[ncl-talk] Uasage of NCL-version 6.6

Tue Sep 7 13:30:42 MDT 2021

NCL has been pretty robust when handling HDF5 files.
-------------------------------
Maybe examine the file via h5dump which, I think, is distributed with the
HDF5 libraries.

*https://www.systutorials.com/docs/linux/man/1-h5dump/*
<https://www.systutorials.com/docs/linux/man/1-h5dump/>

On Tue, Sep 7, 2021 at 8:37 AM Rick Brownrigg via ncl-talk <
ncl-talk at mailman.ucar.edu> wrote:

> 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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