives core dump. I am attaching the code for your reference. <br clear="none"></div><div dir="ltr">I deleted all lines and was trying to read the data. at present it contains one line with addfile. <br clear="none"></div><div dir="ltr"><br clear="none"></div><div dir="ltr">thanks<br clear="none"></div><br clear="none"><a rel="nofollow noopener noreferrer" shape="rect" href="https://overview.mail.yahoo.com/?.src=iOS" target="_blank">Sent from Yahoo Mail for iPhone</a><br clear="none"><br clear="none">
</div></div></div><div id="gmail-m_-2190494404464614471gmail-m_277708533336914142yiv1968575678yqt45779"><div id="gmail-m_-2190494404464614471gmail-m_277708533336914142yiv1968575678yqt22425"><p style="font-size:15px;color:rgb(113,95,250);padding-top:15px;margin-top:0px">On Saturday, August 28, 2021, 10:44 PM, Rick Brownrigg <<a href="mailto:brownrig@ucar.edu" target="_blank">brownrig@ucar.edu</a>> wrote:</p><blockquote><div id="gmail-m_-2190494404464614471gmail-m_277708533336914142yiv1968575678"><div><div dir="ltr"><div>HI,</div><div><br clear="none"></div><div>I was able to open that file just fine, on a Mac, using 6.6.2. Do you know if you're getting the core dump when you try to open the file (addfile())? Or trying to access a particular variable?</div><div><br clear="none"></div><div>The core file can be used with gdb to look at what was happening at the time of the SEGV:</div><div><br clear="none"></div><div> gdb ncl core</div><div> gdb> bt # should print the stack at the time of crash</div><div><br clear="none"></div><div>That said, I don't know that it will help you much without access to the source code. I'd be curious however where the failure is occurring.</div><div><br clear="none"></div><div>Rick</div><div><br clear="none"></div></div><br clear="none"><div><div id="gmail-m_-2190494404464614471gmail-m_277708533336914142yiv1968575678yqt99338"><div dir="ltr">On Sat, Aug 28, 2021 at 8:00 AM Geeta Geeta via ncl-talk <<a rel="nofollow noopener noreferrer" shape="rect" href="mailto:ncl-talk@mailman.ucar.edu" target="_blank">ncl-talk@mailman.ucar.edu</a>> wrote:<br clear="none"></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:Helvetica Neue,Helvetica,Arial,sans-serif;font-size:13px"><div><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear sir. <br clear="none"></div><div dir="ltr">I am using ncl version 6.6.2 in the CONDA enviornment. <br clear="none"></div><div dir="ltr">I am unable to use the command of ncl like ncl_filedump, addfile etc in this enviornment as I am getting core dump. esp when I run it on my h5 data files. <br clear="none"></div><div dir="ltr">I have already uploaded the h5 file (data file) on the ftp server. <br clear="none"></div><div dir="ltr"><br clear="none"></div><div dir="ltr">Copyright (C) 1995-2019 - All Rights Reserved</div> University Corporation for Atmospheric Research<br clear="none"> NCAR Command Language Version 6.6.2<br clear="none"><br clear="none"></div><div dir="ltr"><div dir="ltr"><div>ncl_filedump 3DIMG_01AUG2020_0300_L1B_STD.h5</div> Copyright (C) 1995-2019 - All Rights Reserved<br clear="none"> University Corporation for Atmospheric Research<br clear="none"> NCAR Command Language Version 6.6.2<br clear="none"> The use of this software is governed by a License Agreement.<br clear="none"> See <a rel="nofollow noopener noreferrer" shape="rect" href="http://www.ncl.ucar.edu/" target="_blank">http://www.ncl.ucar.edu/</a> for more details.<br clear="none">Segmentation fault (core dumped)<br clear="none"><div dir="ltr"><br clear="none"></div><div dir="ltr">I donot know how to debug the generated "core file" to know what is wrong. <br clear="none"></div><div dir="ltr"><br clear="none"></div><div dir="ltr">Request you to help me. <br clear="none"></div></div><div><br clear="none"></div></div></div><div><br clear="none"></div><div>Geeta.</div></div></div></div>_______________________________________________<br clear="none">
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