[ncl-talk] Uasage of NCL-version 6.6

Tue Sep 7 08:36:59 MDT 2021

Hi,

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.

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.

I'm not sure what to advise at this point.

Rick

On Sun, Sep 5, 2021 at 2:44 AM Geeta Geeta <geetag54 at yahoo.com> wrote:

> sir, extremely sorry for sending the info without activating the
> environment.  I am sending the output once again.
>
> (base) geeta at geetax230:~/restore/geeta/HEM_IMSRA_DATA$ conda activate
> ncl_stable
> (ncl_stable) geeta at geetax230:~/restore/geeta/HEM_IMSRA_DATA$ gdb ncl core
> GNU gdb (Ubuntu 9.2-0ubuntu1~20.04) 9.2
> Copyright (C) 2020 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <
> http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.
> Type "show copying" and "show warranty" for details.
> This GDB was configured as "x86_64-linux-gnu".
> Type "show configuration" for configuration details.
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>.
> Find the GDB manual and other documentation resources online at:
>     <http://www.gnu.org/software/gdb/documentation/>.
>
> For help, type "help".
> Type "apropos word" to search for commands related to "word"...
> Reading symbols from ncl...
> [New LWP 34114]
> [New LWP 34116]
> [New LWP 34117]
> [New LWP 34115]
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
> Core was generated by `ncl -x hem_rgrid.ncl'.
> Program terminated with signal SIGSEGV, Segmentation fault.
> #0  0x000055e2de11ac45 in NrmStringToQuark ()
> [Current thread is 1 (Thread 0x7f72d8aaab40 (LWP 34114))]
> (gdb) bt
> #0  0x000055e2de11ac45 in NrmStringToQuark ()
> #1  0x000055e2dde5315f in _addH5address ()
> #2  0x000055e2dde5851a in _searchH5byName ()
> #3  0x00007f72e206b38e in H5G_visit_cb () from
> /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103
> #4  0x00007f72e2072ddd in H5G__node_iterate () from
> /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103
> #5  0x00007f72e1fa2a17 in H5B__iterate_helper () from
> /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103
> #6  0x00007f72e1fa3f98 in H5B_iterate () from
> /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103
> #7  0x00007f72e207906d in H5G__stab_iterate () from
> /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103
> #8  0x00007f72e2075aac in H5G__obj_iterate () from
> /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103
> #9  0x00007f72e206cf95 in H5G_visit () from
> /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103
> #10 0x00007f72e20a76bf in H5Lvisit_by_name () from
> /home/geeta/anaconda3/envs/ncl_stable/bin/../lib/libhdf5.so.103
> #11 0x000055e2dde5a966 in H5OpenFile ()
> #12 0x000055e2dddf0a86 in _NclAdvancedFileCreate ()
> #13 0x000055e2dddd47a5 in _NclOpenFile ()
> #14 0x000055e2ddecc936 in _NclIAddFile ()
> #15 0x000055e2ddea4da5 in CallINTRINSIC_FUNC_CALL ()
> #16 0x000055e2ddeaf37d in _NclExecute ()
> #17 0x000055e2ddd835fb in yyparse ()
> #18 0x000055e2ddd78020 in NclDriver ()
> #19 0x00007f72df8740b3 in __libc_start_main (main=0x55e2ddd746d0 <main>,
> argc=3, argv=0x7ffc63c11c08, init=<optimized out>,
>     fini=<optimized out>, rtld_fini=<optimized out>,
> stack_end=0x7ffc63c11bf8) at ../csu/libc-start.c:308
> #20 0x000055e2ddd74701 in _start ()
> (gdb)
>
>
>
>
> Geeta.
>
>
> On Monday, 30 August, 2021, 09:41:00 pm IST, Geeta Geeta <
> geetag54 at yahoo.com> wrote:
>
>
>
> sir, while using addfile, it gives core dump. I am attaching the code for
> your reference.
> I deleted all lines and was trying to read the data. at present it
> contains one line with addfile.
>
> thanks
>
> Sent from Yahoo Mail for iPhone
> <https://overview.mail.yahoo.com/?.src=iOS>
>
> On Saturday, August 28, 2021, 10:44 PM, Rick Brownrigg <brownrig at ucar.edu>
> wrote:
>
> HI,
>
> 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?
>
> The core file can be used with gdb to look at what was happening at the
> time of the SEGV:
>
>      gdb ncl core
>      gdb>  bt       # should print the stack at the time of crash
>
> 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.
>
> Rick
>
>
> On Sat, Aug 28, 2021 at 8:00 AM Geeta Geeta via ncl-talk <
> ncl-talk at mailman.ucar.edu> wrote:
>
> Dear sir.
> I am using ncl version 6.6.2 in the CONDA enviornment.
> 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.
> I have already uploaded the h5 file (data file) on the ftp server.
>
> Copyright (C) 1995-2019 - All Rights Reserved
>  University Corporation for Atmospheric Research
>  NCAR Command Language Version 6.6.2
>
> ncl_filedump 3DIMG_01AUG2020_0300_L1B_STD.h5
>  Copyright (C) 1995-2019 - All Rights Reserved
>  University Corporation for Atmospheric Research
>  NCAR Command Language Version 6.6.2
>  The use of this software is governed by a License Agreement.
>  See http://www.ncl.ucar.edu/ for more details.
> Segmentation fault (core dumped)
>
> I donot know how to debug the generated "core file" to know what is wrong.
>
> Request you to help me.
>
>
> Geeta.
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