SIGABRT on OSX 10.12 (Sierra) after fork() #195

onyxraven · 2016-09-26T16:05:01Z

Crash Log and DiagnosticReport: https://gist.github.com/onyxraven/ce190bc4c9f31db07ec3c27578d33641

When running rspec via spring, ruby almost immediately crashes with the attached crash info. This is within my rails app, but I can try to get a simpler example put together later today.

What it looks like is the libsqlite3.dylib bundled with Sierra may not be safe for use across a fork.

There is a similar report on the python list https://bugs.python.org/issue27126, and someone else added a bug to the ruby bug list https://bugs.ruby-lang.org/issues/12781.

I've attempted to get the gem to use a different version (eg, the one in Homebrew), but so far I've failed to get it to load anything but the version out of /usr/lib/ - If I can get that workaround figured out, it would get me past this issue for the short term.

If ruby is not forking (eg, via SPRING_DISABLE, or other non-forking code), the sqlite3 code still works fine.

kumasento · 2016-09-26T17:01:48Z

I'm facing the same issue.

Yanchek99 · 2016-09-28T02:23:10Z

Same here causing seg faults.

markwpiper · 2016-10-04T18:18:24Z

+1

rhutch117 · 2016-10-04T18:21:30Z

same issue

markwpiper · 2016-10-04T18:33:34Z

Was able to workaround it by installing the sqlite3 gem and forcing it to use the newer version of sqlite from my homebrew installation:

gem uninstall sqlite3
gem install sqlite3 -- --with-sqlite3-include=/usr/local/Cellar/sqlite/3.14.2_1/include --with-sqlite3-lib=/usr/local/Cellar/sqlite/3.14.2_1/lib

electrickite · 2016-10-05T00:27:18Z

Also experiencing this issue on macOS Sierra, specifically with v1.3.11. Seems to occur when running a Rails console under spring or using rake to start Resque workers.

In some cases, I can avoid the segfault by setting the environment variable DISABLE_SPRING=1

jdongelmans · 2016-10-05T12:29:26Z

Also having this issue.
Thanks @markwpiper for the workaround!

ccasabona · 2016-10-08T20:14:05Z

Thanks to markwpiper for a working fix!

tenderlove · 2016-10-08T23:57:44Z

Thanks for reporting this. Seems like we're in the same boat as the Python folks. I'd prefer not to embed SQLite3 but maybe we can ship a version that looks for SQLite3 in homebrew before trying to use the system library. Does this seem reasonable to everyone?

In the mean time, you can shorten @markwpiper's workaround to:

gem install sqlite3 -- --with-sqlite3-dir=/usr/local/Cellar/sqlite/3.14.2_1

excid3 · 2016-10-08T23:58:53Z

Seems like a reasonable solution to me.

tenderlove · 2016-10-09T01:12:21Z

I just pushed 1.3.12. It contains c7226ba, which should fix this problem. You can verify the installed version is linked against homebrew's installed version of SQLite3 by doing otool -L $(gem which sqlite3/sqlite3_native.bundle). The output should look something like this:

[aaron@TC pkg (master)]$ otool -L $(gem which sqlite3/sqlite3_native.bundle)
/Users/aaron/.rbenv/versions/ruby-trunk/lib/ruby/gems/2.4.0/gems/sqlite3-1.3.12/lib/sqlite3/sqlite3_native.bundle:
    /usr/local/opt/sqlite/lib/libsqlite3.0.dylib (compatibility version 9.0.0, current version 9.6.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)
    /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)
    /usr/local/opt/gperftools/lib/libprofiler.0.dylib (compatibility version 5.0.0, current version 5.8.0)
[aaron@TC pkg (master)]$

The important line is where it says /usr/local/opt/sqlite/lib/libsqlite3.0.dylib, which is from homebrew.

I close this if someone can verify the new version fixes the issue. Thank you!

excid3 · 2016-10-09T01:51:12Z

@tenderlove Just tested it, can confirm 1.3.12 works great! 🤘

○ otool -L $(gem which sqlite3/sqlite3_native.bundle)
/Users/chris/.rbenv/versions/2.3.1/lib/ruby/gems/2.3.0/gems/sqlite3-1.3.12/lib/sqlite3/sqlite3_native.bundle:
    /usr/local/opt/sqlite/lib/libsqlite3.0.dylib (compatibility version 9.0.0, current version 9.6.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)
    /usr/local/opt/gmp/lib/libgmp.10.dylib (compatibility version 14.0.0, current version 14.1.0)
    /usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

tenderlove · 2016-10-09T02:01:29Z

@excid3 great! Thank you for testing. I'll close this ticket now. 😄

ccasabona · 2016-10-09T13:37:40Z

I upgraded the version and the fix is working perfectly. Thank you.

Charlie

On Oct 8, 2016, at 10:01 PM, Aaron Patterson notifications@github.com wrote:

@excid3 https://github.com/excid3 great! Thank you for testing. I'll close this ticket now. 😄

—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub #195 (comment), or mute the thread https://github.com/notifications/unsubscribe-auth/AGE6Iol9zelSY-rjze_pSjGMFTW-vGh_ks5qyEr7gaJpZM4KGtDL.

spikex · 2016-10-09T20:09:48Z

Worked for me as well. Thanks!

The `libsqlite3.dylib` is apparently not safe for use in forked processes. The updated gem now prefers the homebrew sqlite3. For further details, see sparklemotion/sqlite3-ruby#195

synth · 2016-11-04T01:25:40Z

This did not work for me running spork with ruby v1.9.3-p547. I uninstalled the gem, uninstalled the brew, and reinstalled both following the above directions.

UPDATE: I've upgraded app to use spring and still same issue. The otool command returns the proper sqlite dylib path. I've tried fixing this six ways to Sunday, so any help in figuring this out would be most appreciated!

Previous version crashing when spring was used. sparklemotion/sqlite3-ruby#195

Previous version was crashing ruby on macOS Sierra when spring was used. sparklemotion/sqlite3-ruby#195

jakeonrails · 2016-12-02T20:39:30Z

I'm still having this issue.

I've tried:

gem install sqlite3 -- --with-sqlite3-dir=/usr/local/Cellar/sqlite/3.14.2_1

I've reinstalled Ruby 2.2.5 via rvm reinstall 2.2.5

I've manually uninstalled sqlite3 and reinstalled

I've uninstalled sqlite from brew and reinstalled

I've tried brew link --force sqlite

I'm running sqlite3 1.3.12.

My otool output:

otool -L $(gem which sqlite3/sqlite3_native.bundle)
/Users/jakemoffatt/.rvm/gems/ruby-2.2.5/gems/sqlite3-1.3.12/lib/sqlite3/sqlite3_native.bundle:
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/usr/local/opt/sqlite/lib/libsqlite3.0.dylib (compatibility version 9.0.0, current version 9.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

Is the problem that the /usr/lib/libz version is shown first? How do I fix that?

My specific error message, migrating a brand new Rails 5 app:

$ rake db:migrate
Running via Spring preloader in process 69525
/Users/jakemoffatt/.rvm/gems/ruby-2.2.5/gems/activerecord-5.0.0.1/lib/active_record/connection_adapters/sqlite3_adapter.rb:27: [BUG] Segmentation fault at 0x00000000000110
ruby 2.2.5p319 (2016-04-26 revision 54774) [x86_64-darwin16]

ascarter · 2016-12-03T05:10:31Z

I think I'm hitting it as well even using Homebrew sqlite3:

$ otool -L $(gem which sqlite3/sqlite3_native.bundle)
/Users/andrew/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/sqlite3-1.3.12/lib/sqlite3/sqlite3_native.bundle:
	/opt/homebrew/opt/sqlite/lib/libsqlite3.0.dylib (compatibility version 9.0.0, current version 9.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

Running tests suites on the depot iteration b1 (pragprog Agile Web Development with Rails 5):

bin/rails test
Running via Spring preloader in process 11300
/Users/andrew/.rbenv/versions/2.3.3/lib/ruby/gems/2.3.0/gems/activerecord-5.0.0.1/lib/active_record/connection_adapters/sqlite3_adapter.rb:27: [BUG] Segmentation fault at 0x00000000000110
ruby 2.3.3p222 (2016-11-21 revision 56859) [x86_64-darwin16]

Installed sqlite3 from homebrew:

$ brew info sqlite
sqlite: stable 3.15.2 (bottled) [keg-only]
Command-line interface for SQLite
https://sqlite.org/
/opt/homebrew/Cellar/sqlite/3.15.2 (11 files, 2.9M)
  Poured from bottle on 2016-12-02 at 20:50:18

Tried:

gem install sqlite3
gem install sqlite3 -- --with-sqlite3-dir=/opt/homebrew/Cellar/sqlite/3.15.2

ccasabona · 2016-12-06T12:47:32Z

Some food for thought for this problem: The problem started after upgrading to OS Sierra. Changes to the source code in development caused a segmentation fault error. Restarting the development server (puma) fixed this. At the time, I was using Rails 5.0.0 and ruby 2.3.1 (or maybe 2.3.0). An issue was put on github rails. The rails team determined that this was not a rails issue, but that it was likely a problem with the sqite gem. My understanding of the problem was that the sqlite gem not using the brew installed sqlite even when brew reported it as linked properly. At the time, a fix was suggested (I think by the gem author) for these steps: gem uninstall sqlite3 match the version number installed by brew install sqlite3 gem install sqlite3 -- --with-sqlite3-include=/usr/local/Cellar/sqlite/3.14.2_1/include --with-sqlite3-lib=/usr/local/Cellar/sqlite/3.14.2_1/lib This was under version 1.3.11 of the sqlite gem. A fix for this was incorporated into a new version of the gem and bumped the version from 1.3.11 to 1.3.12. You could just use the gem without the complicated install command. After installing ruby 2.3.2, the problem came back but only in the test environment when entering or removing a byebug command. I went back to ruby 2.3.1 and the problem went away. When ruby 2.3.3 was installed, the problem did not recur. Currently, I am using: OS Sierra 10.12.1 Ruby 2.3.3 Rails 5.0.0.1 running these commands ~/ brew link sqlite --dry-run Warning: Already linked: /usr/local/Cellar/sqlite/3.15.1 ~/ which sqlite3 /usr/local/bin/sqlite3 I hope this helps someone.

…

On Dec 6, 2016, at 5:32 AM, PineWong ***@***.***> wrote: Me too. macOS 10.12.1 Rails 5.0.0.1 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#195 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGE6IoQdZLK0gQHD31PZ4sUJP3beFFt-ks5rFTnXgaJpZM4KGtDL>.

arthurnn · 2017-01-04T17:58:38Z

I think brew info wasn't working for me, which 427b15e fixed the issue. However that is not released yet. Can you cut another release @tenderlove ?
this is my output after a install of 1.3.12:

[arthurnn@snowball activerecord]$ otool -L $(gem which sqlite3/sqlite3_native.bundle)
/Users/arthurnn/.gem/ruby/2.4.0/gems/sqlite3-1.3.12/lib/sqlite3/sqlite3_native.bundle:
/usr/lib/libsqlite3.dylib (compatibility version 9.0.0, current version 253.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)
/usr/local/opt/gmp/lib/libgmp.10.dylib (compatibility version 14.0.0, current version 14.0.0)
/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

[arthurnn@snowball activerecord]$ brew --prefix sqlite3
/usr/local/opt/sqlite

For now, I am using this as a solution:

 gem install sqlite3 -- --with-sqlite3-dir=$(brew --prefix sqlite3)

tenderlove · 2017-01-04T18:40:48Z

@arthurnn 1.3.13 should be shipped now!

Version 1.3.13 includes the proper fix for the segfaults reported in sparklemotion/sqlite3-ruby#195.

tenderlove closed this as completed Oct 9, 2016

inz mentioned this issue Oct 12, 2016

Update sqlite3 gem sealuzh/cloud-stove#166

Merged

inz added a commit to sealuzh/cloud-stove that referenced this issue Oct 13, 2016

Update sqlite3 gem

4330623

The `libsqlite3.dylib` is apparently not safe for use in forked processes. The updated gem now prefers the homebrew sqlite3. For further details, see sparklemotion/sqlite3-ruby#195

tenderlove mentioned this issue Nov 23, 2016

OS X Sierra sqlite seg fault rails/spring#493

Closed

mrhead added a commit to mrhead/action_cable_chat_app that referenced this issue Nov 24, 2016

Update sqlite3 gem

94b34be

Previous version crashing when spring was used. sparklemotion/sqlite3-ruby#195

mrhead added a commit to mrhead/action_cable_chat_app that referenced this issue Nov 24, 2016

Update sqlite3 gem

db44d3d

Previous version was crashing ruby on macOS Sierra when spring was used. sparklemotion/sqlite3-ruby#195

mrhead mentioned this issue Nov 24, 2016

Update sqlite3 gem mhartl/action_cable_chat_app#3

Closed

pixeltrix added a commit to rails/rails that referenced this issue Mar 4, 2017

Bump sqlite3 gem to 1.3.13

d2011f7

Version 1.3.13 includes the proper fix for the segfaults reported in sparklemotion/sqlite3-ruby#195.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

SIGABRT on OSX 10.12 (Sierra) after fork() #195

SIGABRT on OSX 10.12 (Sierra) after fork() #195

onyxraven commented Sep 26, 2016 •

edited

kumasento commented Sep 26, 2016

Yanchek99 commented Sep 28, 2016

markwpiper commented Oct 4, 2016

rhutch117 commented Oct 4, 2016

markwpiper commented Oct 4, 2016

electrickite commented Oct 5, 2016

jdongelmans commented Oct 5, 2016

ccasabona commented Oct 8, 2016

tenderlove commented Oct 8, 2016

excid3 commented Oct 8, 2016

tenderlove commented Oct 9, 2016

excid3 commented Oct 9, 2016

tenderlove commented Oct 9, 2016

ccasabona commented Oct 9, 2016

spikex commented Oct 9, 2016

synth commented Nov 4, 2016 •

edited

jakeonrails commented Dec 2, 2016

ascarter commented Dec 3, 2016

ccasabona commented Dec 6, 2016 via email

arthurnn commented Jan 4, 2017 •

edited

tenderlove commented Jan 4, 2017

SIGABRT on OSX 10.12 (Sierra) after fork() #195

SIGABRT on OSX 10.12 (Sierra) after fork() #195

Comments

onyxraven commented Sep 26, 2016 • edited

kumasento commented Sep 26, 2016

Yanchek99 commented Sep 28, 2016

markwpiper commented Oct 4, 2016

rhutch117 commented Oct 4, 2016

markwpiper commented Oct 4, 2016

electrickite commented Oct 5, 2016

jdongelmans commented Oct 5, 2016

ccasabona commented Oct 8, 2016

tenderlove commented Oct 8, 2016

excid3 commented Oct 8, 2016

tenderlove commented Oct 9, 2016

excid3 commented Oct 9, 2016

tenderlove commented Oct 9, 2016

ccasabona commented Oct 9, 2016

spikex commented Oct 9, 2016

synth commented Nov 4, 2016 • edited

jakeonrails commented Dec 2, 2016

ascarter commented Dec 3, 2016

ccasabona commented Dec 6, 2016 via email

arthurnn commented Jan 4, 2017 • edited

tenderlove commented Jan 4, 2017

onyxraven commented Sep 26, 2016 •

edited

synth commented Nov 4, 2016 •

edited

arthurnn commented Jan 4, 2017 •

edited