BUNDLE_GLOBAL_GEM_CACHE breaks natively compiled libraries

Describe the problem as clearly as you can

When setting up BUNDLE_GLOBAL_GEM_CACHE=1 it installs the gems correctly. In a CI environment you want to carry that cache over to a next build. When the next CI run happens (which contains only the cache folder from previous execution) the gems "install" correctly but when trying to execute the code it claims the gems with native extensions are missing the compiled extension/library.

You can see an example here:

https://gitlab.com/gitlab-org/gitlab-development-kit/-/jobs/4117614795

LoadError: cannot find 'llhttp-ext' library
/builds/gitlab-org/gitlab-development-kit/gdk/gitlab/vendor/bundle/ruby/3.0.0/gems/ffi-compiler-1.0.1/lib/ffi-compiler/loader.rb:21:in `find'
/builds/gitlab-org/gitlab-development-kit/gdk/gitlab/vendor/bundle/ruby/3.0.0/gems/llhttp-ffi-0.4.0/lib/llhttp.rb:13:in `<module:LLHttp>'
/builds/gitlab-org/gitlab-development-kit/gdk/gitlab/vendor/bundle/ruby/3.0.0/gems/llhttp-ffi-0.4.0/lib/llhttp.rb:6:in `<top (required)>'
<internal:/home/gdk/.asdf/installs/ruby/3.0.5/lib/ruby/site_ruby/3.0.0/rubygems/core_ext/kernel_require.rb>:37:in `require'
<internal:/home/gdk/.asdf/installs/ruby/3.0.5/lib/ruby/site_ruby/3.0.0/rubygems/core_ext/kernel_require.rb>:37:in `require'

Did you try upgrading rubygems & bundler?

Yes, I've tried using latest versions of both:

Bundler version 2.4.12

$ gem --version
3.4.11

Post steps to reproduce the problem

I've tested this locally by setting:

export BUNDLE_GLOBAL_GEM_CACHE=1
export BUNDLE_USER_CACHE=~/.cache/bundle

And doing the following:

1. On the original project: bundle install
2. Go back to another project with fewer gems: bundle clean --force
3. Go back to the original project: bundle install
4. Try to run rails console (and get a lot of missing libraries errors, including pg)

Which command did you run?

• bundle install
• rails console

What were you expecting to happen?

• It should load the code correctly

What actually happened?

• I've got a missing (binary/compiled) library error

If not included with the output of your command, run bundle env and paste the output below

Environment

Bundler       2.4.11
  Platforms   ruby, arm64-darwin-22
Ruby          3.0.5p211 (2022-11-24 revision ba5cf0f7c52d4d35cc6a173c89eda98ceffa2dcf) [arm64-darwin-22]
  Full Path   /Users/brodock/.rvm/rubies/ruby-3.0.5/bin/ruby
  Config Dir  /Users/brodock/.rvm/rubies/ruby-3.0.5/etc
RubyGems      3.4.12
  Gem Home    /Users/brodock/.rvm/gems/ruby-3.0.5
  Gem Path    /Users/brodock/.rvm/gems/ruby-3.0.5:/Users/brodock/.rvm/rubies/ruby-3.0.5/lib/ruby/gems/3.0.0
  User Home   /Users/brodock
  User Path   /Users/brodock/.gem/ruby/3.0.0
  Bin Dir     /Users/brodock/.rvm/gems/ruby-3.0.5/bin
Tools
  Git         2.40.0
  RVM         1.29.12-next master
  rbenv       not installed
  chruby      not installed

Bundler Build Metadata

Built At          2023-04-10
Git SHA           be1d1b4623
Released Version  true

Bundler settings

Environment

Bundler       2.4.11
  Platforms   ruby, arm64-darwin-22
Ruby          3.0.5p211 (2022-11-24 revision ba5cf0f7c52d4d35cc6a173c89eda98ceffa2dcf) [arm64-darwin-22]
  Full Path   /Users/brodock/.rvm/rubies/ruby-3.0.5/bin/ruby
  Config Dir  /Users/brodock/.rvm/rubies/ruby-3.0.5/etc
RubyGems      3.4.12
  Gem Home    /Users/brodock/.rvm/gems/ruby-3.0.5
  Gem Path    /Users/brodock/.rvm/gems/ruby-3.0.5:/Users/brodock/.rvm/rubies/ruby-3.0.5/lib/ruby/gems/3.0.0
  User Home   /Users/brodock
  User Path   /Users/brodock/.gem/ruby/3.0.0
  Bin Dir     /Users/brodock/.rvm/gems/ruby-3.0.5/bin
Tools
  Git         2.40.0
  RVM         1.29.12-next master
  rbenv       not installed
  chruby      not installed

Bundler Build Metadata

Built At          2023-04-10
Git SHA           be1d1b4623
Released Version  true

Bundler settings

build.ffi
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): "--disable-system-libffi"
build.nokogiri
  Set for the current user (/Users/brodock/.bundle/config): "--use-system-libraries"
build.pg
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): "--with-pg-config=/opt/homebrew/bin/pg_config"
  Set for the current user (/Users/brodock/.bundle/config): "--with-pg-config=/opt/homebrew/bin/pg_config"
build.pg_query
  Set for the current user (/Users/brodock/.bundle/config): "--with-ldflags=-Wl,-undefined,dynamic_lookup"
build.re2
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): "--with-re2-dir=/opt/homebrew/opt/re2"
  Set for the current user (/Users/brodock/.bundle/config): "--with-re2-dir=/opt/homebrew/opt/re2"
build.thin
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): "--with-cflags=-Wno-error=implicit-function-declaration"
  Set for the current user (/Users/brodock/.bundle/config): "--with-cflags=-Wno-error=implicit-function-declaration"
build.thrift
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): "--with-cppflags=-Wno-error=compound-token-split-by-macro"
  Set for the current user (/Users/brodock/.bundle/config): "--with-cppflags=-Wno-error=compound-token-split-by-macro"
cache_all
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): false
gem.changelog
  Set for the current user (/Users/brodock/.bundle/config): true
gem.ci
  Set for the current user (/Users/brodock/.bundle/config): "gitlab"
gem.coc
  Set for the current user (/Users/brodock/.bundle/config): false
gem.mit
  Set for the current user (/Users/brodock/.bundle/config): true
gem.rubocop
  Set for the current user (/Users/brodock/.bundle/config): "true"
gem.test
  Set for the current user (/Users/brodock/.bundle/config): "rspec"
global_gem_cache
  Set via BUNDLE_GLOBAL_GEM_CACHE: true
jobs
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): 10
set
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): "without production"
user_cache
  Set via BUNDLE_USER_CACHE: "~/.cache/bundle"
without
  Set for your local app (/Users/brodock/Projetos/Gitlab/gdk-ee/gitlab/.bundle/config): [:production]
  Set for the current user (/Users/brodock/.bundle/config): [:production]

Reproduce the failure with BUNDLE_GLOBAL_GEM_CACHE=1 using bundle install, bundle clean --force, and rails console, focusing on the llhttp-ffi and pg native-extension errors shown in the report. Trace Bundler's global gem cache handling and add coverage so a cache-only subsequent install loads compiled libraries successfully.