Segmentation Fault with mysql2 #1416
Description
Hello,
I'm migrating a Redmine 3.2.0 application to a Debian 12 Bookworm server.
I configured the server with rbenv and ruby 2.3.3.
I'm able to install the gems via bundle version 1.11.2 using the original server's Gemfile under Debian 9 and its Gemfile.lock.
I had a Segmentation Fault issue with MySQL2 and the infamous incorrect version string between the library and the MariaDB client, but I resolved this issue by upgrading MySQL2 to version 0.5.6.
However, I still have a Segmentation Fault with MySQL2, but I no longer get the error message about the MariaDB version.
Mysql2 is compiled with the following options:
bundle config --local build.mysql2 --with-mysql-config=/usr/bin/mysql_config --with-openssl-dir=/opt/openssl-1.0.2u
/opt/openssl-1.0.2u is the directory where OpenSSL is compiled.
The variables are configured as follows:
export PATH=$HOME/.rbenv/shims:$PATH
export PATH=$HOME/.gem/ruby/2.3.0/bin:$PATH
export PATH=/opt/openssl-1.0.2u/bin:$PATH
export BUNDLER_WITHOUT="development test"
export LDFLAGS="-L/opt/openssl-1.0.2u/lib"
export CPPFLAGS="-I/opt/openssl-1.0.2u/include"
Here's the error I get when I run a command like:
RAILS_ENV=production bundle exec rake db:migrate
BigDecimal.new is deprecated; use BigDecimal() method instead.
{:uplevel=>1}
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/htmlentities-4.3.1/lib/htmlentities/mappings/expanded.rb:465: warning: key "inodot" is duplicated and overwritten on line 466
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/bundler/gems/mysql2-36ed43cd1519/lib/mysql2/mysql2.so: [BUG] Segmentation fault at 0x00000000000000
ruby 2.3.3p222 (2016-11-21 revision 56859) [x86_64-linux]
-- Control frame information -----------------------------------------------
c:0030 p:-11760065929212 s:0111 e:000110 TOP [FINISH]
c:0029 p:---- s:0109 e:000108 CFUNC :require
c:0028 p:0012 s:0105 e:000104 BLOCK /home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/activesupport-4.2.6/lib/active_support/dependencies.rb:274
c:0027 p:0059 s:0103 e:000102 METHOD /home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/activesupport-4.2.6/lib/active_support/dependencies.rb:240
c:0026 p:0017 s:0098 e:000097 METHOD /home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/activesupport-4.2.6/lib/active_support/dependencies.rb:274
c:0025 p:0306 s:0093 e:000092 TOP /home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/bundler/gems/mysql2-36ed43cd1519/lib/mysql2.rb:36 [FINISH]
c:0024 p:---- s:0088 e:000087 CFUNC :require
c:0023 p:0042 s:0084 e:000083 BLOCK /home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:77 [FINISH]
c:0022 p:---- s:0080 e:000079 CFUNC :each
c:0021 p:0062 s:0077 e:000076 BLOCK /home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:72 [FINISH]
c:0020 p:---- s:0071 e:000070 CFUNC :each
c:0019 p:0038 s:0068 e:000067 METHOD /home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:61
c:0018 p:0019 s:0064 e:000063 METHOD /home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler.rb:99
c:0017 p:0054 s:0060 e:000059 TOP /home/redmine/redmine-3.2.0/config/application.rb:5 [FINISH]
c:0016 p:---- s:0058 e:000057 CFUNC :require
c:0015 p:0020 s:0054 e:000053 TOP /home/redmine/redmine-3.2.0/config/environment.rb:2 [FINISH]
c:0014 p:---- s:0051 e:000050 CFUNC :require
c:0013 p:0025 s:0047 e:000046 BLOCK config.ru:3 [FINISH]
c:0012 p:---- s:0045 e:000044 CFUNC :instance_eval
c:0011 p:0040 s:0042 e:000041 METHOD /home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/rack-1.6.5/lib/rack/builder.rb:55 [FINISH]
c:0010 p:---- s:0037 e:000036 CFUNC :new
c:0009 p:0015 s:0034 E:001420 EVAL config.ru:1 [FINISH]
c:0008 p:---- s:0032 e:000031 CFUNC :eval
c:0007 p:0163 s:0026 e:000025 METHOD /usr/share/passenger/helper-scripts/rack-preloader.rb:101
c:0006 p:0008 s:0019 e:000018 BLOCK /usr/share/passenger/helper-scripts/rack-preloader.rb:189
c:0005 p:0023 s:0017 e:000016 METHOD /usr/lib/ruby/vendor_ruby/phusion_passenger/loader_shared_helpers.rb:399
c:0004 p:0186 s:0011 e:000010 CLASS /usr/share/passenger/helper-scripts/rack-preloader.rb:188
c:0003 p:0011 s:0006 e:000005 CLASS /usr/share/passenger/helper-scripts/rack-preloader.rb:30
c:0002 p:0038 s:0004 E:000db0 EVAL /usr/share/passenger/helper-scripts/rack-preloader.rb:29 [FINISH]
c:0001 p:0000 s:0002 E:001de0 (none) [FINISH]
-- Ruby level backtrace information ----------------------------------------
/usr/share/passenger/helper-scripts/rack-preloader.rb:29:in `<main>'
/usr/share/passenger/helper-scripts/rack-preloader.rb:30:in `<module:PhusionPassenger>'
/usr/share/passenger/helper-scripts/rack-preloader.rb:188:in `<module:App>'
/usr/lib/ruby/vendor_ruby/phusion_passenger/loader_shared_helpers.rb:399:in `run_block_and_record_step_progress'
/usr/share/passenger/helper-scripts/rack-preloader.rb:189:in `block in <module:App>'
/usr/share/passenger/helper-scripts/rack-preloader.rb:101:in `preload_app'
/usr/share/passenger/helper-scripts/rack-preloader.rb:101:in `eval'
config.ru:1:in `<main>'
config.ru:1:in `new'
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/rack-1.6.5/lib/rack/builder.rb:55:in `initialize'
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/rack-1.6.5/lib/rack/builder.rb:55:in `instance_eval'
config.ru:3:in `block in <main>'
config.ru:3:in `require'
/home/redmine/redmine-3.2.0/config/environment.rb:2:in `<top (required)>'
/home/redmine/redmine-3.2.0/config/environment.rb:2:in `require'
/home/redmine/redmine-3.2.0/config/application.rb:5:in `<top (required)>'
/home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler.rb:99:in `require'
/home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:61:in `require'
/home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:61:in `each'
/home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:72:in `block in require'
/home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:72:in `each'
/home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:77:in `block (2 levels) in require'
/home/***/.gem/ruby/2.3.0/gems/bundler-1.11.2/lib/bundler/runtime.rb:77:in `require'
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/bundler/gems/mysql2-36ed43cd1519/lib/mysql2.rb:36:in `<top (required)>'
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/activesupport-4.2.6/lib/active_support/dependencies.rb:274:in `require'
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/activesupport-4.2.6/lib/active_support/dependencies.rb:240:in `load_dependency'
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/activesupport-4.2.6/lib/active_support/dependencies.rb:274:in `block in require'
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/activesupport-4.2.6/lib/active_support/dependencies.rb:274:in `require'
-- Machine register context ------------------------------------------------
RIP: 0x00007eff674d6867 RBP: 0x00005590cf573830 RSP: 0x00007ffc25209dd8
RAX: 0x0000000000000000 RBX: 0x00005590d38ff450 RCX: 0x0000000000000100
RDX: 0x0000000000000002 RDI: 0x0000000000000000 RSI: 0x0000000000000000
R8: 0x00005590cf578600 R9: 0x000000000000000e R10: 0xd0db1174f35de706
R11: 0x00007eff67554c60 R12: 0x0000000000000002 R13: 0x00005590cf577518
R14: 0x00005590d4743fe0 R15: 0x00007eff66a6d4a0 EFL: 0x0000000000010207
-- C level backtrace information -------------------------------------------
Unexpected size of .debug_line in /home/***/.rbenv/versions/2.3.3/bin/ruby
Unexpected size of .debug_line in /home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/bundler/gems/mysql2-36ed43cd1519/lib/mysql2/mysql2.so
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8a34044]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8a0aea5]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b891837e]
/lib/x86_64-linux-gnu/libc.so.6 [0x7eff673bd050]
/lib/x86_64-linux-gnu/libc.so.6 [0x7eff674d6867]
/opt/openssl-1.0.2u/lib/libcrypto.so.1.0.0(getrn+0x7c) [0x7eff66b25d6c]
/opt/openssl-1.0.2u/lib/libcrypto.so.1.0.0(lh_insert+0xbf) [0x7eff66b2605f]
/opt/openssl-1.0.2u/lib/libcrypto.so.1.0.0(OBJ_NAME_add+0x70) [0x7eff66a6d8f0]
/lib/x86_64-linux-gnu/libcrypto.so.3 [0x7eff62befa2c]
/lib/x86_64-linux-gnu/libcrypto.so.3 [0x7eff62c32269]
/lib/x86_64-linux-gnu/libc.so.6 [0x7eff6740f057]
/lib/x86_64-linux-gnu/libcrypto.so.3(CRYPTO_THREAD_run_once+0x9) [0x7eff62c3fa19]
/lib/x86_64-linux-gnu/libcrypto.so.3(OPENSSL_init_crypto+0x323) [0x7eff62c327e3]
/lib/x86_64-linux-gnu/libssl.so.3(OPENSSL_init_ssl+0x31) [0x7eff6372f711]
/usr/lib/x86_64-linux-gnu/libmariadb.so.3 [0x7eff637e253a]
/usr/lib/x86_64-linux-gnu/libmariadb.so.3 [0x7eff637c8136]
/lib/x86_64-linux-gnu/libc.so.6 [0x7eff6740f057]
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/bundler/gems/mysql2-36ed43cd1519/lib/mysql2/mysql2.so(init_mysql2_client+0x11) [0x7eff65635a51]
/home/***/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/bundler/gems/mysql2-36ed43cd1519/lib/mysql2/mysql2.so(Init_mysql2+0x6d) [0x7eff6563039d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(dln_load+0x106) [0x5590b89bffc6]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b89a6e10]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8863e64]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_f_require+0x13) [0x5590b88643d3]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8996812]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8862571]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8864372]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_f_require+0x13) [0x5590b88643d3]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899688d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_yield+0x1fc) [0x5590b89a5e0c]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_ary_each+0x3c) [0x5590b89c3bcc]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899695d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_yield+0x1fc) [0x5590b89a5e0c]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_ary_each+0x3c) [0x5590b89c3bcc]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899695d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8862571]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8864372]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_f_require+0x13) [0x5590b88643d3]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899688d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8862571]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8864372]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_f_require+0x13) [0x5590b88643d3]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899688d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b89a4de6]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899695d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899c2ea]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(rb_class_new_instance+0x21) [0x5590b88c46b1]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899695d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899a841]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899ad60]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b898e1da]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b899688d]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b8999d8a]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b885d7e9]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(ruby_run_node+0x2f) [0x5590b88605ff]
Passenger AppPreloader: /home/redmine/redmine-3.2.0 [0x5590b885d40b]
/lib/x86_64-linux-gnu/libc.so.6 [0x7eff673a824a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85) [0x7eff673a8305]
Passenger AppPreloader: /home/redmine/redmine-3.2.0(_start+0x21) [0x5590b885d431]
If you have any questions or ideas for a resolution, I'd love to hear them.