Upgrade 5.2.3 to 6.0 failing

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Permanently deleted user
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Hi,

I'm trying to upgrade a Youtrack 5.2.3 instance to 6.0 on CentOS with java-1.7 but failing miserably. I followed the usual steps for upgrading with the new jar, modified the wrapper.conf file according to this thread, getting the following error in wrapper.log on start:

STATUS | wrapper  | 2014/10/31 12:22:01 | –> Wrapper Started as Daemon
STATUS | wrapper  | 2014/10/31 12:22:01 | Java Service Wrapper Community Edition 64-bit 3.5.6
STATUS | wrapper  | 2014/10/31 12:22:01 |   Copyright (C) 1999-2010 Tanuki Software, Ltd. All Rights Reserved.
STATUS | wrapper  | 2014/10/31 12:22:01 |     http://wrapper.tanukisoftware.com
STATUS | wrapper  | 2014/10/31 12:22:01 |
STATUS | wrapper  | 2014/10/31 12:22:02 | Launching a JVM...
INFO   | jvm 1    | 2014/10/31 12:22:02 | WrapperManager: Initializing...
INFO   | jvm 1    | 2014/10/31 12:22:03 | Jetty home folder is http://forum.jetbrains.com/var/www/youtrack/.youtrack
INFO   | jvm 1    | 2014/10/31 12:22:03 | log4j:WARN No appenders could be found for logger (jetbrains.youtrack.standalone.MultiAppWebServer).
INFO   | jvm 1    | 2014/10/31 12:22:03 | log4j:WARN Please initialize the log4j system properly.
INFO   | jvm 1    | 2014/10/31 12:22:03 | 2014-10-31 12:22:03.695:INFO:oejs.Server:jetty-8.y.z-SNAPSHOT
INFO   | jvm 1    | 2014/10/31 12:22:03 | 2014-10-31 12:22:03.731:INFO:oejw.WebInfConfiguration:Extract jar:file:/var/www/youtrack/.youtrack/work/jetbrains.jetpass.server.war!/ to /var/www/youtrack/.youtrack/work/jetty-0.0.0.0-8080-jetbrains.jetpass.server.war-_hub-any-/webapp
INFO   | jvm 1    | 2014/10/31 12:22:07 | log4j:WARN No appenders could be found for logger (org.eclipse.jetty.util.log).
INFO   | jvm 1    | 2014/10/31 12:22:07 | log4j:WARN Please initialize the log4j system properly.
INFO   | jvm 1    | 2014/10/31 12:22:07 | Init web application log4j location: jetbrains/jetpass/server/main/log4j.xml
INFO   | jvm 1    | 2014/10/31 12:22:13 | Oct 31, 2014 12:22:13 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO   | jvm 1    | 2014/10/31 12:22:13 | INFO: Initiating Jersey application, version 'Jersey: 1.12 02/15/2012 04:51 PM'
INFO   | jvm 1    | 2014/10/31 12:22:14 | Oct 31, 2014 12:22:14 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO   | jvm 1    | 2014/10/31 12:22:14 | INFO: Initiating Jersey application, version 'Jersey: 1.12 02/15/2012 04:51 PM'
INFO   | jvm 1    | 2014/10/31 12:22:14 | 12:22:14,533 DEBUG [DefaultServicesManagerImpl    ] Adding registered service ^(https?|imaps?)://.*
INFO   | jvm 1    | 2014/10/31 12:22:14 | 12:22:14,535 INFO  [DefaultServicesManagerImpl    ] Loaded 1 services.
INFO   | jvm 1    | 2014/10/31 12:22:18 | gflogger:  version 20131206
INFO   | jvm 1    | 2014/10/31 12:22:20 | 2014-10-31 12:22:20.502:INFO:oejw.WebInfConfiguration:Extract jar:file:/var/www/youtrack/standalone/youtrack-6.0.12102.jar!/ to /var/www/youtrack/.youtrack/work/jetty-0.0.0.0-8080-youtrack-6.0.12102.jar–any-/webapp
INFO   | jvm 1    | 2014/10/31 12:22:27 | 2014-10-31 12:22:27.140:INFO:oejs.AbstractConnector:Started DispatchProbeSelectChannelConnector@0.0.0.0:8080
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp:
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error: Encountered an error running main:
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error: java.lang.NullPointerException
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.launchBrowser(YoutrackStandalone.java:104)
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.startServer(YoutrackStandalone.java:74)
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.main(YoutrackStandalone.java:37)
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at java.lang.reflect.Method.invoke(Method.java:606)
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at org.tanukisoftware.wrapper.WrapperSimpleApp.run(WrapperSimpleApp.java:272)
INFO   | jvm 1    | 2014/10/31 12:22:27 | WrapperSimpleApp Error:       at java.lang.Thread.run(Thread.java:745)
INFO   | jvm 1    | 2014/10/31 12:22:28 | 2014-10-31 12:22:28.969:INFO:oejsh.ContextHandler:stopped j.m.w.s.r.{,file:/var/www/youtrack/.youtrack/work/jetty-0.0.0.0-8080-youtrack-6.0.12102.jar–any-/webapp/},/var/www/youtrack/standalone/youtrack-6.0.12102.jar
INFO   | jvm 1    | 2014/10/31 12:22:29 | 2014-10-31 12:22:29.155:INFO:oejsh.ContextHandler:stopped j.m.w.s.r.{/hub,file:/var/www/youtrack/.youtrack/work/jetty-0.0.0.0-8080-jetbrains.jetpass.server.war-_hub-any-/webapp/},/var/www/youtrack/.youtrack/work/jetbrains.jetpass.server.war
STATUS | wrapper  | 2014/10/31 12:22:29 | on_exit trigger matched.  Restarting the JVM.  (Exit code: 1)

From here it just gets stuck in the same loop.

I tried starting it directly from command line, with "java -Xmx1500m -Djava.awt.headless=true -jar youtrack.jar 8080", and it starts. The problem is that it runs of course as a new instance in /root/.youtrack/, not using the existing data.

Any ideas what could be wrong with the upgrade?

Thank you.

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Andrey Tigay
Created
Hello Ovidiu,

Just to be clear, did you download the new wrapper.conf and followed the guide ?

Thank you.
0
Avatar
Permanently deleted user
Created
Hi Andrey,

Thanks for the reply. Well, I used the existing one because the 6.0 docs specified the same version in the second step. Just modified it as per the mentioned thread. I'll give the newest version available a try and see how it goes, I see the latest is 3.5.25 whereas the docs mention 3.5.6.

Cheers!
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Unfortunately there's the same error with the linked wrapper.conf in the guide as well:
STATUS | wrapper  | 2014/11/01 14:36:12 | --> Wrapper Started as Daemon
STATUS | wrapper  | 2014/11/01 14:36:12 | Java Service Wrapper Community Edition 64-bit 3.5.6
STATUS | wrapper  | 2014/11/01 14:36:12 |   Copyright (C) 1999-2010 Tanuki Software, Ltd. All Rights Reserved.
STATUS | wrapper  | 2014/11/01 14:36:12 |     http://wrapper.tanukisoftware.com
STATUS | wrapper  | 2014/11/01 14:36:12 | 
STATUS | wrapper  | 2014/11/01 14:36:13 | Launching a JVM...
INFO   | jvm 1    | 2014/11/01 14:36:13 | WrapperManager: Initializing...
INFO   | jvm 1    | 2014/11/01 14:36:15 | Jetty home folder is [/var/www/youtrack/.youtrack]
INFO   | jvm 1    | 2014/11/01 14:36:20 | log4j:WARN No appenders could be found for logger (jetbrains.youtrack.standalone.MultiAppWebServer).
INFO   | jvm 1    | 2014/11/01 14:36:20 | log4j:WARN Please initialize the log4j system properly.
INFO   | jvm 1    | 2014/11/01 14:36:20 | 2014-11-01 14:36:20.667:INFO:oejs.Server:jetty-8.y.z-SNAPSHOT
INFO   | jvm 1    | 2014/11/01 14:36:20 | 2014-11-01 14:36:20.730:INFO:oejw.WebInfConfiguration:Extract jar:file:/var/www/youtrack/.youtrack/work/jetbrains.jetpass.server.war!/ to /var/www/youtrack/.youtrack/work/jetty-0.0.0.0-8080-jetbrains.jetpass.server.war-_hub-any-/webapp
INFO   | jvm 1    | 2014/11/01 14:36:24 | log4j:WARN No appenders could be found for logger (org.eclipse.jetty.util.log).
INFO   | jvm 1    | 2014/11/01 14:36:24 | log4j:WARN Please initialize the log4j system properly.
INFO   | jvm 1    | 2014/11/01 14:36:24 | Init web application log4j location: jetbrains/jetpass/server/main/log4j.xml
INFO   | jvm 1    | 2014/11/01 14:36:30 | Nov 01, 2014 2:36:30 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO   | jvm 1    | 2014/11/01 14:36:30 | INFO: Initiating Jersey application, version 'Jersey: 1.12 02/15/2012 04:51 PM'
INFO   | jvm 1    | 2014/11/01 14:36:31 | Nov 01, 2014 2:36:31 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO   | jvm 1    | 2014/11/01 14:36:31 | INFO: Initiating Jersey application, version 'Jersey: 1.12 02/15/2012 04:51 PM'
INFO   | jvm 1    | 2014/11/01 14:36:32 | 14:36:32,040 DEBUG [DefaultServicesManagerImpl    ] Adding registered service ^(https?|imaps?)://.*
INFO   | jvm 1    | 2014/11/01 14:36:32 | 14:36:32,042 INFO  [DefaultServicesManagerImpl    ] Loaded 1 services.
INFO   | jvm 1    | 2014/11/01 14:36:37 | gflogger:  version 20131206
INFO   | jvm 1    | 2014/11/01 14:36:39 | 2014-11-01 14:36:39.068:INFO:oejw.WebInfConfiguration:Extract jar:file:/var/www/youtrack/standalone/youtrack-6.0.12102.jar!/ to /var/www/youtrack/.youtrack/work/jetty-0.0.0.0-8080-youtrack-6.0.12102.jar--any-/webapp
INFO   | jvm 1    | 2014/11/01 14:36:49 | 2014-11-01 14:36:49.655:INFO:oejs.AbstractConnector:Started DispatchProbeSelectChannelConnector@0.0.0.0:8080
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp: 
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error: Encountered an error running main:
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error: java.lang.NullPointerException
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at jetbrains.youtrack.standalone.YoutrackStandalone.launchBrowser(YoutrackStandalone.java:104)
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at jetbrains.youtrack.standalone.YoutrackStandalone.startServer(YoutrackStandalone.java:74)
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at jetbrains.youtrack.standalone.YoutrackStandalone.main(YoutrackStandalone.java:37)
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at java.lang.reflect.Method.invoke(Method.java:606)
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at org.tanukisoftware.wrapper.WrapperSimpleApp.run(WrapperSimpleApp.java:272)
INFO   | jvm 1    | 2014/11/01 14:36:49 | WrapperSimpleApp Error:     at java.lang.Thread.run(Thread.java:745)
INFO   | jvm 1    | 2014/11/01 14:36:51 | 2014-11-01 14:36:51.485:INFO:oejsh.ContextHandler:stopped j.m.w.s.r.{,file:/var/www/youtrack/.youtrack/work/jetty-0.0.0.0-8080-youtrack-6.0.12102.jar--any-/webapp/},/var/www/youtrack/standalone/youtrack-6.0.12102.jar
INFO   | jvm 1    | 2014/11/01 14:36:51 | 2014-11-01 14:36:51.671:INFO:oejsh.ContextHandler:stopped j.m.w.s.r.{/hub,file:/var/www/youtrack/.youtrack/work/jetty-0.0.0.0-8080-jetbrains.jetpass.server.war-_hub-any-/webapp/},/var/www/youtrack/.youtrack/work/jetbrains.jetpass.server.war
STATUS | wrapper  | 2014/11/01 14:36:51 | on_exit trigger matched.  Restarting the JVM.  (Exit code: 1)
0
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Permanently deleted user
Created
Hi there, I am getting pretty much the same error. We are running the system with the jar solution. I followed the update instructions, but even updating the wrapper to the newest version did not fix the issue here.

Our java version is currently

JavaVersion
java version "1.8.0_25"
Java(TM) SE Runtime Environment (build 1.8.0_25-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.25-b02, mixed mode)


Also I recognized that the md5checksum on the downloaded file is not the same as on the m5checksum file on your download page:

checksum
On http://download-cf.jetbrains.com/charisma/md5_checksum_6.0.12102.txt ---> jar 17e7579c3d7fe0d8bff0ad094960c337
After downloading --> youtrack-6.0.12124.jar ---> ba09f2f0b20cfb0e9336011a2fea4824


We have a 25 user licence, as additional information. Here the error output from the log file:

LOGFILE wrapper.log
STATUS | wrapper  | 2014/11/01 15:43:17 | Launching a JVM...
INFO   | jvm 1    | 2014/11/01 15:43:17 | Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=128m; support was removed in 8.0
INFO   | jvm 1    | 2014/11/01 15:43:17 | WrapperManager: Initializing...
INFO   | jvm 1    | 2014/11/01 15:43:17 | Jetty home folder is [/root/.youtrack]
INFO   | jvm 1    | 2014/11/01 15:43:18 | log4j:WARN No appenders could be found for logger (jetbrains.youtrack.standalone.MultiAppWebServer).
INFO   | jvm 1    | 2014/11/01 15:43:18 | log4j:WARN Please initialize the log4j system properly.
INFO   | jvm 1    | 2014/11/01 15:43:18 | 2014-11-01 15:43:18.144:INFO:oejs.Server:jetty-8.y.z-SNAPSHOT
INFO   | jvm 1    | 2014/11/01 15:43:18 | 2014-11-01 15:43:18.185:INFO:oejw.WebInfConfiguration:Extract jar:file:/root/.youtrack/work/jetbrains.jetpass.server.war!/ to /root/.youtrack/work/jetty-0.0.0.0-8080-jetbrains.jetpass.server.war-_hub-any-/webapp
INFO   | jvm 1    | 2014/11/01 15:43:20 | log4j:WARN No appenders could be found for logger (org.eclipse.jetty.util.log).
INFO   | jvm 1    | 2014/11/01 15:43:20 | log4j:WARN Please initialize the log4j system properly.
INFO   | jvm 1    | 2014/11/01 15:43:20 | Init web application log4j location: jetbrains/jetpass/server/main/log4j.xml
INFO   | jvm 1    | 2014/11/01 15:43:28 | Nov 01, 2014 3:43:28 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO   | jvm 1    | 2014/11/01 15:43:28 | INFORMATION: Initiating Jersey application, version 'Jersey: 1.12 02/15/2012 04:51 PM'
INFO   | jvm 1    | 2014/11/01 15:43:29 | Nov 01, 2014 3:43:29 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO   | jvm 1    | 2014/11/01 15:43:29 | INFORMATION: Initiating Jersey application, version 'Jersey: 1.12 02/15/2012 04:51 PM'
INFO   | jvm 1    | 2014/11/01 15:43:30 | 15:43:30,438 DEBUG [DefaultServicesManagerImpl    ] Adding registered service ^(https?|imaps?)://.*
INFO   | jvm 1    | 2014/11/01 15:43:30 | 15:43:30,443 INFO  [DefaultServicesManagerImpl    ] Loaded 1 services.
INFO   | jvm 1    | 2014/11/01 15:43:34 | gflogger:  version 20131206
INFO   | jvm 1    | 2014/11/01 15:43:34 | 2014-11-01 15:43:34.755:INFO:oejw.WebInfConfiguration:Extract jar:file:/home/youtrack/standalone/youtrack-6.0.12124.jar!/ to /root/.youtrack/work/jetty-0.0.0.0-8080-youtrack-6.0.12124.jar--any-/webapp
INFO   | jvm 1    | 2014/11/01 15:43:39 | 2014-11-01 15:43:38.949:INFO:oejs.AbstractConnector:Started DispatchProbeSelectChannelConnector@0.0.0.0:8080
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp:
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error: Encountered an error running main:
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error: java.lang.NullPointerException
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.launchBrowser(YoutrackStandalone.java:104)
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.startServer(YoutrackStandalone.java:74)
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.main(YoutrackStandalone.java:37)
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at java.lang.reflect.Method.invoke(Method.java:483)
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at org.tanukisoftware.wrapper.WrapperSimpleApp.run(WrapperSimpleApp.java:290)
INFO   | jvm 1    | 2014/11/01 15:43:39 | WrapperSimpleApp Error:       at java.lang.Thread.run(Thread.java:745)
INFO   | jvm 1    | 2014/11/01 15:43:40 | 2014-11-01 15:43:40.792:INFO:oejsh.ContextHandler:stopped j.m.w.s.r.{,file:/root/.youtrack/work/jetty-0.0.0.0-8080-youtrack-6.0.12124.jar--any-/webapp/},/home/youtrack/standalone/youtrack-6.0.12124.jar
INFO   | jvm 1    | 2014/11/01 15:43:41 | 2014-11-01 15:43:40.935:INFO:oejsh.ContextHandler:stopped j.m.w.s.r.{/hub,file:/root/.youtrack/work/jetty-0.0.0.0-8080-jetbrains.jetpass.server.war-_hub-any-/webapp/},/root/.youtrack/work/jetbrains.jetpass.server.war
STATUS | wrapper  | 2014/11/01 15:43:41 | on_exit trigger matched.  Restarting the JVM.  (Exit code: 1)



Sorry here the one with the correct memory settings

LOGFILE wrapper.log
tail -f logs/wrapper.log
STATUS | wrapper  | 2014/11/01 16:05:47 |   Copyright (C) 1999-2014 Tanuki Software, Ltd. All Rights Reserved.
STATUS | wrapper  | 2014/11/01 16:05:47 |     http://wrapper.tanukisoftware.com
STATUS | wrapper  | 2014/11/01 16:05:47 |
STATUS | wrapper  | 2014/11/01 16:05:48 | Launching a JVM...
INFO   | jvm 1    | 2014/11/01 16:05:48 | WrapperManager: Initializing...
INFO   | jvm 1    | 2014/11/01 16:05:48 | Jetty home folder is [/root/.youtrack]
INFO   | jvm 1    | 2014/11/01 16:05:49 | log4j:WARN No appenders could be found for logger (jetbrains.youtrack.standalone.MultiAppWebServer).
INFO   | jvm 1    | 2014/11/01 16:05:49 | log4j:WARN Please initialize the log4j system properly.
INFO   | jvm 1    | 2014/11/01 16:05:49 | 2014-11-01 16:05:49.169:INFO:oejs.Server:jetty-8.y.z-SNAPSHOT
INFO   | jvm 1    | 2014/11/01 16:05:49 | 2014-11-01 16:05:49.210:INFO:oejw.WebInfConfiguration:Extract jar:file:/root/.youtrack/work/jetbrains.jetpass.server.war!/ to /root/.youtrack/work/jetty-0.0.0.0-8080-jetbrains.jetpass.server.war-_hub-any-/webapp
INFO   | jvm 1    | 2014/11/01 16:05:51 | log4j:WARN No appenders could be found for logger (org.eclipse.jetty.util.log).
INFO   | jvm 1    | 2014/11/01 16:05:51 | log4j:WARN Please initialize the log4j system properly.
INFO   | jvm 1    | 2014/11/01 16:05:51 | Init web application log4j location: jetbrains/jetpass/server/main/log4j.xml
INFO   | jvm 1    | 2014/11/01 16:05:58 | Nov 01, 2014 4:05:58 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO   | jvm 1    | 2014/11/01 16:05:58 | INFORMATION: Initiating Jersey application, version 'Jersey: 1.12 02/15/2012 04:51 PM'
INFO   | jvm 1    | 2014/11/01 16:05:59 | Nov 01, 2014 4:05:59 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO   | jvm 1    | 2014/11/01 16:05:59 | INFORMATION: Initiating Jersey application, version 'Jersey: 1.12 02/15/2012 04:51 PM'
INFO   | jvm 1    | 2014/11/01 16:06:00 | 16:06:00,102 DEBUG [DefaultServicesManagerImpl    ] Adding registered service ^(https?|imaps?)://.*
INFO   | jvm 1    | 2014/11/01 16:06:00 | 16:06:00,109 INFO  [DefaultServicesManagerImpl    ] Loaded 1 services.
INFO   | jvm 1    | 2014/11/01 16:06:03 | gflogger:  version 20131206
INFO   | jvm 1    | 2014/11/01 16:06:04 | 2014-11-01 16:06:03.964:INFO:oejw.WebInfConfiguration:Extract jar:file:/home/youtrack/standalone/youtrack-6.0.12124.jar!/ to /root/.youtrack/work/jetty-0.0.0.0-8080-youtrack-6.0.12124.jar--any-/webapp
INFO   | jvm 1    | 2014/11/01 16:06:09 | 2014-11-01 16:06:09.718:INFO:oejs.AbstractConnector:Started DispatchProbeSelectChannelConnector@0.0.0.0:8080
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp:
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error: Encountered an error running main:
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error: java.lang.NullPointerException
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.launchBrowser(YoutrackStandalone.java:104)
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.startServer(YoutrackStandalone.java:74)
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at jetbrains.youtrack.standalone.YoutrackStandalone.main(YoutrackStandalone.java:37)
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at java.lang.reflect.Method.invoke(Method.java:483)
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at org.tanukisoftware.wrapper.WrapperSimpleApp.run(WrapperSimpleApp.java:290)
INFO   | jvm 1    | 2014/11/01 16:06:09 | WrapperSimpleApp Error:       at java.lang.Thread.run(Thread.java:745)
INFO   | jvm 1    | 2014/11/01 16:06:11 | 2014-11-01 16:06:11.563:INFO:oejsh.ContextHandler:stopped j.m.w.s.r.{,file:/root/.youtrack/work/jetty-0.0.0.0-8080-youtrack-6.0.12124.jar--any-/webapp/},/home/youtrack/standalone/youtrack-6.0.12124.jar
INFO   | jvm 1    | 2014/11/01 16:06:11 | 2014-11-01 16:06:11.720:INFO:oejsh.ContextHandler:stopped j.m.w.s.r.{/hub,file:/root/.youtrack/work/jetty-0.0.0.0-8080-jetbrains.jetpass.server.war-_hub-any-/webapp/},/root/.youtrack/work/jetbrains.jetpass.server.war
STATUS | wrapper  | 2014/11/01 16:06:12 | on_exit trigger matched.  Restarting the JVM.  (Exit code: 1)
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Regarding the md5sum issue, you're comparing two different packages, see the filenames: checksum is for 6.0.12102, youtrack jar is 6.0.12124.
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Well that is what I am saying, that link leads to the download for the md5 checksum, even so the filename of the youtrack build is different. So there might already be a problem with that.
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Alright I will keep a list of what has already been accomplished. Tested to blow away the work folder in the home directory.
Usually helps with the jetty servlet container but in this case not.
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I managed to solve the issue thanks to this thread: http://forum.jetbrains.com/thread/YouTrack-1819

Added 
wrapper.java.additional.17=-Djetbrains.youtrack.disableBrowser=true
to wrapper.conf and it started. wrapper.java.additional.9 parameter was already present in the wrapper.conf file.

Thank you @ghingis!
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Perfect thanks for that. Works fine now.

Would be nice to have that documented, with the current documentation the youtrack is not working at all. Even with an installation from scratch. That does not make such a good impression.
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