Logstash pipeline can't be stopped after upgrading

We have just recently updated Logstash from version 2.3.4 to 2.4.0. It seems that since updating Logstash we have been having throughput issues (I suspect we are dropping logs somewhere, either in Filebeats or in our Logstash shippers). I noticed that running service logstash restart has been consistently failing after the upgrade. Additionally, when I attempt to restart the service I see the following errors appear in the logs:

{"timestamp":"2016-09-16T04:15:18.832000-0400","message":"The shutdown process appears to be stalled due to busy or blocked plugins. Check the logs for more information.","level":"error"}
{"timestamp":"2016-09-16T04:15:26.915000-0400","message":{"events_filtered":120177,"events_consumed":119811,"worker_count":16,"inflight_count":1125,"worker_states":[{"status":"dead","alive":false,"index":0,"inflight_count":0},{"status":"run","alive":true,"index":1,"inflight_count":0},{"status":"run","alive":true,"index":2,"inflight_count":125},{"status":"dead","alive":false,"index":3,"inflight_count":0},{"status":"run","alive":true,"index":4,"inflight_count":125},{"status":"run","alive":true,"index":5,"inflight_count":125},{"status":"run","alive":true,"index":6,"inflight_count":125},{"status":"run","alive":true,"index":7,"inflight_count":125},{"status":"run","alive":true,"index":8,"inflight_count":125},{"status":"dead","alive":false,"index":9,"inflight_count":0},{"status":"run","alive":true,"index":10,"inflight_count":125},{"status":"run","alive":true,"index":11,"inflight_count":125},{"status":"dead","alive":false,"index":12,"inflight_count":0},{"status":"dead","alive":false,"index":13,"inflight_count":0},{"status":"dead","alive":false,"index":14,"inflight_count":0},{"status":"sleep","alive":true,"index":15,"inflight_count":125}],"output_info":[{"type":"http","config":{"http_method":"get","url":"http://127.0.0.1:8500/v1/agent/check/pass/service:logstash:1","__ALLOW_ENV__":false},"is_multi_worker":false,"events_received":326,"workers":["LogStash::Outputs::Http: {\"http_method\"=>\"get\", \"url\"=>\"http://127.0.0.1:8500/v1/agent/check/pass/service:logstash:1\", \"codec\"=><LogStash::Codecs::Plain charset=>\"UTF-8\">, \"workers\"=>1, \"request_timeout\"=>60, \"socket_timeout\"=>10, \"connect_timeout\"=>10, \"follow_redirects\"=>true, \"pool_max\"=>50, \"pool_max_per_route\"=>25, \"keepalive\"=>true, \"automatic_retries\"=>1, \"retry_non_idempotent\"=>false, \"validate_after_inactivity\"=>200, \"ssl_certificate_validation\"=>true, \"keystore_type\"=>\"JKS\", \"truststore_type\"=>\"JKS\", \"cookies\"=>true, \"verify_ssl\"=>true, \"format\"=>\"json\"}"],"busy_workers":0},{"type":"sqs","config":{"batch":"false","queue":"logstash","region":"us-east-1","workers":16,"__ALLOW_ENV__":false},"is_multi_worker":true,"events_received":120177,"workers":["LogStash::Outputs::SQS: {\"batch\"=>false, \"queue\"=>\"logstash\", \"region\"=>\"us-east-1\", \"workers\"=>16, \"codec\"=><LogStash::Codecs::Plain charset=>\"UTF-8\">, \"use_ssl\"=>true, 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\"region\"=>\"us-east-1\", \"workers\"=>16, \"codec\"=><LogStash::Codecs::Plain charset=>\"UTF-8\">, \"use_ssl\"=>true, \"batch_events\"=>10, \"batch_timeout\"=>5}","LogStash::Outputs::SQS: {\"batch\"=>false, \"queue\"=>\"logstash\", \"region\"=>\"us-east-1\", \"workers\"=>16, \"codec\"=><LogStash::Codecs::Plain charset=>\"UTF-8\">, \"use_ssl\"=>true, \"batch_events\"=>10, \"batch_timeout\"=>5}","LogStash::Outputs::SQS: {\"batch\"=>false, \"queue\"=>\"logstash\", \"region\"=>\"us-east-1\", \"workers\"=>16, \"codec\"=><LogStash::Codecs::Plain charset=>\"UTF-8\">, \"use_ssl\"=>true, \"batch_events\"=>10, \"batch_timeout\"=>5}"],"busy_workers":10},{"type":"statsd","config":{"count":{"logstash_events":"%{[events][count]}"},"gauge":{"logstash_event_rate.1m":"%{[events][rate_1m]}","logstash_event_rate.5m":"%{[events][rate_5m]}","logstash_event_rate.15m":"%{[events][rate_15m]}"},"__ALLOW_ENV__":false},"is_multi_worker":false,"events_received":365,"workers":["LogStash::Outputs::Statsd: 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\"workers\"=>1}"],"busy_workers":0}],"thread_info":[{"thread_id":29,"name":"[main]>worker1","plugin":["LogStash::Filters::Metrics",{"add_field":{"type":"metric"},"add_tag":"metric","meter":["events"]}],"backtrace":["[...]/vendor/jruby/lib/ruby/1.9/net/http.rb:777:in `initialize'","[...]/vendor/jruby/lib/ruby/1.9/net/http.rb:777:in `connect'","[...]/vendor/jruby/lib/ruby/1.9/net/http.rb:756:in `do_start'","[...]/vendor/jruby/lib/ruby/1.9/net/http.rb:751:in `start'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/core/http/connection_pool.rb:327:in `start_session'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/core/http/connection_pool.rb:127:in `session_for'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/core/http/net_http_handler.rb:56:in `handle'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/core/client.rb:253:in `make_sync_request'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/core/client.rb:282:in 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{"timestamp":"2016-09-16T04:15:31.210000-0400","message":"Pipeline aborted due to error","exception":"NoMethodError","backtrace":["/opt/logstash/vendor/bundle/jruby/1.9/gems/stud-0.0.22/lib/stud/buffer.rb:186:in `buffer_flush'","/opt/logstash/vendor/bundle/jruby/1.9/gems/logstash-output-sqs-2.0.5/lib/logstash/outputs/sqs.rb:134:in `close'","/opt/logstash/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/plugin.rb:38:in `do_close'","/opt/logstash/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/output_delegator.rb:144:in `do_close'","org/jruby/RubyFixnum.java:275:in `times'","/opt/logstash/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/output_delegator.rb:142:in `do_close'","org/jruby/RubyArray.java:1613:in `each'","/opt/logstash/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/pipeline.rb:405:in `shutdown_workers'","/opt/logstash/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/pipeline.rb:151:in `run'","/opt/logstash/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/agent.rb:491:in `start_pipeline'"],"level":"error"}
{"timestamp":"2016-09-16T04:16:50.375000-0400","message":"Pipeline main started"}
{"timestamp":"2016-09-16T04:18:09.261000-0400","message":"SIGTERM received. Shutting down the agent.","level":"warn"}
{"timestamp":"2016-09-16T04:18:09.262000-0400","message":"stopping pipeline","id":"main"}
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`log_client_request'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/core/client.rb:477:in `client_request'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/core/client.rb:373:in `return_or_raise'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/core/client.rb:476:in `client_request'","(eval):3:in `send_message'","[...]/vendor/bundle/jruby/1.9/gems/aws-sdk-v1-1.66.0/lib/aws/sqs/queue.rb:125:in `send_message'","[...]/vendor/bundle/jruby/1.9/gems/logstash-output-sqs-2.0.5/lib/logstash/outputs/sqs.rb:124:in `receive'","[...]/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/outputs/base.rb:109:in `multi_receive'","[...]/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/outputs/base.rb:109:in `each'","[...]/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/outputs/base.rb:109:in `multi_receive'","[...]/vendor/bundle/jruby/1.9/gems/logstash-core-2.4.0-java/lib/logstash/output_delegator.rb:130:in 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`select'"},{"thread_id":46,"name":"[main]>worker13","plugin":["LogStash::Filters::Metrics",{"add_field":{"type":"metric"},"add_tag":"metric","meter":["events"]}],"current_call":"[...]/vendor/jruby/lib/ruby/1.9/net/protocol.rb:143:in `select'"},{"thread_id":47,"name":"[main]>worker14","plugin":["LogStash::Filters::Metrics",{"add_field":{"type":"metric"},"add_tag":"metric","meter":["events"]}],"current_call":"[...]/vendor/jruby/lib/ruby/1.9/net/protocol.rb:143:in `select'"},{"thread_id":48,"name":"[main]>worker15","plugin":["LogStash::Filters::Metrics",{"add_field":{"type":"metric"},"add_tag":"metric","meter":["events"]}],"current_call":"[...]/vendor/jruby/lib/ruby/1.9/net/http.rb:777:in `initialize'"}]},"level":"warn"}

This issue might be similar or related to #5932. Our Logstash configuration is:

input {
  beats {
    port => 5044
  }
}
input {
  file {
    add_field => {
      "role" => "logstash_shipper"
    }
    path => "/var/log/logstash/logstash.log"
    type => "logstash"
  }
}
input {
  heartbeat {
    add_field => {
      "role" => "logstash_shipper"
    }
    interval => "10"
    type => "heartbeat"
  }
}
filter {
  metrics {
    add_field => {
      type => "metric"
    }
    add_tag => "metric"
    meter => ["events"]
  }
}
output {
  if [type] == "heartbeat" {
    http {
      http_method => "get"
      url => "http://127.0.0.1:8500/v1/agent/check/pass/service:logstash:1"
    }
  }
}
output {
  sqs {
    batch => false
    queue => "logstash"
    region => "us-east-1"
    workers => 16
  }
}
output {
  if "metric" in [tags] {
    statsd {
      count => {
        "logstash_events" => "%{[events][count]}"
      }
      gauge => {
        "logstash_event_rate.1m" => "%{[events][rate_1m]}"
        "logstash_event_rate.5m" => "%{[events][rate_5m]}"
        "logstash_event_rate.15m" => "%{[events][rate_15m]}"
      }
    }
  }
}

elastic / logstash

Logstash pipeline can't be stopped after upgrading #5933