rails s できない

前提・実現したいこと

Rails 5.0.7

rails s をするとエラーが出ます。

発生している問題・エラーメッセージ

You've tried to invoke Spring when it's already loaded (i.e. the Spring constant is defined).

This is probably because you generated binstubs with Spring 1.0, and you now have a Spring version > 1.0 on your system. To solve this, upgrade your bundle to the latest Spring version and then run `bundle exec spring binstub --all` to regenerate your binstubs. This is a one-time step necessary to upgrade from 1.0 to 1.1.

Here's the backtrace:

/Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/activesupport-5.0.7.2/lib/active_support/dependencies.rb:287:in `load'
/Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/activesupport-5.0.7.2/lib/active_support/dependencies.rb:287:in `block in load'
/Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/activesupport-5.0.7.2/lib/active_support/dependencies.rb:259:in `load_dependency'
/Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/activesupport-5.0.7.2/lib/active_support/dependencies.rb:287:in `load'
/Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/spring-2.1.0/lib/spring/binstub.rb:11:in `<top (required)>'
/Users/username/.rbenv/versions/2.5.1/lib/ruby/site_ruby/2.5.0/rubygems/core_ext/kernel_require.rb:92:in `require'
/Users/username/.rbenv/versions/2.5.1/lib/ruby/site_ruby/2.5.0/rubygems/core_ext/kernel_require.rb:92:in `require'
/Users/username/projects/bookcafe-review-app/bin/spring:16:in `<top (required)>'
bin/rails:5:in `load'
bin/rails:5:in `<main>'

試したこと

以前は正常に動いていたのですが、直前にLaravelやpythonの環境構築をしてアプリを触っていました。
それ以外にRailsは全く触ってなかったのでそこらへんが問題ではないかと推測しています。

エラーメッセージにあるように

undle exec spring binstub --all

やこのエラーを調べた時、スプリングを一度停止させるなど試しましたがうまくいきませんでした。
そもそもspringは起動していませんでした。

また試しにbundle installするとspringがバージョンアップされてしまいたくさんbin以下にたくさんファイルが追加され
その状態でrails sすると

Beginning in Rails 4, Rails ships with a `rails` binstub at ./bin/rails that
should be used instead of the Bundler-generated `rails` binstub.

If you are seeing this message, your binstub at ./bin/rails was generated by
Bundler instead of Rails.

You might need to regenerate your `rails` binstub locally and add it to source
control:

 rails app:update:bin           # Bear in mind this generates other binstubs
                                # too that you may or may not want (like yarn)

If you already have Rails binstubs in source control, you might be
inadvertently overwriting them during deployment by using bundle install
with the --binstubs option.

If your application was created prior to Rails 4, here's how to upgrade:

  bundle config --delete bin    # Turn off Bundler's stub generator
  rails app:update:bin          # Use the new Rails executables
  git add bin                   # Add bin/ to source control

You may need to remove bin/ from your .gitignore as well.

When you install a gem whose executable you want to use in your app,
generate it and add it to source control:

  bundle binstubs some-gem-name
  git add bin/new-executable

NOTE: Gem::Specification#rubyforge_project= is deprecated with no replacement. It will be removed on or after 2019-12-01.
Gem::Specification#rubyforge_project= called from /Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/specifications/erubis-2.7.0.gemspec:17.
NOTE: Gem::Specification#rubyforge_project= is deprecated with no replacement. It will be removed on or after 2019-12-01.
Gem::Specification#rubyforge_project= called from /Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/specifications/rack-test-0.6.3.gemspec:17.
NOTE: Gem::Specification#rubyforge_project= is deprecated with no replacement. It will be removed on or after 2019-12-01.
Gem::Specification#rubyforge_project= called from /Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/specifications/coderay-1.1.2.gemspec:21.
NOTE: Gem::Specification#rubyforge_project= is deprecated with no replacement. It will be removed on or after 2019-12-01.
Gem::Specification#rubyforge_project= called from /Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/specifications/coffee-script-source-1.12.2.gemspec:16.
Traceback (most recent call last):
        8: from /Users/username/.rbenv/versions/2.5.1/bin/rails:23:in `<main>'
        7: from /Users/username/.rbenv/versions/2.5.1/bin/rails:23:in `load'
        6: from /Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/railties-6.0.2.2/exe/rails:10:in `<top (required)>'
        5: from /Users/username/.rbenv/versions/2.5.1/lib/ruby/site_ruby/2.5.0/rubygems/core_ext/kernel_require.rb:35:in `require'
        4: from /Users/username/.rbenv/versions/2.5.1/lib/ruby/site_ruby/2.5.0/rubygems/core_ext/kernel_require.rb:161:in `rescue in require'
        3: from /Users/username/.rbenv/versions/2.5.1/lib/ruby/site_ruby/2.5.0/rubygems.rb:208:in `try_activate'
        2: from /Users/username/.rbenv/versions/2.5.1/lib/ruby/site_ruby/2.5.0/rubygems.rb:215:in `rescue in try_activate'
        1: from /Users/username/.rbenv/versions/2.5.1/lib/ruby/site_ruby/2.5.0/rubygems/specification.rb:1367:in `activate'
/Users/username/.rbenv/versions/2.5.1/lib/ruby/site_ruby/2.5.0/rubygems/specification.rb:2233:in `check_version_conflict': can't activate railties-5.0.7.2, already activated railties-6.0.2.2 (Gem::LoadError)

追記

rails app:update:bin
こちらのコマンドを実行したところエラーが発生しました。

rails
1LoadError: dlopen(/Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/mysql2-0.5.3/lib/mysql2/mysql2.bundle, 9): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
2  Referenced from: /Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/mysql2-0.5.3/lib/mysql2/mysql2.bundle
3  Reason: image not found - /Users/username/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/mysql2-0.5.3/lib/mysql2/mysql2.bundle
4/Users/username/projects/bookcafe-review-app/config/application.rb:6:in `<top (required)>'
5/Users/username/projects/bookcafe-review-app/Rakefile:6:in `require_relative'
6/Users/username/projects/bookcafe-review-app/Rakefile:6:in `<top (required)>'
7/Users/username/projects/bookcafe-review-app/bin/rails:11:in `require'
8/Users/username/projects/bookcafe-review-app/bin/rails:11:in `<top (required)>'
9/Users/username/projects/bookcafe-review-app/bin/spring:16:in `<top (required)>'
10bin/rails:5:in `load'
11bin/rails:5:in `<main>'
12(See full trace by running task with --trace)