[Octave-bug-tracker] [bug #64999] [octave forge] (netcff) Octave segfaults on exit after running test_netcdf

[Rafael Laboissière]

URL:
  <https://savannah.gnu.org/bugs/?64999>

                 Summary: [octave forge] (netcff) Octave segfaults on exit
after running test_netcdf
                   Group: GNU Octave
               Submitter: rlaboiss
               Submitted: Fri 08 Dec 2023 08:19:50 AM UTC
                Category: Octave Forge Package
                Severity: 3 - Normal
                Priority: 5 - Normal
              Item Group: Segfault, Bus Error, etc.
                  Status: None
             Assigned to: None
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: other
         Discussion Lock: Any
        Operating System: GNU/Linux
           Fixed Release: None
         Planned Release: None


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Follow-up Comments:


-------------------------------------------------------
Date: Fri 08 Dec 2023 08:19:50 AM UTC By: Rafael Laboissière <rlaboiss>
I am experiencing segmentation faults when using the netcdf package.

I am using:

* Octave 8.4.0
* netcdf package 1.0.17
* libnetcdf 4.9.2
* g++ 13.2.0

This is what happens for me:


$ octave-cli --silent
octave:1> pkg load netcdf
octave:2> test_netcdf
Using NetCDF library version "4.9.2 of Sep  4 2023 05:51:05 $"
run test_netcdf_constant..............   OK  
run test_netcdf_create................   OK  
run test_netcdf_low_level_interface...   OK  
run test_netcdf_unlim................. warning: variable size 0 or currently
too large to process
warning: called from
    getVar at line 31 column 28
    test_netcdf_unlim at line 30 column 3
    test_netcdf at line 50 column 7

  OK  
run test_netcdf_datatypes.............   OK  
run test_netcdf_scalar_variable.......   OK  
run test_netcdf_attributes............   OK  
run test_netcdf_high_level_interface..   OK  
run test_netcdf_ncwriteschema.........   OK  
run test_netcdf_ncwriteschema_unlim...   OK  
run test_netcdf_ncwriteschema_chunking   OK  
run test_netcdf_ncwriteschema_group...   OK  
run test_netcdf_user_types............   OK  
run bug_47014.........................   OK  
octave:3> exit
fatal: caught signal Segmentation fault -- stopping myself...
Segmentation fault


The same thing happens when feeding the commands through a pipe:


$ echo 'pkg load netcdf; test_netcdf' | octave-cli --silent
Using NetCDF library version "4.9.2 of Sep  4 2023 05:51:05 $"
run test_netcdf_constant..............   OK  
run test_netcdf_create................   OK  
run test_netcdf_low_level_interface...   OK  
run test_netcdf_unlim................. warning: variable size 0 or currently
too large to process
warning: called from
    getVar at line 31 column 28
    test_netcdf_unlim at line 30 column 3
    test_netcdf at line 50 column 7

  OK  
run test_netcdf_datatypes.............   OK  
run test_netcdf_scalar_variable.......   OK  
run test_netcdf_attributes............   OK  
run test_netcdf_high_level_interface..   OK  
run test_netcdf_ncwriteschema.........   OK  
run test_netcdf_ncwriteschema_unlim...   OK  
run test_netcdf_ncwriteschema_chunking   OK  
run test_netcdf_ncwriteschema_group...   OK  
run test_netcdf_user_types............   OK  
run bug_47014.........................   OK  
fatal: caught signal Segmentation fault -- stopping myself...
Segmentation fault


Here is the backtrace in gdb:


$ gdb octave-cli
(gdb) run < tmp
Starting program: /usr/bin/octave-cli < tmp
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New Thread 0x7fffed5ff6c0 (LWP 2322115)]
[New Thread 0x7fffe49ff6c0 (LWP 2322116)]
Using NetCDF library version "4.9.2 of Sep  4 2023 05:51:05 $"
run test_netcdf_constant..............   OK  
run test_netcdf_create................   OK  
run test_netcdf_low_level_interface...   OK  
run test_netcdf_unlim................. warning: variable size 0 or currently
too large to process
warning: called from
    getVar at line 31 column 28
    test_netcdf_unlim at line 30 column 3
    test_netcdf at line 50 column 7

  OK  
run test_netcdf_datatypes.............   OK  
run test_netcdf_scalar_variable.......   OK  
run test_netcdf_attributes............   OK  
run test_netcdf_high_level_interface..   OK  
run test_netcdf_ncwriteschema.........   OK  
run test_netcdf_ncwriteschema_unlim...   OK  
run test_netcdf_ncwriteschema_chunking   OK  
run test_netcdf_ncwriteschema_group...   OK  
run test_netcdf_user_types............   OK  
run bug_47014.........................   OK  

Thread 1 "octave-cli" received signal SIGSEGV, Segmentation fault.
0x00007fffe3ff3ea0 in ?? ()
(gdb) bt
#0  0x00007fffe3ff3ea0 in ?? ()
#1  0x00007ffff551279c in ?? () from
/lib/x86_64-linux-gnu/libhdf5_serial.so.103
#2  0x00007ffff55761a5 in H5I_clear_type () from
/lib/x86_64-linux-gnu/libhdf5_serial.so.103
#3  0x00007ffff55128ce in H5FD_term_package () from
/lib/x86_64-linux-gnu/libhdf5_serial.so.103
#4  0x00007ffff544d1cc in H5_term_library () from
/lib/x86_64-linux-gnu/libhdf5_serial.so.103
#5  0x00007ffff544e5c1 in H5close () from
/lib/x86_64-linux-gnu/libhdf5_serial.so.103
#6  0x00007ffff79c7ffd in octave::load_save_system::~load_save_system() ()
from /usr/lib/x86_64-linux-gnu/octave/8.4.0/liboctinterp.so.11
#7  0x00007ffff79a05e6 in octave::interpreter::~interpreter() () from
/usr/lib/x86_64-linux-gnu/octave/8.4.0/liboctinterp.so.11
#8  0x00007ffff70b4abf in octave::application::~application() () from
/usr/lib/x86_64-linux-gnu/octave/8.4.0/liboctinterp.so.11
#9  0x00005555555563cb in ?? ()
#10 0x00007ffff58456ca in __libc_start_call_main
(main=main@entry=0x5555555561b0, argc=argc@entry=1,
argv=argv@entry=0x7fffffffde58) at ../sysdeps/nptl/libc_start_call_main.h:58
#11 0x00007ffff5845785 in __libc_start_main_impl (main=0x5555555561b0, argc=1,
argv=0x7fffffffde58, init=<optimized out>, fini=<optimized out>,
rtld_fini=<optimized out>, stack_end=0x7fffffffde48)
    at ../csu/libc-start.c:360
#12 0x00005555555564e1 in ?? ()
-verbatin-







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