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  1. Attempting to load properties file in current directory: openmrs-standalone-runtime.properties
  2. Using runtime properties file: openmrs-standalone-runtime.properties
  3. Mar 11, 2013 7:30:56 AM org.apache.catalina.startup.Embedded start
  4. INFO: Starting tomcat server
  5. Mar 11, 2013 7:30:57 AM org.apache.catalina.core.StandardEngine start
  6. INFO: Starting Servlet Engine: Apache Tomcat/6.0.26
  7. [/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld][--no-defaults][--port=3316][--collation-server=utf8_general_ci][--max_allowed_packet=96M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database][--datadir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data][--pid-file=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid]
  8. [MysqldResource] launching mysqld (driver_launched_mysqld_1)
  9. Exception in thread "driver_launched_mysqld_1" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  10. at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
  11. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
  12. at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
  13. at com.mysql.management.util.Shell$Default.run(Shell.java:140)
  14. at java.lang.Thread.run(Thread.java:662)
  15. Caused by: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  16. at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
  17. at java.lang.Runtime.exec(Runtime.java:593)
  18. at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
  19. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
  20. ... 3 more
  21. Caused by: java.io.IOException: java.io.IOException: error=13, Permission denied
  22. at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
  23. at java.lang.ProcessImpl.start(ProcessImpl.java:65)
  24. at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
  25. ... 6 more
  26. [MysqldResource]
  27. [MysqldResource] mysqld pid-file not found: /media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid
  28. SQL: null
  29. ErrorCode: 0
  30. com.mysql.management.util.SQLRuntimeException: User initialization error. Can not connect as openmrs with password. Can not connect as root without password. URL: jdbc:mysql://127.0.0.1:3316/mysql
  31. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:70)
  32. at com.mysql.management.MysqldResource.start(MysqldResource.java:223)
  33. at com.mysql.management.MysqldResource.start(MysqldResource.java:168)
  34. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.ensureMysqlStarted(ServerLauncherSocketFactory.java:145)
  35. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.connect(ServerLauncherSocketFactory.java:72)
  36. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  37. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2288)
  38. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  39. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  40. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  41. at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
  42. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  43. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  44. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  45. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  46. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  47. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  48. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  49. at org.openmrs.util.DatabaseUpdater.getConnection(DatabaseUpdater.java:424)
  50. at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:362)
  51. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:614)
  52. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:587)
  53. at org.openmrs.util.DatabaseUpdater.updatesRequired(DatabaseUpdater.java:259)
  54. at org.openmrs.web.Listener.setupNeeded(Listener.java:170)
  55. at org.openmrs.web.Listener.contextInitialized(Listener.java:142)
  56. at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3972)
  57. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4467)
  58. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  59. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  60. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  61. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
  62. at org.apache.catalina.startup.Embedded.start(Embedded.java:825)
  63. at org.openmrs.standalone.TomcatManager.run(TomcatManager.java:73)
  64. at org.openmrs.standalone.ApplicationController.startServer(ApplicationController.java:381)
  65. at org.openmrs.standalone.ApplicationController.access$000(ApplicationController.java:29)
  66. at org.openmrs.standalone.ApplicationController$1.construct(ApplicationController.java:128)
  67. at org.openmrs.standalone.SwingWorker$2.run(SwingWorker.java:125)
  68. at java.lang.Thread.run(Thread.java:662)
  69. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  70.  
  71. The last packet successfully received from the server was 1,362,976,707,710 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  72. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  73. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  74. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  75. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  76. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  77. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
  78. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  79. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  80. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  81. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  82. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  83. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  84. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  85. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  86. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  87. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  88. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:64)
  89. ... 37 more
  90. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  91.  
  92. The last packet successfully received from the server was 1,362,976,707,710 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  93. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  94. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  95. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  96. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  97. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  98. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
  99. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
  100. ... 48 more
  101. Caused by: java.net.ConnectException: Connection refused
  102. at java.net.PlainSocketImpl.socketConnect(Native Method)
  103. at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
  104. at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
  105. at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
  106. at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
  107. at java.net.Socket.connect(Socket.java:529)
  108. at java.net.Socket.connect(Socket.java:478)
  109. at java.net.Socket.<init>(Socket.java:375)
  110. at java.net.Socket.<init>(Socket.java:218)
  111. at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
  112. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  113. ... 49 more
  114. [/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld][--no-defaults][--port=3316][--collation-server=utf8_general_ci][--max_allowed_packet=96M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database][--datadir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data][--pid-file=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid]
  115. [MysqldResource] launching mysqld (driver_launched_mysqld_2)
  116. Exception in thread "driver_launched_mysqld_2" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  117. at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
  118. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
  119. at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
  120. at com.mysql.management.util.Shell$Default.run(Shell.java:140)
  121. at java.lang.Thread.run(Thread.java:662)
  122. Caused by: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  123. at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
  124. at java.lang.Runtime.exec(Runtime.java:593)
  125. at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
  126. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
  127. ... 3 more
  128. Caused by: java.io.IOException: java.io.IOException: error=13, Permission denied
  129. at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
  130. at java.lang.ProcessImpl.start(ProcessImpl.java:65)
  131. at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
  132. ... 6 more
  133. [MysqldResource]
  134. [MysqldResource] mysqld pid-file not found: /media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid
  135. SQL: null
  136. ErrorCode: 0
  137. com.mysql.management.util.SQLRuntimeException: User initialization error. Can not connect as openmrs with password. Can not connect as root without password. URL: jdbc:mysql://127.0.0.1:3316/mysql
  138. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:70)
  139. at com.mysql.management.MysqldResource.start(MysqldResource.java:223)
  140. at com.mysql.management.MysqldResource.start(MysqldResource.java:168)
  141. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.ensureMysqlStarted(ServerLauncherSocketFactory.java:145)
  142. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.connect(ServerLauncherSocketFactory.java:72)
  143. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  144. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2288)
  145. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  146. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  147. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  148. at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
  149. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  150. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  151. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  152. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  153. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  154. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  155. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  156. at org.openmrs.util.DatabaseUpdater.getConnection(DatabaseUpdater.java:424)
  157. at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:362)
  158. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:614)
  159. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:587)
  160. at org.openmrs.util.DatabaseUpdater.updatesRequired(DatabaseUpdater.java:259)
  161. at org.openmrs.web.Listener.setupNeeded(Listener.java:170)
  162. at org.openmrs.web.Listener.contextInitialized(Listener.java:142)
  163. at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3972)
  164. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4467)
  165. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  166. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  167. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  168. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
  169. at org.apache.catalina.startup.Embedded.start(Embedded.java:825)
  170. at org.openmrs.standalone.TomcatManager.run(TomcatManager.java:73)
  171. at org.openmrs.standalone.ApplicationController.startServer(ApplicationController.java:381)
  172. at org.openmrs.standalone.ApplicationController.access$000(ApplicationController.java:29)
  173. at org.openmrs.standalone.ApplicationController$1.construct(ApplicationController.java:128)
  174. at org.openmrs.standalone.SwingWorker$2.run(SwingWorker.java:125)
  175. at java.lang.Thread.run(Thread.java:662)
  176. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  177.  
  178. The last packet successfully received from the server was 1,362,977,131,667 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  179. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  180. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  181. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  182. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  183. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  184. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
  185. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  186. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  187. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  188. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  189. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  190. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  191. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  192. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  193. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  194. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  195. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:64)
  196. ... 37 more
  197. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  198.  
  199. The last packet successfully received from the server was 1,362,977,131,666 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  200. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  201. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  202. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  203. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  204. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  205. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
  206. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
  207. ... 48 more
  208. Caused by: java.net.ConnectException: Connection refused
  209. at java.net.PlainSocketImpl.socketConnect(Native Method)
  210. at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
  211. at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
  212. at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
  213. at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
  214. at java.net.Socket.connect(Socket.java:529)
  215. at java.net.Socket.connect(Socket.java:478)
  216. at java.net.Socket.<init>(Socket.java:375)
  217. at java.net.Socket.<init>(Socket.java:218)
  218. at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
  219. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  220. ... 49 more
  221. [/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld][--no-defaults][--port=3316][--collation-server=utf8_general_ci][--max_allowed_packet=96M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database][--datadir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data][--pid-file=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid]
  222. [MysqldResource] launching mysqld (driver_launched_mysqld_3)
  223. Exception in thread "driver_launched_mysqld_3" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  224. at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
  225. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
  226. at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
  227. at com.mysql.management.util.Shell$Default.run(Shell.java:140)
  228. at java.lang.Thread.run(Thread.java:662)
  229. Caused by: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  230. at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
  231. at java.lang.Runtime.exec(Runtime.java:593)
  232. at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
  233. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
  234. ... 3 more
  235. Caused by: java.io.IOException: java.io.IOException: error=13, Permission denied
  236. at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
  237. at java.lang.ProcessImpl.start(ProcessImpl.java:65)
  238. at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
  239. ... 6 more
  240. [MysqldResource]
  241. [MysqldResource] mysqld pid-file not found: /media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid
  242. SQL: null
  243. ErrorCode: 0
  244. com.mysql.management.util.SQLRuntimeException: User initialization error. Can not connect as openmrs with password. Can not connect as root without password. URL: jdbc:mysql://127.0.0.1:3316/mysql
  245. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:70)
  246. at com.mysql.management.MysqldResource.start(MysqldResource.java:223)
  247. at com.mysql.management.MysqldResource.start(MysqldResource.java:168)
  248. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.ensureMysqlStarted(ServerLauncherSocketFactory.java:145)
  249. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.connect(ServerLauncherSocketFactory.java:72)
  250. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  251. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2288)
  252. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  253. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  254. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  255. at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
  256. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  257. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  258. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  259. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  260. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  261. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  262. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  263. at org.openmrs.util.DatabaseUpdater.getConnection(DatabaseUpdater.java:424)
  264. at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:362)
  265. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:614)
  266. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:587)
  267. at org.openmrs.util.DatabaseUpdater.updatesRequired(DatabaseUpdater.java:259)
  268. at org.openmrs.web.Listener.setupNeeded(Listener.java:170)
  269. at org.openmrs.web.Listener.contextInitialized(Listener.java:142)
  270. at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3972)
  271. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4467)
  272. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  273. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  274. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  275. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
  276. at org.apache.catalina.startup.Embedded.start(Embedded.java:825)
  277. at org.openmrs.standalone.TomcatManager.run(TomcatManager.java:73)
  278. at org.openmrs.standalone.ApplicationController.startServer(ApplicationController.java:381)
  279. at org.openmrs.standalone.ApplicationController.access$000(ApplicationController.java:29)
  280. at org.openmrs.standalone.ApplicationController$1.construct(ApplicationController.java:128)
  281. at org.openmrs.standalone.SwingWorker$2.run(SwingWorker.java:125)
  282. at java.lang.Thread.run(Thread.java:662)
  283. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  284.  
  285. The last packet successfully received from the server was 1,362,977,557,443 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  286. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  287. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  288. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  289. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  290. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  291. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
  292. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  293. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  294. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  295. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  296. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  297. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  298. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  299. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  300. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  301. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  302. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:64)
  303. ... 37 more
  304. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  305.  
  306. The last packet successfully received from the server was 1,362,977,557,443 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  307. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  308. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  309. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  310. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  311. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  312. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
  313. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
  314. ... 48 more
  315. Caused by: java.net.ConnectException: Connection refused
  316. at java.net.PlainSocketImpl.socketConnect(Native Method)
  317. at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
  318. at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
  319. at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
  320. at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
  321. at java.net.Socket.connect(Socket.java:529)
  322. at java.net.Socket.connect(Socket.java:478)
  323. at java.net.Socket.<init>(Socket.java:375)
  324. at java.net.Socket.<init>(Socket.java:218)
  325. at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
  326. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  327. ... 49 more
  328. ERROR - Listener.contextInitialized(154) |2013-03-11 07:52:39,946| Got exception while starting up:
  329. java.lang.RuntimeException: Error occurred while trying to get the updates needed for the database. Unable to get a connection to the database. Please check your openmrs runtime properties file and make sure you have the correct connection.username and connection.password set
  330. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:628)
  331. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:587)
  332. at org.openmrs.util.DatabaseUpdater.updatesRequired(DatabaseUpdater.java:259)
  333. at org.openmrs.web.Listener.setupNeeded(Listener.java:170)
  334. at org.openmrs.web.Listener.contextInitialized(Listener.java:142)
  335. at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3972)
  336. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4467)
  337. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  338. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  339. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  340. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
  341. at org.apache.catalina.startup.Embedded.start(Embedded.java:825)
  342. at org.openmrs.standalone.TomcatManager.run(TomcatManager.java:73)
  343. at org.openmrs.standalone.ApplicationController.startServer(ApplicationController.java:381)
  344. at org.openmrs.standalone.ApplicationController.access$000(ApplicationController.java:29)
  345. at org.openmrs.standalone.ApplicationController$1.construct(ApplicationController.java:128)
  346. at org.openmrs.standalone.SwingWorker$2.run(SwingWorker.java:125)
  347. at java.lang.Thread.run(Thread.java:662)
  348. Caused by: java.lang.Exception: Unable to get a connection to the database. Please check your openmrs runtime properties file and make sure you have the correct connection.username and connection.password set
  349. at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:365)
  350. at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:614)
  351. ... 17 more
  352. Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
  353. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  354. at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
  355. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  356. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  357. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  358. at com.mysql.jdbc.Util.getInstance(Util.java:381)
  359. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:984)
  360. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
  361. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926)
  362. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2364)
  363. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  364. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  365. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  366. at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
  367. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  368. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  369. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  370. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  371. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  372. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  373. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  374. at org.openmrs.util.DatabaseUpdater.getConnection(DatabaseUpdater.java:424)
  375. at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:362)
  376. ... 18 more
  377. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  378.  
  379. The last packet successfully received from the server was 1,362,977,557,925 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  380. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  381. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  382. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  383. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  384. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  385. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
  386. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2288)
  387. ... 31 more
  388. Caused by: java.net.ConnectException: Connection refused
  389. at java.net.PlainSocketImpl.socketConnect(Native Method)
  390. at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
  391. at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
  392. at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
  393. at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
  394. at java.net.Socket.connect(Socket.java:529)
  395. at java.net.Socket.connect(Socket.java:478)
  396. at java.net.Socket.<init>(Socket.java:375)
  397. at java.net.Socket.<init>(Socket.java:218)
  398. at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
  399. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.connect(ServerLauncherSocketFactory.java:74)
  400. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  401. ... 32 more
  402. [/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld][--no-defaults][--port=3316][--collation-server=utf8_general_ci][--max_allowed_packet=96M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database][--datadir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data][--pid-file=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid]
  403. [MysqldResource] launching mysqld (driver_launched_mysqld_4)
  404. Exception in thread "driver_launched_mysqld_4" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  405. at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
  406. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
  407. at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
  408. at com.mysql.management.util.Shell$Default.run(Shell.java:140)
  409. at java.lang.Thread.run(Thread.java:662)
  410. Caused by: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  411. at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
  412. at java.lang.Runtime.exec(Runtime.java:593)
  413. at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
  414. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
  415. ... 3 more
  416. Caused by: java.io.IOException: java.io.IOException: error=13, Permission denied
  417. at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
  418. at java.lang.ProcessImpl.start(ProcessImpl.java:65)
  419. at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
  420. ... 6 more
  421. [MysqldResource]
  422. [MysqldResource] mysqld pid-file not found: /media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid
  423. SQL: null
  424. ErrorCode: 0
  425. com.mysql.management.util.SQLRuntimeException: User initialization error. Can not connect as openmrs with password. Can not connect as root without password. URL: jdbc:mysql://127.0.0.1:3316/mysql
  426. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:70)
  427. at com.mysql.management.MysqldResource.start(MysqldResource.java:223)
  428. at com.mysql.management.MysqldResource.start(MysqldResource.java:168)
  429. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.ensureMysqlStarted(ServerLauncherSocketFactory.java:145)
  430. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.connect(ServerLauncherSocketFactory.java:72)
  431. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  432. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2288)
  433. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  434. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  435. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  436. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  437. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  438. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  439. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  440. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  441. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  442. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  443. at org.openmrs.web.filter.initialization.InitializationFilter.isDatabaseEmpty(InitializationFilter.java:1711)
  444. at org.openmrs.web.filter.initialization.InitializationFilter.init(InitializationFilter.java:1006)
  445. at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:295)
  446. at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:422)
  447. at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:115)
  448. at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:3838)
  449. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4488)
  450. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  451. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  452. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  453. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
  454. at org.apache.catalina.startup.Embedded.start(Embedded.java:825)
  455. at org.openmrs.standalone.TomcatManager.run(TomcatManager.java:73)
  456. at org.openmrs.standalone.ApplicationController.startServer(ApplicationController.java:381)
  457. at org.openmrs.standalone.ApplicationController.access$000(ApplicationController.java:29)
  458. at org.openmrs.standalone.ApplicationController$1.construct(ApplicationController.java:128)
  459. at org.openmrs.standalone.SwingWorker$2.run(SwingWorker.java:125)
  460. at java.lang.Thread.run(Thread.java:662)
  461. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  462.  
  463. The last packet successfully received from the server was 1,362,977,984,549 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  464. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  465. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  466. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  467. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  468. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  469. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
  470. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  471. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  472. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  473. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  474. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  475. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  476. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  477. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  478. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  479. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  480. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:64)
  481. ... 34 more
  482. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  483.  
  484. The last packet successfully received from the server was 1,362,977,984,549 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  485. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  486. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  487. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  488. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  489. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  490. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
  491. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
  492. ... 45 more
  493. Caused by: java.net.ConnectException: Connection refused
  494. at java.net.PlainSocketImpl.socketConnect(Native Method)
  495. at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
  496. at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
  497. at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
  498. at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
  499. at java.net.Socket.connect(Socket.java:529)
  500. at java.net.Socket.connect(Socket.java:478)
  501. at java.net.Socket.<init>(Socket.java:375)
  502. at java.net.Socket.<init>(Socket.java:218)
  503. at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
  504. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  505. ... 46 more
  506. [/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld][--no-defaults][--port=3316][--collation-server=utf8_general_ci][--max_allowed_packet=96M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database][--datadir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data][--pid-file=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid]
  507. [MysqldResource] launching mysqld (driver_launched_mysqld_5)
  508. Exception in thread "driver_launched_mysqld_5" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  509. at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
  510. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
  511. at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
  512. at com.mysql.management.util.Shell$Default.run(Shell.java:140)
  513. at java.lang.Thread.run(Thread.java:662)
  514. Caused by: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  515. at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
  516. at java.lang.Runtime.exec(Runtime.java:593)
  517. at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
  518. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
  519. ... 3 more
  520. Caused by: java.io.IOException: java.io.IOException: error=13, Permission denied
  521. at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
  522. at java.lang.ProcessImpl.start(ProcessImpl.java:65)
  523. at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
  524. ... 6 more
  525. [MysqldResource]
  526. [MysqldResource] mysqld pid-file not found: /media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid
  527. SQL: null
  528. ErrorCode: 0
  529. com.mysql.management.util.SQLRuntimeException: User initialization error. Can not connect as openmrs with password. Can not connect as root without password. URL: jdbc:mysql://127.0.0.1:3316/mysql
  530. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:70)
  531. at com.mysql.management.MysqldResource.start(MysqldResource.java:223)
  532. at com.mysql.management.MysqldResource.start(MysqldResource.java:168)
  533. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.ensureMysqlStarted(ServerLauncherSocketFactory.java:145)
  534. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.connect(ServerLauncherSocketFactory.java:72)
  535. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  536. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2288)
  537. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  538. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  539. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  540. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  541. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  542. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  543. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  544. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  545. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  546. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  547. at org.openmrs.web.filter.initialization.InitializationFilter.isDatabaseEmpty(InitializationFilter.java:1711)
  548. at org.openmrs.web.filter.initialization.InitializationFilter.init(InitializationFilter.java:1006)
  549. at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:295)
  550. at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:422)
  551. at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:115)
  552. at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:3838)
  553. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4488)
  554. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  555. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  556. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  557. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
  558. at org.apache.catalina.startup.Embedded.start(Embedded.java:825)
  559. at org.openmrs.standalone.TomcatManager.run(TomcatManager.java:73)
  560. at org.openmrs.standalone.ApplicationController.startServer(ApplicationController.java:381)
  561. at org.openmrs.standalone.ApplicationController.access$000(ApplicationController.java:29)
  562. at org.openmrs.standalone.ApplicationController$1.construct(ApplicationController.java:128)
  563. at org.openmrs.standalone.SwingWorker$2.run(SwingWorker.java:125)
  564. at java.lang.Thread.run(Thread.java:662)
  565. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  566.  
  567. The last packet successfully received from the server was 1,362,978,408,950 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  568. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  569. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  570. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  571. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  572. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  573. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
  574. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  575. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  576. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  577. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  578. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  579. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  580. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  581. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  582. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  583. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  584. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:64)
  585. ... 34 more
  586. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  587.  
  588. The last packet successfully received from the server was 1,362,978,408,950 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  589. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  590. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  591. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  592. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  593. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  594. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
  595. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
  596. ... 45 more
  597. Caused by: java.net.ConnectException: Connection refused
  598. at java.net.PlainSocketImpl.socketConnect(Native Method)
  599. at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
  600. at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
  601. at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
  602. at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
  603. at java.net.Socket.connect(Socket.java:529)
  604. at java.net.Socket.connect(Socket.java:478)
  605. at java.net.Socket.<init>(Socket.java:375)
  606. at java.net.Socket.<init>(Socket.java:218)
  607. at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
  608. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  609. ... 46 more
  610. [/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld][--no-defaults][--port=3316][--collation-server=utf8_general_ci][--max_allowed_packet=96M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database][--datadir=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data][--pid-file=/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid]
  611. [MysqldResource] launching mysqld (driver_launched_mysqld_6)
  612. Exception in thread "driver_launched_mysqld_6" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  613. at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
  614. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
  615. at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
  616. at com.mysql.management.util.Shell$Default.run(Shell.java:140)
  617. at java.lang.Thread.run(Thread.java:662)
  618. Caused by: java.io.IOException: Cannot run program "/media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/bin/mysqld": java.io.IOException: error=13, Permission denied
  619. at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
  620. at java.lang.Runtime.exec(Runtime.java:593)
  621. at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
  622. at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
  623. ... 3 more
  624. Caused by: java.io.IOException: java.io.IOException: error=13, Permission denied
  625. at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
  626. at java.lang.ProcessImpl.start(ProcessImpl.java:65)
  627. at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
  628. ... 6 more
  629. [MysqldResource]
  630. [MysqldResource] mysqld pid-file not found: /media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid
  631. SQL: null
  632. ErrorCode: 0
  633. com.mysql.management.util.SQLRuntimeException: User initialization error. Can not connect as openmrs with password. Can not connect as root without password. URL: jdbc:mysql://127.0.0.1:3316/mysql
  634. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:70)
  635. at com.mysql.management.MysqldResource.start(MysqldResource.java:223)
  636. at com.mysql.management.MysqldResource.start(MysqldResource.java:168)
  637. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.ensureMysqlStarted(ServerLauncherSocketFactory.java:145)
  638. at com.mysql.management.driverlaunched.ServerLauncherSocketFactory.connect(ServerLauncherSocketFactory.java:72)
  639. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  640. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2288)
  641. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  642. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  643. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  644. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  645. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  646. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  647. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  648. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  649. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  650. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  651. at org.openmrs.web.filter.initialization.InitializationFilter.isDatabaseEmpty(InitializationFilter.java:1711)
  652. at org.openmrs.web.filter.initialization.InitializationFilter.init(InitializationFilter.java:1006)
  653. at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:295)
  654. at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:422)
  655. at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:115)
  656. at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:3838)
  657. at org.apache.catalina.core.StandardContext.start(StandardContext.java:4488)
  658. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  659. at org.apache.catalina.core.StandardHost.start(StandardHost.java:785)
  660. at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
  661. at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
  662. at org.apache.catalina.startup.Embedded.start(Embedded.java:825)
  663. at org.openmrs.standalone.TomcatManager.run(TomcatManager.java:73)
  664. at org.openmrs.standalone.ApplicationController.startServer(ApplicationController.java:381)
  665. at org.openmrs.standalone.ApplicationController.access$000(ApplicationController.java:29)
  666. at org.openmrs.standalone.ApplicationController$1.construct(ApplicationController.java:128)
  667. at org.openmrs.standalone.SwingWorker$2.run(SwingWorker.java:125)
  668. at java.lang.Thread.run(Thread.java:662)
  669. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  670.  
  671. The last packet successfully received from the server was 1,362,978,834,752 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  672. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  673. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  674. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  675. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  676. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  677. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
  678. at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:773)
  679. at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
  680. at sun.reflect.GeneratedConstructorAccessor9.newInstance(Unknown Source)
  681. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  682. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  683. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  684. at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
  685. at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
  686. at java.sql.DriverManager.getConnection(DriverManager.java:582)
  687. at java.sql.DriverManager.getConnection(DriverManager.java:185)
  688. at com.mysql.management.util.InitializeUser.initializeUser(InitializeUser.java:64)
  689. ... 34 more
  690. Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
  691.  
  692. The last packet successfully received from the server was 1,362,978,834,752 milliseconds ago. The last packet sent successfully to the server was 0 milliseconds ago.
  693. at sun.reflect.GeneratedConstructorAccessor8.newInstance(Unknown Source)
  694. at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
  695. at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
  696. at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
  697. at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
  698. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:341)
  699. at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
  700. ... 45 more
  701. Caused by: java.net.ConnectException: Connection refused
  702. at java.net.PlainSocketImpl.socketConnect(Native Method)
  703. at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)
  704. at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)
  705. at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200)
  706. at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
  707. at java.net.Socket.connect(Socket.java:529)
  708. at java.net.Socket.connect(Socket.java:478)
  709. at java.net.Socket.<init>(Socket.java:375)
  710. at java.net.Socket.<init>(Socket.java:218)
  711. at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:253)
  712. at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:290)
  713. ... 46 more
  714. Mar 11, 2013 8:13:58 AM org.apache.coyote.http11.Http11Protocol init
  715. INFO: Initializing Coyote HTTP/1.1 on http-8081
  716. Mar 11, 2013 8:13:58 AM org.apache.coyote.http11.Http11Protocol start
  717. INFO: Starting Coyote HTTP/1.1 on http-8081
  718. Mar 11, 2013 1:29:43 PM org.apache.coyote.http11.Http11Protocol destroy
  719. INFO: Stopping Coyote HTTP/1.1 on http-8081
  720. [MysqldResource] Mysqld not running. No file: /media/KJoseph/Projects/openMRS/openmrs-standalone-1.9.1/database/data/MysqldResource.pid
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