iodine issue: External LLVMFunction pthread_atfork cannot be found

[AlexeyMatskevich]

RuntimeError: External LLVMFunction pthread_atfork cannot be found.
  <internal:core> core/kernel.rb:293:in `require_relative'
  /home/aleksei/.asdf/installs/ruby/truffleruby+graalvm-20.3.0/graalvm/jre/languages/ruby/lib/gems/gems/iodine-0.7.43/lib/iodine.rb:6:in `<top (required)>'
  <internal:core> core/kernel.rb:234:in `gem_original_require'
  /home/aleksei/.asdf/installs/ruby/truffleruby+graalvm-20.3.0/graalvm/jre/languages/ruby/lib/gems/gems/iodine-0.7.43/exe/iodine:4:in `<top (required)>'
  <internal:core> core/kernel.rb:401:in `load'
  <internal:core> core/kernel.rb:401:in `load'
  /home/aleksei/.asdf/installs/ruby/truffleruby+graalvm-20.3.0/bin/iodine:23:in `<top (required)>'
  <internal:core> core/kernel.rb:401:in `load'
  <internal:core> core/kernel.rb:401:in `load'

[ [ SubstrateSegfaultHandler caught a segfault. ] ]

To reproduce:

gem install iodine
iodine

[eregon]

Thanks for the report.

I can reproduce.
This might be caused by not linking to libpthread, but actually it seems like it is linked to it:

$ gem i iodine

$ iodine --experimental-options --cexts-log-load --help
<internal:core> core/kernel.rb:293:in `require_relative': External LLVMFunction pthread_atfork cannot be found. (RuntimeError)
	from /home/eregon/.rubies/truffleruby-dev/lib/gems/gems/iodine-0.7.43/lib/iodine.rb:6:in `<top (required)>'
	from <internal:core> core/kernel.rb:234:in `gem_original_require'
	from /home/eregon/.rubies/truffleruby-dev/lib/mri/rubygems/core_ext/kernel_require.rb:72:in `require'
	from /home/eregon/.rubies/truffleruby-dev/lib/gems/gems/iodine-0.7.43/exe/iodine:4:in `<top (required)>'
	from <internal:core> core/kernel.rb:400:in `load'
	from <internal:core> core/kernel.rb:400:in `load'
	from /home/eregon/.rubies/truffleruby-dev/bin/iodine:23:in `<main>'

$  ldd /home/eregon/.rubies/truffleruby-dev/lib/gems/gems/iodine-0.7.43/lib/iodine/iodine.so
	linux-vdso.so.1 (0x00007ffcef965000)
	libtruffleruby.so => /home/eregon/.rubies/truffleruby-dev/lib/cext/libtruffleruby.so (0x00007fda8ad56000)
	libgraalvm-llvm.so.1 => /home/eregon/.rubies/truffleruby-dev/lib/sulong/native/lib/libgraalvm-llvm.so.1 (0x00007fda8ad49000)
	libssl.so.1.1 => /lib64/libssl.so.1.1 (0x00007fda8ac8e000)
	libcrypto.so.1.1 => /lib64/libcrypto.so.1.1 (0x00007fda8a9a1000)
	libc.so.6 => /lib64/libc.so.6 (0x00007fda8a7d7000)
	/lib64/ld-linux-x86-64.so.2 (0x00007fda8b0bf000)
	libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fda8a7b5000)
	libz.so.1 => /lib64/libz.so.1 (0x00007fda8a799000)
	libdl.so.2 => /lib64/libdl.so.2 (0x00007fda8a792000)

$ nm /lib64/libpthread.so.0 | grep pthread_atfork
0000000000011ba0 t .annobin___dyn_pthread_atfork.end
0000000000011b90 t .annobin___dyn_pthread_atfork.start
0000000000011b90 t .annobin_old_pthread_atfork.c
0000000000011ba0 t .annobin_old_pthread_atfork.c_end
0000000000007b15 t .annobin_old_pthread_atfork.c_end.exit
0000000000007b15 t .annobin_old_pthread_atfork.c_end.hot
0000000000007b15 t .annobin_old_pthread_atfork.c_end.startup
0000000000007b15 t .annobin_old_pthread_atfork.c_end.unlikely
0000000000007b15 t .annobin_old_pthread_atfork.c.exit
0000000000007b15 t .annobin_old_pthread_atfork.c.hot
0000000000007b15 t .annobin_old_pthread_atfork.c.startup
0000000000007b15 t .annobin_old_pthread_atfork.c.unlikely
0000000000011b90 t __dyn_pthread_atfork
0000000000011b90 T pthread_atfork@GLIBC_2.2.5

I think this is a Sulong or NFI issue, so I'll move the issue to oracle/graal.

[oubidar-Abderrahim]

Could you please provide more detailed steps to reproduce this issue? that would be helpful

[AlexeyMatskevich]

a) With rbenv

1. Install rbenv
2. Install truffleruby+graalvm-20.3.0 from ruby-build with rbenv install truffleruby+graalvm-20.3.0
3. Switch to truffleruby with rbenv shell truffleruby+graalvm-20.3.0
4. Check ruby version

ruby -v
truffleruby 20.3.0, like ruby 2.6.6, GraalVM CE Native [x86_64-linux]

5. Install iodine with gem install iodine
6. Run iodine with iodine or try to check iodine version with iodine -v

b) With docker

1. Pull container with docker pull flavorjones/truffleruby:20.3.0-buster
2. Connect to container with docker run -it --rm flavorjones/truffleruby:20.3.0-buster bash
3. Install iodine with gem install iodine
4. Run iodine with iodine or try to check iodine version with iodine -v

iodine -v
<internal:core> core/kernel.rb:293:in `require_relative': External LLVMFunction pthread_atfork cannot be found. (RuntimeError)
        from /home/alex/.rbenv/versions/truffleruby+graalvm-20.3.0/graalvm/jre/languages/ruby/lib/gems/gems/iodine-0.7.43/lib/iodine.rb:6:in `<top (required)>'
        from <internal:core> core/kernel.rb:234:in `gem_original_require'
        from /home/alex/.rbenv/versions/truffleruby+graalvm-20.3.0/graalvm/jre/languages/ruby/lib/mri/rubygems/core_ext/kernel_require.rb:54:in `require'
        from /home/alex/.rbenv/versions/truffleruby+graalvm-20.3.0/graalvm/jre/languages/ruby/lib/gems/gems/iodine-0.7.43/exe/iodine:4:in `<top (required)>'
        from <internal:core> core/kernel.rb:401:in `load'
        from <internal:core> core/kernel.rb:401:in `load'
        from /home/alex/.rbenv/versions/truffleruby+graalvm-20.3.0/bin/iodine:23:in `<main>'

Get full backtrace

[oubidar-Abderrahim]

The issue is tracked internally on GR-29336

[oubidar-Abderrahim]

This is not planned

[eregon]

The pthread_atfork stuff seems to work now since truffleruby runs extensions natively oracle/truffleruby#3118 on master.
But we get another error, because rb_get_argv() isn't implemented yet on TruffleRuby.

$ chruby truffleruby-dev
$ gem i iodine
$ iodine --experimental-options --cexts-log-load --help
/home/eregon/.rubies/truffleruby-dev/bin/ruby: symbol lookup error: /home/eregon/.rubies/truffleruby-dev/lib/gems/gems/iodine-0.7.57/lib/iodine/iodine_ext.so: undefined symbol: rb_get_argv

If you care about that, please file an issue at https://github.com/oracle/truffleruby/issues.