Sonar stops working every few days: jdbc connection error - java

I have a Sonar server which is used once a day from maven/jenkins and every few days, say every 4 or 5 days, it crashes and and shows the message "We're sorry, but something went wrong".
In the log, the error is always about a jdbc connection problem. I thought that it was a problem with the database but then if I restart the sonar server everything goes fine again.
So, it looks like a memory leak or something in the sonar server that makes it crash every few days until someone restarts it. Does that makes sense?. This is the configuration I have:
sonar.jdbc.username: xxxx
sonar.jdbc.password: xxxx
sonar.jdbc.url: jdbc:mysql://x.x.x.x:3306/sonar?useUnicode=true&characterEncoding=utf8&rewriteBatchedStatements=true
#----- Connection pool settings
sonar.jdbc.maxActive: 20
sonar.jdbc.maxIdle: 5
sonar.jdbc.minIdle: 2
sonar.jdbc.maxWait: 5000
sonar.jdbc.minEvictableIdleTimeMillis: 600000
sonar.jdbc.timeBetweenEvictionRunsMillis: 30000
sonar.updatecenter.activate=true
http.proxyHost=xxxx
http.proxyPort=3128
sonar.notifications.delay=60
That's it. And this is the error log:
INFO o.s.s.p.ServerImpl SonarQube Server / 3.7.3 /
INFO o.s.c.p.Database Create JDBC datasource for jdbc:mysql://x.x.x.x:3306/sonar?useUnicode=true&characterEncoding=utf8&rewriteBatchedStatements=true
ERROR o.s.c.p.Database Can not connect to database.
Please check connectivity and settings (see the properties prefixed by 'sonar.jdbc.').
org.apache.commons.dbcp.SQLNestedException:
Cannot create PoolableConnectionFactory (Communications link failure
The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)
.
.
.
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException:
Communications link failure
The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
.
.
.
Caused by: java.net.ConnectException: Connection refused
.
.
.
INFO jruby.rack An exception happened during JRuby-Rack startup
no connection available
--- System
jruby 1.6.8 (ruby-1.8.7-p357) (2012-09-18 1772b40) (Java HotSpot(TM) 64-Bit Server VM 1.6.0_43) [linux-amd64-java]
Time: Thu Jan 02 08:04:08 -0500 2014
Server: jetty/7.6.11.v20130520
jruby.home: file:/opt/sonar/war/sonar-server/WEB-INF/lib/jruby-complete-1.6.8.jar!/META-INF/jruby.home
--- Context Init Parameters:
jruby.compat.version = 1.8
jruby.max.runtimes = 1
jruby.min.runtimes = 1
jruby.rack.logging = slf4j
public.root = /
rails.env = production
--- Backtrace
ActiveRecord::ConnectionNotEstablished: no connection available
set_native_database_types at arjdbc/jdbc/RubyJdbcConnection.java:517
initialize at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-jdbc-adapter-1.1.3/lib/arjdbc/jdbc/connection.rb:61
initialize at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-jdbc-adapter-1.1.3/lib/arjdbc/jdbc/adapter.rb:31
jdbc_connection at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-jdbc-adapter-1.1.3/lib/arjdbc/jdbc/connection_methods.rb:6
send at org/jruby/RubyKernel.java:2109
new_connection at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_pool.rb:223
checkout_new_connection at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_pool.rb:245
checkout at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_pool.rb:188
loop at org/jruby/RubyKernel.java:1439
checkout at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_pool.rb:184
mon_synchronize at file:/opt/sonar/war/sonar-server/WEB-INF/lib/jruby-complete-1.6.8.jar!/META-INF/jruby.home/lib/ruby/1.8/monitor.rb:191
checkout at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_pool.rb:183
connection at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_pool.rb:98
retrieve_connection at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_pool.rb:326
retrieve_connection at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_specification.rb:123
connection at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/connection_adapters/abstract/connection_specification.rb:115
initialize at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/migration.rb:440
up at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/migration.rb:401
migrate at /opt/sonar/war/sonar-server/WEB-INF/gems/gems/activerecord-2.3.15/lib/active_record/migration.rb:383
upgrade_and_start at /opt/sonar/war/sonar-server/WEB-INF/lib/database_version.rb:62
automatic_setup at /opt/sonar/war/sonar-server/WEB-INF/lib/database_version.rb:74
(root) at /opt/sonar/war/sonar-server/WEB-INF/config/environment.rb:213
load at org/jruby/RubyKernel.java:1087
load_environment at /opt/sonar/war/sonar-server/WEB-INF/config/environment.rb:23
load_environment at file:/opt/sonar/war/sonar-server/WEB-INF/lib/jruby-rack-1.1.10.jar!/jruby/rack/rails_booter.rb:65
(root) at <script>:1
--- RubyGems
Gem.dir: /opt/sonar/war/sonar-server/WEB-INF/gems
Gem.path:
/opt/sonar/war/sonar-server/WEB-INF/gems
Activated gems:
rake-0.9.2.2
activesupport-2.3.15
activerecord-2.3.15
rack-1.1.3
actionpack-2.3.15
actionmailer-2.3.15
activeresource-2.3.15
rails-2.3.15
color-tools-1.3.0
i18n-0.4.2
json-jruby-1.2.3-universal-java-1.6
activerecord-jdbc-adapter-1.1.3
fastercsv-1.4.0
--- Bundler
undefined method `bundle_path' for Bundler:Module
--- JRuby-Rack Config
compat_version = RUBY1_8
default_logger = org.jruby.rack.logging.StandardOutLogger#4fbbe4e1
err = java.io.PrintStream#d2284af
filter_adds_html = true
filter_verifies_resource = false
ignore_environment = false
initial_memory_buffer_size =
initial_runtimes = 1
jms_connection_factory =
jms_jndi_properties =
logger = org.jruby.rack.logging.Slf4jLogger#566dc8f0
logger_class_name = slf4j
logger_name = jruby.rack
maximum_memory_buffer_size =
maximum_runtimes = 1
num_initializer_threads =
out = java.io.PrintStream#6aeeefcf
rackup =
rackup_path =
rewindable = true
runtime_arguments =
runtime_timeout_seconds =
serial_initialization = false
servlet_context = ServletContext#o.e.j.w.WebAppContext{/,file:/opt/sonar/war/sonar-server/},file:/opt/sonar/war/sonar-server
ERROR jruby.rack unable to create shared application instance
org.jruby.rack.RackInitializationException: no connection available
.
.
.
org.jruby.exceptions.RaiseException:
(ConnectionNotEstablished) no connection available
.
.
.
ERROR jruby.rack Error: application initialization failed
org.jruby.rack.RackInitializationException: no connection available
.
.
.
org.jruby.exceptions.RaiseException:
(ConnectionNotEstablished) no connection available
Any help will be appreciated :)

This sounds familiar to me :P Try asking your operators if they have some automated 'cleansing' operation that just kills periodically open database connections automatically in order to prevent leaked connections to the database.

It happened to me, in a Windows 2012 Server and SQL Server 2012 database in a different server. It seems that sonar service maintains a connection open, created at start up time, so any disconnection (networking, database restart, etc.) causes this unrecoverable connection problem. Restarting the Sonar (SonarQube) Windows service solved the problem to me. But, if this problem is frequent, as in your case, it would be a good idea to schedule a service restart task, or find out what is taking the connection down.

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[#|2011-02-24T12:59:03.046+0330|INFO|glassfish3.0.1|javax.enterprise.system.tool
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ontainer.web.com.sun.web.security|_ThreadID=25;_ThreadName=http-thread-pool-4848
-(2);|Web login failed: Login failed: javax.security.auth.login.LoginException:
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[#|2011-02-24T12:59:10.843+0330|WARNING|glassfish3.0.1|org.apache.catalina.conne
ctor.Request|_ThreadID=25;_ThreadName=http-thread-pool-4848-(2);|PWC4011: Unable
to set request character encoding to UTF-8 from context , because request param
eters have already been read, or ServletRequest.getReader() has already been cal
led|#]
[#|2011-02-24T12:59:16.093+0330|INFO|glassfish3.0.1|org.glassfish.admingui|_Thre
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tes()|#]
[#|2011-02-24T12:59:37.578+0330|INFO|glassfish3.0.1|javax.enterprise.system.std.
com.sun.enterprise.v3.services.impl|_ThreadID=25;_ThreadName=http-thread-pool-48
48-(2);|Cannot refresh Catalog : Connection timed out: connect|#]
[#|2011-02-24T13:08:09.015+0330|INFO|glassfish3.0.1|org.glassfish.admingui|_Thre
adID=28;_ThreadName=http-thread-pool-4848-(1);|admin console: initSessionAttribu
tes()|#]
[#|2011-02-24T13:08:30.125+0330|INFO|glassfish3.0.1|javax.enterprise.system.std.
com.sun.enterprise.v3.services.impl|_ThreadID=28;_ThreadName=http-thread-pool-48
48-(1);|Cannot refresh Catalog : Connection timed out: connect|#]
[#|2011-02-24T13:14:16.546+0330|WARNING|glassfish3.0.1|com.sun.grizzly.config.Gr
izzlyServiceListener|_ThreadID=17;_ThreadName=Thread-13;|Interrupting idle Threa
d: http-thread-pool-4848-(2)|#]
It seems that Glassfish has a lot of trouble recently caused by the new version 3.1. The admin console tries to look for new updates at start-up. If the update server will not respond in a certain time, the update count fails or take a long time.
You could first try to choose a different update server with glassfishs update tool. You will find it in glassfish/bin folder.
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