Seg Fault when an incomplete record is in the database

[bschwal]

I imported a csv file into a SOS container without realizing the last line of the csv was truncated such that only a couple of the fields existed. When I try to view the data in the file that matches this record (using sos_cmd or python API) the query seg faults. I would not have expected this record to be imported into the database in the first place.

[tom95858]

@bschwal could you please send me the git commit-id at the top of your source tree?

[bschwal]

My sha's ovis: 66c8c5528ec595b40ea42fea74bd562c43db1e47 sos: 3177b4c7149e0ac4380c89f0c2248717ccac2066

[tom95858]

Thanks, do you have a core dump?

[bschwal]

Just a small dump into /var/log/messages:

systemd-coredump[1904265]: Process 1904134 (python3) of user 0 dumped core.#012#012Stack trace of thread 1904134:#012#0 0x00007f73b15dd210 sos_value_cmp (libsos.so.0)#012#1 0x00007f73b15dac19 eq_fn (libsos.so.0)#012#2 0x00007f73b15dba04 sos_filter_eval (libsos.so.0)#012#3 0x00007f73b15dbb15 next_match (libsos.so.0)#012#4 0x00007f73b1895231 pyx_pf_6python_3Sos_12QueryInputer_12input (Sos.so)#012#5 0x00007f73b1894a03 pyx_pw_6python_3Sos_12QueryInputer_13input (Sos.so)#012#6 0x00007f73b3251f04 PyCFunction_Call (libpython3.6m.so.1.0)#012#7 0x00007f73b18f6458 Pyx_PyObject_Call (Sos.so)#012#8 0x00007f73b18b2ef7 __pyx_pf_6python_3Sos_5Query_12query (Sos.so)#012#9 0x00007f73b18b29a0 pyx_pw_6python_3Sos_5Query_13query (Sos.so)#012#10 0x00007f73b3259301 call_function (libpython3.6m.so.1.0)#012#11 0x00007f73b325a904 _PyEval_EvalFrameDefault (libpython3.6m.so.1.0)#012#12 0x00007f73b31b5754 _PyEval_EvalCodeWithName (libpython3.6m.so.1.0)#012#13 0x00007f73b3235de0 fast_function (libpython3.6m.so.1.0)#012#14 0x00007f73b3259087 call_function (libpython3.6m.so.1.0)#012#15 0x00007f73b3259cc8 _PyEval_EvalFrameDefault (libpython3.6m.so.1.0)#012#16 0x00007f73b31b5754 _PyEval_EvalCodeWithName (libpython3.6m.so.1.0)#012#17 0x00007f73b3235de0 fast_function (libpython3.6m.so.1.0)#012#18 0x00007f73b3259087 call_function (libpython3.6m.so.1.0)#012#19 0x00007f73b325a904 _PyEval_EvalFrameDefault (libpython3.6m.so.1.0)#012#20 0x00007f73b31b5754 _PyEval_EvalCodeWithName (libpython3.6m.so.1.0)#012#21 0x00007f73b31b6af3 PyEval_EvalCode (libpython3.6m.so.1.0)#012#22 0x00007f73b32c56d2 run_mod (libpython3.6m.so.1.0)#012#23 0x00007f73b319637d PyRun_FileExFlags (libpython3.6m.so.1.0)#012#24 0x00007f73b319b478 PyRun_SimpleFileExFlags (libpython3.6m.so.1.0)#012#25 0x00007f73b319bdc7 Py_Main.cold.3363 (libpython3.6m.so.1.0)#012#26 0x00005647302aeb96 main (platform-python3.6)#012#27 0x00007f73b23727b3 libc_start_main (libc.so.6)#012#28 0x00005647302aed1e _start (platform-python3.6)#012#012Stack trace of thread 1904200:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904206:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904207:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904135:#012#0 0x00007f73b2417fc8 nanosleep (libc.so.6)#012#1 0x00007f73b2417ece sleep (libc.so.6)#012#2 0x00007f73b13baf45 gc_thread_fn (libods.so.0)#012#3 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#4 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904204:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904203:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904202:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904201:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904222:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904205:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904224:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904225:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904223:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904209:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904210:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904226:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904208:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904212:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904213:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904211:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread (libpthread.so.0)#012#3 0x00007f73b244bf23 clone (libc.so.6)#012#012Stack trace of thread 1904215:#012#0 0x00007f73b2eaa2fc pthread_cond_wait@@GLIBC_2.3.2 (libpthread.so.0)#012#1 0x00007f71876960cb blas_thread_server (libopenblasp-r0-085ca80a.3.9.so)#012#2 0x00007f73b2ea414a start_thread

[bschwal]

I can send in email how to replicate if you wish, I left the "bad" container in place.

[tom95858]

Hi Ben,

Yes, please send the instructions to reproduce.

Thanks, Tom

On Fri, May 14, 2021 at 2:03 PM bschwal @.***> wrote:

I can send in email how to replicate if you wish, I left the "bad" container in place.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ovis-hpc/sos/issues/44#issuecomment-841472562, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABVTPXHYEQJCFVV2MI3TWO3TNV6ZPANCNFSM4443RQKQ .

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