can't deploy 2.0.1

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can't deploy 2.0.1

Sofia Robb
Hello,

Is anyone else having troubles deploying the new version of apollo? When I move the war file into my webapp directory and restart tomcat, my tomcat stops working (localhost:8080 won't even load).


ps -ef | grep java
tomcat   15347     1 87 11:37 ?        00:00:24 /usr/lib/jvm/jre/bin/java -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



This is from my catalina.out file

Dec 28, 2015 11:29:58 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Dec 28, 2015 11:30:43 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 432 ms
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks,
Sofia




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Re: can't deploy 2.0.1

nathandunn

A few questions:

0 - try refreshing your browser cache or with a browser you don’t usually use.  shift-reload or use an incognito window
1 - what do you see in the console (JS) log (and on-screen) if you go to http://localhost:8080/apollo  ?
I would (a) stop tomcat, (b) sudo rm -rf /var/lib/tomcat/webapps/apollo  (c) recopy the war file over (d) start tomcat  . . . this is a Tomcat thing, not an Apollo one.
3 - wasn’t sure if you were meaning to set memory (or if its set somewhere else).  I don’t see that error, so its probably fine, but it will eventually result in problems unless you have a 1 GB max limit set. 

Nathan

On Dec 28, 2015, at 9:50 AM, Sofia Robb <[hidden email]> wrote:

Hello,

Is anyone else having troubles deploying the new version of apollo? When I move the war file into my webapp directory and restart tomcat, my tomcat stops working (localhost:8080 won't even load).


ps -ef | grep java
tomcat   15347     1 87 11:37 ?        00:00:24 /usr/lib/jvm/jre/bin/java -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



This is from my catalina.out file

Dec 28, 2015 11:29:58 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Dec 28, 2015 11:30:43 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 432 ms
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks,
Sofia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: can't deploy 2.0.1

Sofia Robb
i am actually running 2.0.2 (here is the war that is made target/apollo-2.0.2-SNAPSHOT.war, that I copy over)

Nothing i try seems to help. When I go to localhost:8080/apollo it just tries and tries to load it until i stop it, it will run for hours, with nothing showing up in the browser or in the logs

0 -  reloading or using incognito does not change anything. 
1 - I have no errors showing up in the console, or in my catalina log file
2 - I am on a new machine without my old copy, 2.0.2 is the only copy I have. I tried stoping, deleting, copying new war, starting, but it still doesn't work.
3- I now have my mem set, and still no good.

i am at a loss. Do you have any tips on how to debug this. 

ps -ef | grep java
vm/jre/bin/java -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



On Mon, Dec 28, 2015 at 10:58 AM, Nathan Dunn <[hidden email]> wrote:

A few questions:

0 - try refreshing your browser cache or with a browser you don’t usually use.  shift-reload or use an incognito window
1 - what do you see in the console (JS) log (and on-screen) if you go to http://localhost:8080/apollo  ?
I would (a) stop tomcat, (b) sudo rm -rf /var/lib/tomcat/webapps/apollo  (c) recopy the war file over (d) start tomcat  . . . this is a Tomcat thing, not an Apollo one.
3 - wasn’t sure if you were meaning to set memory (or if its set somewhere else).  I don’t see that error, so its probably fine, but it will eventually result in problems unless you have a 1 GB max limit set. 

Nathan

On Dec 28, 2015, at 9:50 AM, Sofia Robb <[hidden email]> wrote:

Hello,

Is anyone else having troubles deploying the new version of apollo? When I move the war file into my webapp directory and restart tomcat, my tomcat stops working (localhost:8080 won't even load).


ps -ef | grep java
tomcat   15347     1 87 11:37 ?        00:00:24 /usr/lib/jvm/jre/bin/java -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



This is from my catalina.out file

Dec 28, 2015 11:29:58 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Dec 28, 2015 11:30:43 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 432 ms
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks,
Sofia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: can't deploy 2.0.1

Sofia Robb
In reply to this post by Sofia Robb
The only error I get in my catalina log is when I stop tomcat:

Jan 06, 2016 11:32:17 AM org.apache.catalina.startup.Catalina stop
SEVERE: Catalina.stop
org.apache.catalina.LifecycleException: An invalid Lifecycle transition was attempted ([before_stop]) for component [StandardServer[8005]] in state [DESTROYED]
        at org.apache.catalina.util.LifecycleBase.invalidTransition(LifecycleBase.java:409)
        at org.apache.catalina.util.LifecycleBase.stop(LifecycleBase.java:219)
        at org.apache.catalina.startup.Catalina.stop(Catalina.java:762)
        at org.apache.catalina.startup.Catalina$CatalinaShutdownHook.run(Catalina.java:908)

Jan 06, 2016 11:33:31 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Jan 06, 2016 11:33:32 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Jan 06, 2016 11:33:32 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Jan 06, 2016 11:33:32 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 724 ms
Jan 06, 2016 11:33:32 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Jan 06, 2016 11:33:32 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Jan 06, 2016 11:33:32 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollotest.war
Jan 06, 2016 11:33:39 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Jan 06, 2016 11:33:39 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined



On Mon, Dec 28, 2015 at 10:50 AM, Sofia Robb <[hidden email]> wrote:
Hello,

Is anyone else having troubles deploying the new version of apollo? When I move the war file into my webapp directory and restart tomcat, my tomcat stops working (localhost:8080 won't even load).


ps -ef | grep java
tomcat   15347     1 87 11:37 ?        00:00:24 /usr/lib/jvm/jre/bin/java -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



This is from my catalina.out file

Dec 28, 2015 11:29:58 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Dec 28, 2015 11:30:43 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 432 ms
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks,
Sofia





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: can't deploy 2.0.1

nathandunn
In reply to this post by Sofia Robb

It looks like everything is being done correctly . . . at least on the server side.  

Two other ideas:
(1) when you start your server, is there anything else on the same port? 
(2) have you tried: “./apollo clean-all”  “./apollo run-local”  ?   

Again, I haven’t tried the master, though it would surprise me if it wasn’t working as I’ve already added a few minor fixes without incident.   2.0.1 should definitely work. 

What does your “not working” screen look like? 

Nathan

On Jan 6, 2016, at 9:39 AM, Sofia Robb <[hidden email]> wrote:

i am actually running 2.0.2 (here is the war that is made target/apollo-2.0.2-SNAPSHOT.war, that I copy over)

Nothing i try seems to help. When I go to localhost:8080/apollo it just tries and tries to load it until i stop it, it will run for hours, with nothing showing up in the browser or in the logs

0 -  reloading or using incognito does not change anything. 
1 - I have no errors showing up in the console, or in my catalina log file
2 - I am on a new machine without my old copy, 2.0.2 is the only copy I have. I tried stoping, deleting, copying new war, starting, but it still doesn't work.
3- I now have my mem set, and still no good.

i am at a loss. Do you have any tips on how to debug this. 

ps -ef | grep java
vm/jre/bin/java -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



On Mon, Dec 28, 2015 at 10:58 AM, Nathan Dunn <[hidden email]> wrote:

A few questions:

0 - try refreshing your browser cache or with a browser you don’t usually use.  shift-reload or use an incognito window
1 - what do you see in the console (JS) log (and on-screen) if you go to http://localhost:8080/apollo  ?
I would (a) stop tomcat, (b) sudo rm -rf /var/lib/tomcat/webapps/apollo  (c) recopy the war file over (d) start tomcat  . . . this is a Tomcat thing, not an Apollo one.
3 - wasn’t sure if you were meaning to set memory (or if its set somewhere else).  I don’t see that error, so its probably fine, but it will eventually result in problems unless you have a 1 GB max limit set. 

Nathan

On Dec 28, 2015, at 9:50 AM, Sofia Robb <[hidden email]> wrote:

Hello,

Is anyone else having troubles deploying the new version of apollo? When I move the war file into my webapp directory and restart tomcat, my tomcat stops working (localhost:8080 won't even load).


ps -ef | grep java
tomcat   15347     1 87 11:37 ?        00:00:24 /usr/lib/jvm/jre/bin/java -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



This is from my catalina.out file

Dec 28, 2015 11:29:58 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Dec 28, 2015 11:30:43 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 432 ms
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks,
Sofia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: can't deploy 2.0.1

Sofia Robb
Ok, skype will be good. I'll find you online tomorrow. my id is srobb1.

When i try ./apollo run-local 8085

it gets stuck here:

| Running Grails application
Configuring Shiro ...
Shiro Configured



On Wed, Jan 6, 2016 at 10:49 AM, Nathan Dunn <[hidden email]> wrote:

It looks like everything is being done correctly . . . at least on the server side.  

Two other ideas:
(1) when you start your server, is there anything else on the same port? 
(2) have you tried: “./apollo clean-all”  “./apollo run-local”  ?   

Again, I haven’t tried the master, though it would surprise me if it wasn’t working as I’ve already added a few minor fixes without incident.   2.0.1 should definitely work. 

What does your “not working” screen look like? 

Nathan

On Jan 6, 2016, at 9:39 AM, Sofia Robb <[hidden email]> wrote:

i am actually running 2.0.2 (here is the war that is made target/apollo-2.0.2-SNAPSHOT.war, that I copy over)

Nothing i try seems to help. When I go to localhost:8080/apollo it just tries and tries to load it until i stop it, it will run for hours, with nothing showing up in the browser or in the logs

0 -  reloading or using incognito does not change anything. 
1 - I have no errors showing up in the console, or in my catalina log file
2 - I am on a new machine without my old copy, 2.0.2 is the only copy I have. I tried stoping, deleting, copying new war, starting, but it still doesn't work.
3- I now have my mem set, and still no good.

i am at a loss. Do you have any tips on how to debug this. 

ps -ef | grep java
vm/jre/bin/java -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



On Mon, Dec 28, 2015 at 10:58 AM, Nathan Dunn <[hidden email]> wrote:

A few questions:

0 - try refreshing your browser cache or with a browser you don’t usually use.  shift-reload or use an incognito window
1 - what do you see in the console (JS) log (and on-screen) if you go to http://localhost:8080/apollo  ?
I would (a) stop tomcat, (b) sudo rm -rf /var/lib/tomcat/webapps/apollo  (c) recopy the war file over (d) start tomcat  . . . this is a Tomcat thing, not an Apollo one.
3 - wasn’t sure if you were meaning to set memory (or if its set somewhere else).  I don’t see that error, so its probably fine, but it will eventually result in problems unless you have a 1 GB max limit set. 

Nathan

On Dec 28, 2015, at 9:50 AM, Sofia Robb <[hidden email]> wrote:

Hello,

Is anyone else having troubles deploying the new version of apollo? When I move the war file into my webapp directory and restart tomcat, my tomcat stops working (localhost:8080 won't even load).


ps -ef | grep java
tomcat   15347     1 87 11:37 ?        00:00:24 /usr/lib/jvm/jre/bin/java -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



This is from my catalina.out file

Dec 28, 2015 11:29:58 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Dec 28, 2015 11:30:43 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 432 ms
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks,
Sofia



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Re: can't deploy 2.0.1

nathandunn
Sounds good.

You should see something after about 30 seconds (or sooner) after the shiro configured message. 

Nathan

On Jan 6, 2016, at 10:36 AM, Sofia Robb <[hidden email]> wrote:

Ok, skype will be good. I'll find you online tomorrow. my id is srobb1.

When i try ./apollo run-local 8085

it gets stuck here:

| Running Grails application
Configuring Shiro ...
Shiro Configured



On Wed, Jan 6, 2016 at 10:49 AM, Nathan Dunn <[hidden email]> wrote:

It looks like everything is being done correctly . . . at least on the server side.  

Two other ideas:
(1) when you start your server, is there anything else on the same port? 
(2) have you tried: “./apollo clean-all”  “./apollo run-local”  ?   

Again, I haven’t tried the master, though it would surprise me if it wasn’t working as I’ve already added a few minor fixes without incident.   2.0.1 should definitely work. 

What does your “not working” screen look like? 

Nathan

On Jan 6, 2016, at 9:39 AM, Sofia Robb <[hidden email]> wrote:

i am actually running 2.0.2 (here is the war that is made target/apollo-2.0.2-SNAPSHOT.war, that I copy over)

Nothing i try seems to help. When I go to localhost:8080/apollo it just tries and tries to load it until i stop it, it will run for hours, with nothing showing up in the browser or in the logs

0 -  reloading or using incognito does not change anything. 
1 - I have no errors showing up in the console, or in my catalina log file
2 - I am on a new machine without my old copy, 2.0.2 is the only copy I have. I tried stoping, deleting, copying new war, starting, but it still doesn't work.
3- I now have my mem set, and still no good.

i am at a loss. Do you have any tips on how to debug this. 

ps -ef | grep java
vm/jre/bin/java -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



On Mon, Dec 28, 2015 at 10:58 AM, Nathan Dunn <[hidden email]> wrote:

A few questions:

0 - try refreshing your browser cache or with a browser you don’t usually use.  shift-reload or use an incognito window
1 - what do you see in the console (JS) log (and on-screen) if you go to http://localhost:8080/apollo  ?
I would (a) stop tomcat, (b) sudo rm -rf /var/lib/tomcat/webapps/apollo  (c) recopy the war file over (d) start tomcat  . . . this is a Tomcat thing, not an Apollo one.
3 - wasn’t sure if you were meaning to set memory (or if its set somewhere else).  I don’t see that error, so its probably fine, but it will eventually result in problems unless you have a 1 GB max limit set. 

Nathan

On Dec 28, 2015, at 9:50 AM, Sofia Robb <[hidden email]> wrote:

Hello,

Is anyone else having troubles deploying the new version of apollo? When I move the war file into my webapp directory and restart tomcat, my tomcat stops working (localhost:8080 won't even load).


ps -ef | grep java
tomcat   15347     1 87 11:37 ?        00:00:24 /usr/lib/jvm/jre/bin/java -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



This is from my catalina.out file

Dec 28, 2015 11:29:58 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Dec 28, 2015 11:30:43 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 432 ms
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks,
Sofia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: can't deploy 2.0.1

Sofia Robb
OK!! All Fixed! Thank you Nathan!!

I had a silly miss type.

In my apollo-config.groovy i incorrectly added :8080 to localhost

I had this:
dataSource.url = "jdbc:postgresql://localhost:8080/apollo"

instead the correct syntax
dataSource.url = "jdbc:postgresql://localhost/apollo"

Thanks,
Sofia




On Wed, Jan 6, 2016 at 12:08 PM, Lbl <[hidden email]> wrote:
Sounds good.

You should see something after about 30 seconds (or sooner) after the shiro configured message. 

Nathan

On Jan 6, 2016, at 10:36 AM, Sofia Robb <[hidden email]> wrote:

Ok, skype will be good. I'll find you online tomorrow. my id is srobb1.

When i try ./apollo run-local 8085

it gets stuck here:

| Running Grails application
Configuring Shiro ...
Shiro Configured



On Wed, Jan 6, 2016 at 10:49 AM, Nathan Dunn <[hidden email]> wrote:

It looks like everything is being done correctly . . . at least on the server side.  

Two other ideas:
(1) when you start your server, is there anything else on the same port? 
(2) have you tried: “./apollo clean-all”  “./apollo run-local”  ?   

Again, I haven’t tried the master, though it would surprise me if it wasn’t working as I’ve already added a few minor fixes without incident.   2.0.1 should definitely work. 

What does your “not working” screen look like? 

Nathan

On Jan 6, 2016, at 9:39 AM, Sofia Robb <[hidden email]> wrote:

i am actually running 2.0.2 (here is the war that is made target/apollo-2.0.2-SNAPSHOT.war, that I copy over)

Nothing i try seems to help. When I go to localhost:8080/apollo it just tries and tries to load it until i stop it, it will run for hours, with nothing showing up in the browser or in the logs

0 -  reloading or using incognito does not change anything. 
1 - I have no errors showing up in the console, or in my catalina log file
2 - I am on a new machine without my old copy, 2.0.2 is the only copy I have. I tried stoping, deleting, copying new war, starting, but it still doesn't work.
3- I now have my mem set, and still no good.

i am at a loss. Do you have any tips on how to debug this. 

ps -ef | grep java
vm/jre/bin/java -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



On Mon, Dec 28, 2015 at 10:58 AM, Nathan Dunn <[hidden email]> wrote:

A few questions:

0 - try refreshing your browser cache or with a browser you don’t usually use.  shift-reload or use an incognito window
1 - what do you see in the console (JS) log (and on-screen) if you go to http://localhost:8080/apollo  ?
I would (a) stop tomcat, (b) sudo rm -rf /var/lib/tomcat/webapps/apollo  (c) recopy the war file over (d) start tomcat  . . . this is a Tomcat thing, not an Apollo one.
3 - wasn’t sure if you were meaning to set memory (or if its set somewhere else).  I don’t see that error, so its probably fine, but it will eventually result in problems unless you have a 1 GB max limit set. 

Nathan

On Dec 28, 2015, at 9:50 AM, Sofia Robb <[hidden email]> wrote:

Hello,

Is anyone else having troubles deploying the new version of apollo? When I move the war file into my webapp directory and restart tomcat, my tomcat stops working (localhost:8080 won't even load).


ps -ef | grep java
tomcat   15347     1 87 11:37 ?        00:00:24 /usr/lib/jvm/jre/bin/java -classpath /usr/share/tomcat/bin/bootstrap.jar:/usr/share/tomcat/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar -Dcatalina.base=/usr/share/tomcat -Dcatalina.home=/usr/share/tomcat -Djava.endorsed.dirs= -Djava.io.tmpdir=/var/cache/tomcat/temp -Djava.util.logging.config.file=/usr/share/tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager org.apache.catalina.startup.Bootstrap start



This is from my catalina.out file

Dec 28, 2015 11:29:58 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:06 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.StandardServer await
INFO: A valid shutdown command was received via the shutdown port. Stopping the Server instance.
Dec 28, 2015 11:30:43 AM org.apache.coyote.AbstractProtocol pause
INFO: Pausing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:43 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Dec 28, 2015 11:30:44 AM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 432 ms
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Dec 28, 2015 11:30:44 AM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.54
Dec 28, 2015 11:30:44 AM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat/webapps/apollo.war
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Dec 28, 2015 11:30:48 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined


Thanks,
Sofia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.