segfault upon "using GSL" on Julia master

[chriscoey]

I'm on Ubuntu. I didn't get this segfault until after I rebuilt Julia master a few days ago. I rebuilt again just now and I still get the segfault. I get the segfault with both GSL#v0.5.0 and GSL#master.

coey@che:~/julia$ j
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.2.0-DEV.544 (2019-03-25)
 _/ |\__'_|_|_|\__'_|  |  Commit ea0c6e9e76 (0 days old master)
|__/                   |

julia> using GSL

signal (11): Segmentation fault
in expression starting at REPL[1]:1
unknown function (ip: 0x7fc07c6770df)
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_struct at /home/coey/julia/src/dump.c:1870
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_value_phic at /home/coey/julia/src/dump.c:1625 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2043
jl_deserialize_value_array at /home/coey/julia/src/dump.c:1542
jl_deserialize_value at /home/coey/julia/src/dump.c:2034
jl_deserialize_struct at /home/coey/julia/src/dump.c:1870
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_value_array at /home/coey/julia/src/dump.c:1542
jl_deserialize_value at /home/coey/julia/src/dump.c:2034
jl_deserialize_struct at /home/coey/julia/src/dump.c:1870
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_value_array at /home/coey/julia/src/dump.c:1542
jl_deserialize_value at /home/coey/julia/src/dump.c:2034
jl_deserialize_struct at /home/coey/julia/src/dump.c:1870
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_struct at /home/coey/julia/src/dump.c:1870
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_value_array at /home/coey/julia/src/dump.c:1542
jl_deserialize_value at /home/coey/julia/src/dump.c:2034
jl_deserialize_struct at /home/coey/julia/src/dump.c:1870
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_struct at /home/coey/julia/src/dump.c:1870
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_value_array at /home/coey/julia/src/dump.c:1542
jl_deserialize_value at /home/coey/julia/src/dump.c:2034
jl_deserialize_struct at /home/coey/julia/src/dump.c:1870
jl_deserialize_value_any at /home/coey/julia/src/dump.c:1969 [inlined]
jl_deserialize_value at /home/coey/julia/src/dump.c:2166
jl_deserialize_value at /home/coey/julia/src/dump.c:1784
jl_deserialize_value_array at /home/coey/julia/src/dump.c:1542
jl_deserialize_value at /home/coey/julia/src/dump.c:2034
_jl_restore_incremental at /home/coey/julia/src/dump.c:3162
jl_restore_incremental at /home/coey/julia/src/dump.c:3221
_include_from_serialized at ./loading.jl:617
_require_search_from_serialized at ./loading.jl:713
_require at ./loading.jl:938
require at ./loading.jl:859
require at ./loading.jl:854
jl_apply_generic at /home/coey/julia/src/gf.c:2226
jl_apply at /home/coey/julia/src/julia.h:1594 [inlined]
call_require at /home/coey/julia/src/toplevel.c:398 [inlined]
eval_import_path at /home/coey/julia/src/toplevel.c:435
jl_toplevel_eval_flex at /home/coey/julia/src/toplevel.c:639
jl_toplevel_eval_flex at /home/coey/julia/src/toplevel.c:746
jl_toplevel_eval_in at /home/coey/julia/src/toplevel.c:826
eval at ./boot.jl:327
jl_apply_generic at /home/coey/julia/src/gf.c:2226
eval_user_input at /home/coey/julia/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:86
macro expansion at /home/coey/julia/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:118 [inlined]
#26 at ./task.jl:269
jl_apply_generic at /home/coey/julia/src/gf.c:2226
jl_apply at /home/coey/julia/src/julia.h:1594 [inlined]
start_task at /home/coey/julia/src/task.c:583
unknown function (ip: 0xffffffffffffffff)
Allocations: 1186985 (Pool: 1186717; Big: 268); GC: 1
Segmentation fault (core dumped)

[giordano]

Any chance to try on julia v1.1 stable?

[chriscoey]

I just tried it with 1.1 stable and there was no segfault with GSL recompiling. So only 1.2 master causes it.

[chriscoey]

The error also happens on a different Ubuntu machine with 5 days old Julia master (Commit f611b46e72)

[simonbyrne]

I updated the Travis config to test on nightly: it appears there as well.

[giordano]

Would you be able to run git bisect in julia repository to search for the offending commit?

[giordano]

You have a hint from appveyor about the last good revision: https://ci.appveyor.com/project/simonbyrne/gsl-jl/history

[chriscoey]

OK I'm trying the bisect now

fyi during bisect I am getting OutOfMemoryError() for some commits (eg f44a37f333) before the later commits that segfault.

[chriscoey]

OK bisection yielded:

c8510e31dc2af6f97358bb7f3b50ef88355feffc is the first bad commit
commit c8510e31dc2af6f97358bb7f3b50ef88355feffc
Author: Jameson Nash <vtjnash@gmail.com>
Date:   Thu Feb 7 14:22:09 2019 -0500

    internals: share slotnames table via Method
    
    Also store a few other unnecessary properties in CodeInfo,
    which some users might be interested in having.

:040000 040000 ce99966cc2a77c0546fb67cc4e6f5b11392dd84c 30d4e91efac48df7d7f62b0a42418273234a9b3a M	base
:040000 040000 4b3af633a0aa965d1594d0f5692ec4805fe667ec 7cc2215313e13bb816a3b6972ba7c3050107ee1b M	src
:040000 040000 9a61a0ede933df0c64fef3141d3c6af107724b90 c6caf524dc70b5d6afcc34448cee240d48ca1530 M	stdlib
:040000 040000 7c38d5fd8690d788579c09c6e8c0944fcdbea57b 00dbf7186646ef48c63c082d75ac2d0eee36ece5 M	test

@vtjnash

[giordano]

I've opened an issue in Julia at JuliaLang/julia#31488

[giordano]

JuliaLang/julia#31488 has been fixed and I confirm that using GSL works for me and tests pass locally, thus I'm going to close this issue. Thanks @chriscoey for the report and the precious bisection!