Error Forked Grails VM exited with error

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Error Forked Grails VM exited with error

Quanwei Zhang
Hi:

I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.

I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"

I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.

Node Version: 10
Npm Version: 6
Yarn Version: 1
javac 1.8.0_191 found
javac installed
JDK 1.8 found: javac 1.8.0_191
Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
No log file found in classpath.
Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
:installJBrowseWebOnly
JBrowse already exists
From https://github.com/gmod/jbrowse
 * tag                 1.15.4-release -> FETCH_HEAD
Already up to date.
yarn install v1.12.3
[1/4] Resolving packages...
success Already up-to-date.
Done in 0.48s.
yarn install v1.12.3
info No lockfile found.
[1/4] Resolving packages...
[2/4] Fetching packages...
[3/4] Linking dependencies...
[4/4] Building fresh packages...
success Saved lockfile.
Done in 0.78s.
Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Evaluating plugin WebApollo=[included:true]
Plugin jbrowse/plugins/WebApollo exists and appears valid.
Evaluating plugin RegexSequenceSearch=[included:true]
Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
Evaluating plugin HideTrackLabels=[included:true]
Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.

> @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> webpack

clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
jbrowse-glob-loader: building 203 JBrowse modules
jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
jbrowse-glob-loader: adding plugin module WebApollo/Permission
jbrowse-glob-loader: adding plugin module WebApollo/main
jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
jbrowse-glob-loader: adding plugin module WebApollo/EUtils
jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
jbrowse-glob-loader: adding plugin module HideTrackLabels/main
jbrowse-glob-loader: adding plugin module DebugEvents/main
jbrowse-glob-loader: adding plugin module CategoryUrl/main
jbrowse-glob-loader: discovered a total of 247 modules
jbrowse-glob-loader: skipping entry point module JBrowse/main
Hash: 9eaefe2aad6bc3d71862
Version: webpack 3.12.0
Time: 9380ms
                    Asset       Size         Chunks                    Chunk Names
          0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]        
              0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
              2.bundle.js     145 kB              2  [emitted]        
              3.bundle.js     531 kB              3  [emitted]  [big] 
              4.bundle.js     398 kB              4  [emitted]  [big] 
              5.bundle.js    1.68 kB              5  [emitted]        
              6.bundle.js  920 bytes              6  [emitted]        
    run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
        browser.bundle.js     364 kB              8  [emitted]  [big]  browser
           main.bundle.js     375 kB              9  [emitted]  [big]  main
              1.bundle.js     456 kB              1  [emitted]  [big] 
          1.bundle.js.map     611 kB              1  [emitted]        
          2.bundle.js.map     200 kB              2  [emitted]        
          3.bundle.js.map     691 kB              3  [emitted]        
          4.bundle.js.map     504 kB              4  [emitted]        
          5.bundle.js.map    1.87 kB              5  [emitted]        
          6.bundle.js.map    1.13 kB              6  [emitted]        
run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
    browser.bundle.js.map     517 kB              8  [emitted]         browser
       main.bundle.js.map     537 kB              9  [emitted]         main
 dojo/resources/blank.gif   43 bytes                 [emitted]        
 [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
 [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
 [373] ./src/JBrowse/main.js 13 kB {9} [built]
 [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
 [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
 [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
 [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
 [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
 [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
 [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
 [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
 [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
 [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
 [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
 [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
    + 1485 hidden modules
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 54.871 secs

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
| Compiling 6 source files

| Compiling 6 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application
Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
| Server running. Browse to http://localhost:8080/apollo
Configuring Shiro ...
Shiro Configured
| Parent process shutdown. Exiting...
| Error Forked Grails VM exited with error

Best
Quanwei




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: Error Forked Grails VM exited with error

nathandunn

Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though). 

A couple of things to try:

1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are.  

2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:


And re-deploying it. 

Nathan





On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:

Hi:

I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.

I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"

I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.

Node Version: 10
Npm Version: 6
Yarn Version: 1
javac 1.8.0_191 found
javac installed
JDK 1.8 found: javac 1.8.0_191
Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
No log file found in classpath.
Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
:installJBrowseWebOnly
JBrowse already exists
From https://github.com/gmod/jbrowse
 * tag                 1.15.4-release -> FETCH_HEAD
Already up to date.
yarn install v1.12.3
[1/4] Resolving packages...
success Already up-to-date.
Done in 0.48s.
yarn install v1.12.3
info No lockfile found.
[1/4] Resolving packages...
[2/4] Fetching packages...
[3/4] Linking dependencies...
[4/4] Building fresh packages...
success Saved lockfile.
Done in 0.78s.
Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Evaluating plugin WebApollo=[included:true]
Plugin jbrowse/plugins/WebApollo exists and appears valid.
Evaluating plugin RegexSequenceSearch=[included:true]
Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
Evaluating plugin HideTrackLabels=[included:true]
Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.

> @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> webpack

clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
jbrowse-glob-loader: building 203 JBrowse modules
jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
jbrowse-glob-loader: adding plugin module WebApollo/Permission
jbrowse-glob-loader: adding plugin module WebApollo/main
jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
jbrowse-glob-loader: adding plugin module WebApollo/EUtils
jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
jbrowse-glob-loader: adding plugin module HideTrackLabels/main
jbrowse-glob-loader: adding plugin module DebugEvents/main
jbrowse-glob-loader: adding plugin module CategoryUrl/main
jbrowse-glob-loader: discovered a total of 247 modules
jbrowse-glob-loader: skipping entry point module JBrowse/main
Hash: 9eaefe2aad6bc3d71862
Version: webpack 3.12.0
Time: 9380ms
                    Asset       Size         Chunks                    Chunk Names
          0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]        
              0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
              2.bundle.js     145 kB              2  [emitted]        
              3.bundle.js     531 kB              3  [emitted]  [big] 
              4.bundle.js     398 kB              4  [emitted]  [big] 
              5.bundle.js    1.68 kB              5  [emitted]        
              6.bundle.js  920 bytes              6  [emitted]        
    run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
        browser.bundle.js     364 kB              8  [emitted]  [big]  browser
           main.bundle.js     375 kB              9  [emitted]  [big]  main
              1.bundle.js     456 kB              1  [emitted]  [big] 
          1.bundle.js.map     611 kB              1  [emitted]        
          2.bundle.js.map     200 kB              2  [emitted]        
          3.bundle.js.map     691 kB              3  [emitted]        
          4.bundle.js.map     504 kB              4  [emitted]        
          5.bundle.js.map    1.87 kB              5  [emitted]        
          6.bundle.js.map    1.13 kB              6  [emitted]        
run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
    browser.bundle.js.map     517 kB              8  [emitted]         browser
       main.bundle.js.map     537 kB              9  [emitted]         main
 dojo/resources/blank.gif   43 bytes                 [emitted]        
 [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
 [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
 [373] ./src/JBrowse/main.js 13 kB {9} [built]
 [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
 [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
 [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
 [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
 [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
 [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
 [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
 [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
 [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
 [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
 [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
 [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
    + 1485 hidden modules
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 54.871 secs

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
| Compiling 6 source files

| Compiling 6 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application
Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
| Server running. Browse to http://localhost:8080/apollo
Configuring Shiro ...
Shiro Configured
| Parent process shutdown. Exiting...
| Error Forked Grails VM exited with error

Best
Quanwei



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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Re: Error Forked Grails VM exited with error

Quanwei Zhang
Dear Nathan:

Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
Do you have any suggestion?


.....
BUILD SUCCESSFUL

Total time: 57.359 secs

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
| Compiling 7 source files

| Compiling 7 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application

Configuring Shiro ...

Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8084/apollo


#Change in the BuildConfig.groovy file
//forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
grails.project.fork = [
        // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
        //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],

        compile: false,
        test   : false,
        run    : false,
        war    : false,
        console : false
        // configure settings for the test-app JVM, uses the daemon by default
        //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
        // configure settings for the run-app JVM
        //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
        // configure settings for the run-war JVM
        //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
        // configure settings for the Console UI JVM
        //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]

]

if (System.getProperty("grails.debug")) {
    //grails.project.fork.war += [debug: true]
    grails.project.fork.run = false
    println "Using debug for run"
}


Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:

Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though). 

A couple of things to try:

1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are.  

2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:


And re-deploying it. 

Nathan





On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:

Hi:

I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.

I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"

I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.

Node Version: 10
Npm Version: 6
Yarn Version: 1
javac 1.8.0_191 found
javac installed
JDK 1.8 found: javac 1.8.0_191
Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
No log file found in classpath.
Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
:installJBrowseWebOnly
JBrowse already exists
From https://github.com/gmod/jbrowse
 * tag                 1.15.4-release -> FETCH_HEAD
Already up to date.
yarn install v1.12.3
[1/4] Resolving packages...
success Already up-to-date.
Done in 0.48s.
yarn install v1.12.3
info No lockfile found.
[1/4] Resolving packages...
[2/4] Fetching packages...
[3/4] Linking dependencies...
[4/4] Building fresh packages...
success Saved lockfile.
Done in 0.78s.
Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
Evaluating plugin WebApollo=[included:true]
Plugin jbrowse/plugins/WebApollo exists and appears valid.
Evaluating plugin RegexSequenceSearch=[included:true]
Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
Evaluating plugin HideTrackLabels=[included:true]
Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.

> @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> webpack

clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
jbrowse-glob-loader: building 203 JBrowse modules
jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
jbrowse-glob-loader: adding plugin module WebApollo/Permission
jbrowse-glob-loader: adding plugin module WebApollo/main
jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
jbrowse-glob-loader: adding plugin module WebApollo/EUtils
jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
jbrowse-glob-loader: adding plugin module HideTrackLabels/main
jbrowse-glob-loader: adding plugin module DebugEvents/main
jbrowse-glob-loader: adding plugin module CategoryUrl/main
jbrowse-glob-loader: discovered a total of 247 modules
jbrowse-glob-loader: skipping entry point module JBrowse/main
Hash: 9eaefe2aad6bc3d71862
Version: webpack 3.12.0
Time: 9380ms
                    Asset       Size         Chunks                    Chunk Names
          0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]        
              0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
              2.bundle.js     145 kB              2  [emitted]        
              3.bundle.js     531 kB              3  [emitted]  [big] 
              4.bundle.js     398 kB              4  [emitted]  [big] 
              5.bundle.js    1.68 kB              5  [emitted]        
              6.bundle.js  920 bytes              6  [emitted]        
    run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
        browser.bundle.js     364 kB              8  [emitted]  [big]  browser
           main.bundle.js     375 kB              9  [emitted]  [big]  main
              1.bundle.js     456 kB              1  [emitted]  [big] 
          1.bundle.js.map     611 kB              1  [emitted]        
          2.bundle.js.map     200 kB              2  [emitted]        
          3.bundle.js.map     691 kB              3  [emitted]        
          4.bundle.js.map     504 kB              4  [emitted]        
          5.bundle.js.map    1.87 kB              5  [emitted]        
          6.bundle.js.map    1.13 kB              6  [emitted]        
run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
    browser.bundle.js.map     517 kB              8  [emitted]         browser
       main.bundle.js.map     537 kB              9  [emitted]         main
 dojo/resources/blank.gif   43 bytes                 [emitted]        
 [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
 [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
 [373] ./src/JBrowse/main.js 13 kB {9} [built]
 [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
 [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
 [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
 [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
 [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
 [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
 [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
 [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
 [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
 [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
 [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
 [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
    + 1485 hidden modules
:javac
:gwtc

BUILD SUCCESSFUL

Total time: 54.871 secs

This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
| Compiling 6 source files

| Compiling 6 source files.....
***
Metrics servlet injected into web.xml
Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
***
| Running Grails application
Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
| Server running. Browse to http://localhost:8080/apollo
Configuring Shiro ...
Shiro Configured
| Parent process shutdown. Exiting...
| Error Forked Grails VM exited with error

Best
Quanwei



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.





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: Error Forked Grails VM exited with error

nathandunn

A few questions:

1 - If you type:

    netstat -tan | grep 8084  

What do you see?

2 - Also, what do you see in the tomcat logs?

3 - If you go to the network developer tab of your browser for that page, what do you see?

4 - What is the name of war file you generated?

5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo


Nathan

> On Jan 9, 2019, at 9:51 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Dear Nathan:
>
> Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
> Do you have any suggestion?
>
>
> .....
> BUILD SUCCESSFUL
>
> Total time: 57.359 secs
>
> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> | Compiling 7 source files
>
> | Compiling 7 source files.....
> ***
> Metrics servlet injected into web.xml
> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> ***
> | Running Grails application
>
> Configuring Shiro ...
>
> Shiro Configured
> Starting Quartz Scheduler in QuartzFactoryBean
> | Server running. Browse to http://localhost:8084/apollo
>
>
> #Change in the BuildConfig.groovy file
> //forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> grails.project.fork = [
>         // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
>         //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
>
>         compile: false,
>         test   : false,
>         run    : false,
>         war    : false,
>         console : false
>         // configure settings for the test-app JVM, uses the daemon by default
>         //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
>         // configure settings for the run-app JVM
>         //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
>         // configure settings for the run-war JVM
>         //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
>         // configure settings for the Console UI JVM
>         //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> ]
>
> if (System.getProperty("grails.debug")) {
>     //grails.project.fork.war += [debug: true]
>     grails.project.fork.run = false
>     println "Using debug for run"
> }
>
>
> Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:
>
> Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though).
>
> A couple of things to try:
>
> 1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are.  
>
> 2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:
>
> https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L14
>
> And re-deploying it.
>
> Nathan
>
>
>
>
>
>> On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:
>>
>> Hi:
>>
>> I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.
>>
>> I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
>> export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"
>>
>> I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.
>>
>> Node Version: 10
>> Npm Version: 6
>> Yarn Version: 1
>> javac 1.8.0_191 found
>> javac installed
>> JDK 1.8 found: javac 1.8.0_191
>> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
>> No log file found in classpath.
>> Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
>> Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
>> :installJBrowseWebOnly
>> JBrowse already exists
>> From https://github.com/gmod/jbrowse
>>  * tag                 1.15.4-release -> FETCH_HEAD
>> Already up to date.
>> yarn install v1.12.3
>> [1/4] Resolving packages...
>> success Already up-to-date.
>> Done in 0.48s.
>> yarn install v1.12.3
>> info No lockfile found.
>> [1/4] Resolving packages...
>> [2/4] Fetching packages...
>> [3/4] Linking dependencies...
>> [4/4] Building fresh packages...
>> success Saved lockfile.
>> Done in 0.78s.
>> Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
>> Evaluating plugin WebApollo=[included:true]
>> Plugin jbrowse/plugins/WebApollo exists and appears valid.
>> Evaluating plugin RegexSequenceSearch=[included:true]
>> Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
>> Evaluating plugin HideTrackLabels=[included:true]
>> Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.
>>
>> > @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
>> > webpack
>>
>> clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
>> jbrowse-glob-loader: building 203 JBrowse modules
>> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
>> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
>> jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
>> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
>> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
>> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
>> jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
>> jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
>> jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
>> jbrowse-glob-loader: adding plugin module WebApollo/Permission
>> jbrowse-glob-loader: adding plugin module WebApollo/main
>> jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
>> jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
>> jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
>> jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
>> jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
>> jbrowse-glob-loader: adding plugin module WebApollo/EUtils
>> jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
>> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
>> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
>> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
>> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
>> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
>> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
>> jbrowse-glob-loader: adding plugin module DebugEvents/main
>> jbrowse-glob-loader: adding plugin module CategoryUrl/main
>> jbrowse-glob-loader: discovered a total of 247 modules
>> jbrowse-glob-loader: skipping entry point module JBrowse/main
>> Hash: 9eaefe2aad6bc3d71862
>> Version: webpack 3.12.0
>> Time: 9380ms
>>                     Asset       Size         Chunks                    Chunk Names
>>           0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]        
>>               0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big]  
>>               2.bundle.js     145 kB              2  [emitted]        
>>               3.bundle.js     531 kB              3  [emitted]  [big]  
>>               4.bundle.js     398 kB              4  [emitted]  [big]  
>>               5.bundle.js    1.68 kB              5  [emitted]        
>>               6.bundle.js  920 bytes              6  [emitted]        
>>     run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
>>         browser.bundle.js     364 kB              8  [emitted]  [big]  browser
>>            main.bundle.js     375 kB              9  [emitted]  [big]  main
>>               1.bundle.js     456 kB              1  [emitted]  [big]  
>>           1.bundle.js.map     611 kB              1  [emitted]        
>>           2.bundle.js.map     200 kB              2  [emitted]        
>>           3.bundle.js.map     691 kB              3  [emitted]        
>>           4.bundle.js.map     504 kB              4  [emitted]        
>>           5.bundle.js.map    1.87 kB              5  [emitted]        
>>           6.bundle.js.map    1.13 kB              6  [emitted]        
>> run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
>>     browser.bundle.js.map     517 kB              8  [emitted]         browser
>>        main.bundle.js.map     537 kB              9  [emitted]         main
>>  dojo/resources/blank.gif   43 bytes                 [emitted]        
>>  [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
>>  [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
>>  [373] ./src/JBrowse/main.js 13 kB {9} [built]
>>  [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
>>  [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
>>  [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
>>  [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
>>  [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
>>  [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
>>  [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
>>  [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
>>  [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
>>  [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
>>  [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
>>  [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
>>     + 1485 hidden modules
>> :javac
>> :gwtc
>>
>> BUILD SUCCESSFUL
>>
>> Total time: 54.871 secs
>>
>> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
>> | Compiling 6 source files
>>
>> | Compiling 6 source files.....
>> ***
>> Metrics servlet injected into web.xml
>> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
>> ***
>> | Running Grails application
>> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
>> | Server running. Browse to http://localhost:8080/apollo
>> Configuring Shiro ...
>> Shiro Configured
>> | Parent process shutdown. Exiting...
>> | Error Forked Grails VM exited with error
>>
>> Best
>> Quanwei
>>
>>
>>
>> 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/
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>
>
>
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Re: Error Forked Grails VM exited with error

Quanwei Zhang
Thank you very much. I am not not familiar with those things, but please see below that I get. Any ideas from the information below?

1 - If you type:

    netstat -tan | grep 8084   

What do you see?

$ netstat -tan | grep 8084  
tcp4       0      0  *.8084                 *.*                    LISTEN


2 - Also, what do you see in the tomcat logs?

Do you mean the log files below. It seems strange that there is no log file generated today.

$ ls -l /usr/local/Cellar/tomcat/9.0.14/libexec/logs/
total 56
-rw-r-----  1 qwzhang  admin  8666 Jan  7 18:14 catalina.2019-01-07.log
-rw-r-----  1 qwzhang  admin  8714 Jan  7 18:14 catalina.out
-rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 host-manager.2019-01-07.log
-rw-r-----  1 qwzhang  admin   650 Jan  7 18:14 localhost.2019-01-07.log
-rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 localhost_access_log.2019-01-07.txt
-rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 manager.2019-01-07.log


3 - If you go to the network developer tab of your browser for that page, what do you see?
It shows Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server "localhost"

4 - What is the name of war file you generated?
Sorry I am not familiar with this. Would you please tell me where to find the war file?

5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
When I tried "./apollo run-local 8085" I get the following message. Maybe I already tried the port when I tested it.
Running Grails application
Error Server failed to start for port 8085: Address already in use (Bind failed) (Use --stacktrace to see the full trace)
If I try "./apollo run-local 8083" and try to connect http://localhost:8084/apollo, still get the same information.
Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server "localhost"


Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午1:22写道:

A few questions:

1 - If you type:

    netstat -tan | grep 8084   

What do you see?

2 - Also, what do you see in the tomcat logs?

3 - If you go to the network developer tab of your browser for that page, what do you see?

4 - What is the name of war file you generated?

5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo


Nathan

> On Jan 9, 2019, at 9:51 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Dear Nathan:
>
> Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
> Do you have any suggestion?
>
>
> .....
> BUILD SUCCESSFUL
>
> Total time: 57.359 secs
>
> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> | Compiling 7 source files
>
> | Compiling 7 source files.....
> ***
> Metrics servlet injected into web.xml
> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> ***
> | Running Grails application
>
> Configuring Shiro ...
>
> Shiro Configured
> Starting Quartz Scheduler in QuartzFactoryBean
> | Server running. Browse to http://localhost:8084/apollo
>
>
> #Change in the BuildConfig.groovy file
> //forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> grails.project.fork = [
>         // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
>         //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
>
>         compile: false,
>         test   : false,
>         run    : false,
>         war    : false,
>         console : false
>         // configure settings for the test-app JVM, uses the daemon by default
>         //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
>         // configure settings for the run-app JVM
>         //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
>         // configure settings for the run-war JVM
>         //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
>         // configure settings for the Console UI JVM
>         //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> ]
>
> if (System.getProperty("grails.debug")) {
>     //grails.project.fork.war += [debug: true]
>     grails.project.fork.run = false
>     println "Using debug for run"
> }
>
>
> Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:
>
> Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though).
>
> A couple of things to try:
>
> 1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are. 
>
> 2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:
>
> https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L14
>
> And re-deploying it.
>
> Nathan
>
>
>
>
>
>> On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:
>>
>> Hi:
>>
>> I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.
>>
>> I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
>> export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"
>>
>> I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.
>>
>> Node Version: 10
>> Npm Version: 6
>> Yarn Version: 1
>> javac 1.8.0_191 found
>> javac installed
>> JDK 1.8 found: javac 1.8.0_191
>> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
>> No log file found in classpath.
>> Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
>> Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
>> :installJBrowseWebOnly
>> JBrowse already exists
>> From https://github.com/gmod/jbrowse
>>  * tag                 1.15.4-release -> FETCH_HEAD
>> Already up to date.
>> yarn install v1.12.3
>> [1/4] Resolving packages...
>> success Already up-to-date.
>> Done in 0.48s.
>> yarn install v1.12.3
>> info No lockfile found.
>> [1/4] Resolving packages...
>> [2/4] Fetching packages...
>> [3/4] Linking dependencies...
>> [4/4] Building fresh packages...
>> success Saved lockfile.
>> Done in 0.78s.
>> Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
>> Evaluating plugin WebApollo=[included:true]
>> Plugin jbrowse/plugins/WebApollo exists and appears valid.
>> Evaluating plugin RegexSequenceSearch=[included:true]
>> Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
>> Evaluating plugin HideTrackLabels=[included:true]
>> Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.
>>
>> > @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
>> > webpack
>>
>> clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
>> jbrowse-glob-loader: building 203 JBrowse modules
>> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
>> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
>> jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
>> jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
>> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
>> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
>> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
>> jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
>> jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
>> jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
>> jbrowse-glob-loader: adding plugin module WebApollo/Permission
>> jbrowse-glob-loader: adding plugin module WebApollo/main
>> jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
>> jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
>> jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
>> jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
>> jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
>> jbrowse-glob-loader: adding plugin module WebApollo/EUtils
>> jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
>> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
>> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
>> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
>> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
>> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
>> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
>> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
>> jbrowse-glob-loader: adding plugin module DebugEvents/main
>> jbrowse-glob-loader: adding plugin module CategoryUrl/main
>> jbrowse-glob-loader: discovered a total of 247 modules
>> jbrowse-glob-loader: skipping entry point module JBrowse/main
>> Hash: 9eaefe2aad6bc3d71862
>> Version: webpack 3.12.0
>> Time: 9380ms
>>                     Asset       Size         Chunks                    Chunk Names
>>           0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]         
>>               0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
>>               2.bundle.js     145 kB              2  [emitted]         
>>               3.bundle.js     531 kB              3  [emitted]  [big] 
>>               4.bundle.js     398 kB              4  [emitted]  [big] 
>>               5.bundle.js    1.68 kB              5  [emitted]         
>>               6.bundle.js  920 bytes              6  [emitted]         
>>     run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
>>         browser.bundle.js     364 kB              8  [emitted]  [big]  browser
>>            main.bundle.js     375 kB              9  [emitted]  [big]  main
>>               1.bundle.js     456 kB              1  [emitted]  [big] 
>>           1.bundle.js.map     611 kB              1  [emitted]         
>>           2.bundle.js.map     200 kB              2  [emitted]         
>>           3.bundle.js.map     691 kB              3  [emitted]         
>>           4.bundle.js.map     504 kB              4  [emitted]         
>>           5.bundle.js.map    1.87 kB              5  [emitted]         
>>           6.bundle.js.map    1.13 kB              6  [emitted]         
>> run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
>>     browser.bundle.js.map     517 kB              8  [emitted]         browser
>>        main.bundle.js.map     537 kB              9  [emitted]         main
>>  dojo/resources/blank.gif   43 bytes                 [emitted]         
>>  [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
>>  [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
>>  [373] ./src/JBrowse/main.js 13 kB {9} [built]
>>  [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
>>  [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
>>  [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
>>  [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
>>  [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
>>  [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
>>  [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
>>  [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
>>  [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
>>  [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
>>  [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
>>  [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
>>     + 1485 hidden modules
>> :javac
>> :gwtc
>>
>> BUILD SUCCESSFUL
>>
>> Total time: 54.871 secs
>>
>> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
>> | Compiling 6 source files
>>
>> | Compiling 6 source files.....
>> ***
>> Metrics servlet injected into web.xml
>> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
>> ***
>> | Running Grails application
>> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
>> | Server running. Browse to http://localhost:8080/apollo
>> Configuring Shiro ...
>> Shiro Configured
>> | Parent process shutdown. Exiting...
>> | Error Forked Grails VM exited with error
>>
>> Best
>> Quanwei
>>
>>
>>
>> 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.
>
>
>
>
> 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.





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: Error Forked Grails VM exited with error

nathandunn



> On Jan 9, 2019, at 11:13 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Thank you very much. I am not not familiar with those things, but please see below that I get. Any ideas from the information below?
>
> 1 - If you type:
>
>     netstat -tan | grep 8084  
>
> What do you see?
>
> $ netstat -tan | grep 8084  
> tcp4       0      0  *.8084                 *.*                    LISTEN

This is good!

>
> 2 - Also, what do you see in the tomcat logs?
>
> Do you mean the log files below. It seems strange that there is no log file generated today.
>
> $ ls -l /usr/local/Cellar/tomcat/9.0.14/libexec/logs/
> total 56
> -rw-r-----  1 qwzhang  admin  8666 Jan  7 18:14 catalina.2019-01-07.log
> -rw-r-----  1 qwzhang  admin  8714 Jan  7 18:14 catalina.out
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 host-manager.2019-01-07.log
> -rw-r-----  1 qwzhang  admin   650 Jan  7 18:14 localhost.2019-01-07.log
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 localhost_access_log.2019-01-07.txt
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 manager.2019-01-07.log

In a separate terminal do:

tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out

This is give output if anything happens.

>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
> It shows Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server “localhost"

If you connect to http://localhost:8084/   do you see something?

Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

(Relevant to below)

> 4 - What is the name of war file you generated?
> Sorry I am not familiar with this. Would you please tell me where to find the war file?


Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.

This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

e.g.,:

cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war

When tomcat starts it will unwrap the war file into a directory called “apollo”

>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
> When I tried "./apollo run-local 8085" I get the following message. Maybe I already tried the port when I tested it.
> Running Grails application
> Error Server failed to start for port 8085: Address already in use (Bind failed) (Use --stacktrace to see the full trace)
> If I try "./apollo run-local 8083" and try to connect http://localhost:8084/apollo, still get the same information.
> Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server "localhost"
>

You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

But hopefully step 4 works.

Nathan

> Best
> Quanwei
>
> Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午1:22写道:
>
> A few questions:
>
> 1 - If you type:
>
>     netstat -tan | grep 8084  
>
> What do you see?
>
> 2 - Also, what do you see in the tomcat logs?
>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
>
> 4 - What is the name of war file you generated?
>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
>
>
> Nathan
>
> > On Jan 9, 2019, at 9:51 AM, Quanwei Zhang <[hidden email]> wrote:
> >
> > Dear Nathan:
> >
> > Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
> > Do you have any suggestion?
> >
> >
> > .....
> > BUILD SUCCESSFUL
> >
> > Total time: 57.359 secs
> >
> > This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> > | Compiling 7 source files
> >
> > | Compiling 7 source files.....
> > ***
> > Metrics servlet injected into web.xml
> > Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> > ***
> > | Running Grails application
> >
> > Configuring Shiro ...
> >
> > Shiro Configured
> > Starting Quartz Scheduler in QuartzFactoryBean
> > | Server running. Browse to http://localhost:8084/apollo
> >
> >
> > #Change in the BuildConfig.groovy file
> > //forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > grails.project.fork = [
> >         // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
> >         //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >
> >         compile: false,
> >         test   : false,
> >         run    : false,
> >         war    : false,
> >         console : false
> >         // configure settings for the test-app JVM, uses the daemon by default
> >         //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >         // configure settings for the run-app JVM
> >         //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the run-war JVM
> >         //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the Console UI JVM
> >         //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > ]
> >
> > if (System.getProperty("grails.debug")) {
> >     //grails.project.fork.war += [debug: true]
> >     grails.project.fork.run = false
> >     println "Using debug for run"
> > }
> >
> >
> > Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:
> >
> > Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though).
> >
> > A couple of things to try:
> >
> > 1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are.  
> >
> > 2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:
> >
> > https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L14
> >
> > And re-deploying it.
> >
> > Nathan
> >
> >
> >
> >
> >
> >> On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:
> >>
> >> Hi:
> >>
> >> I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.
> >>
> >> I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
> >> export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"
> >>
> >> I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.
> >>
> >> Node Version: 10
> >> Npm Version: 6
> >> Yarn Version: 1
> >> javac 1.8.0_191 found
> >> javac installed
> >> JDK 1.8 found: javac 1.8.0_191
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> No log file found in classpath.
> >> Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
> >> Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> :installJBrowseWebOnly
> >> JBrowse already exists
> >> From https://github.com/gmod/jbrowse
> >>  * tag                 1.15.4-release -> FETCH_HEAD
> >> Already up to date.
> >> yarn install v1.12.3
> >> [1/4] Resolving packages...
> >> success Already up-to-date.
> >> Done in 0.48s.
> >> yarn install v1.12.3
> >> info No lockfile found.
> >> [1/4] Resolving packages...
> >> [2/4] Fetching packages...
> >> [3/4] Linking dependencies...
> >> [4/4] Building fresh packages...
> >> success Saved lockfile.
> >> Done in 0.78s.
> >> Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> Evaluating plugin WebApollo=[included:true]
> >> Plugin jbrowse/plugins/WebApollo exists and appears valid.
> >> Evaluating plugin RegexSequenceSearch=[included:true]
> >> Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
> >> Evaluating plugin HideTrackLabels=[included:true]
> >> Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.
> >>
> >> > @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> >> > webpack
> >>
> >> clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
> >> jbrowse-glob-loader: building 203 JBrowse modules
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
> >> jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
> >> jbrowse-glob-loader: adding plugin module WebApollo/Permission
> >> jbrowse-glob-loader: adding plugin module WebApollo/main
> >> jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
> >> jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/EUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
> >> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
> >> jbrowse-glob-loader: adding plugin module DebugEvents/main
> >> jbrowse-glob-loader: adding plugin module CategoryUrl/main
> >> jbrowse-glob-loader: discovered a total of 247 modules
> >> jbrowse-glob-loader: skipping entry point module JBrowse/main
> >> Hash: 9eaefe2aad6bc3d71862
> >> Version: webpack 3.12.0
> >> Time: 9380ms
> >>                     Asset       Size         Chunks                    Chunk Names
> >>           0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]        
> >>               0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big]  
> >>               2.bundle.js     145 kB              2  [emitted]        
> >>               3.bundle.js     531 kB              3  [emitted]  [big]  
> >>               4.bundle.js     398 kB              4  [emitted]  [big]  
> >>               5.bundle.js    1.68 kB              5  [emitted]        
> >>               6.bundle.js  920 bytes              6  [emitted]        
> >>     run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
> >>         browser.bundle.js     364 kB              8  [emitted]  [big]  browser
> >>            main.bundle.js     375 kB              9  [emitted]  [big]  main
> >>               1.bundle.js     456 kB              1  [emitted]  [big]  
> >>           1.bundle.js.map     611 kB              1  [emitted]        
> >>           2.bundle.js.map     200 kB              2  [emitted]        
> >>           3.bundle.js.map     691 kB              3  [emitted]        
> >>           4.bundle.js.map     504 kB              4  [emitted]        
> >>           5.bundle.js.map    1.87 kB              5  [emitted]        
> >>           6.bundle.js.map    1.13 kB              6  [emitted]        
> >> run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
> >>     browser.bundle.js.map     517 kB              8  [emitted]         browser
> >>        main.bundle.js.map     537 kB              9  [emitted]         main
> >>  dojo/resources/blank.gif   43 bytes                 [emitted]        
> >>  [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
> >>  [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
> >>  [373] ./src/JBrowse/main.js 13 kB {9} [built]
> >>  [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
> >>  [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
> >>  [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
> >>  [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
> >>  [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
> >>  [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
> >>  [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
> >>  [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
> >>  [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
> >>  [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
> >>  [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
> >>  [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
> >>     + 1485 hidden modules
> >> :javac
> >> :gwtc
> >>
> >> BUILD SUCCESSFUL
> >>
> >> Total time: 54.871 secs
> >>
> >> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> >> | Compiling 6 source files
> >>
> >> | Compiling 6 source files.....
> >> ***
> >> Metrics servlet injected into web.xml
> >> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> >> ***
> >> | Running Grails application
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> | Server running. Browse to http://localhost:8080/apollo
> >> Configuring Shiro ...
> >> Shiro Configured
> >> | Parent process shutdown. Exiting...
> >> | Error Forked Grails VM exited with error
> >>
> >> Best
> >> Quanwei
> >>
> >>
> >>
> >> 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.
> >
> >
> >
> >
> > 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.
>
>
>
>
> 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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Re: Error Forked Grails VM exited with error

Quanwei Zhang
Thank you so much your patient and time. But I still can not get it work. Please see below for the information you asked

1. tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out
By the above command I get information like below. But is seems they are all old information (no information for today)
07-Jan-2019 18:14:50.418 SEVERE [main] org.apache.catalina.core.StandardServer.await Failed to create server shutdown socket on address [localhost] and port [8005] (base port [8005] and offset [0])
 java.net.BindException: Can't assign requested address (Bind failed)
        at java.net.PlainSocketImpl.socketBind(Native Method)
        at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
        at java.net.ServerSocket.bind(ServerSocket.java:375)
        at java.net.ServerSocket.<init>(ServerSocket.java:237)
        at org.apache.catalina.core.StandardServer.await(StandardServer.java:587)
        at org.apache.catalina.startup.Catalina.await(Catalina.java:725)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:671)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:350)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:492)

07-Jan-2019 18:14:50.419 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.429 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.430 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
07-Jan-2019 18:14:50.450 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.453 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]

2. If you connect to http://localhost:8084/   do you see something?

I can not see anything, just saying can not connect.

3. Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

$        ls /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
ROOT        docs        examples    host-manager    manager


4. Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.
This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
e.g.,:
cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war
When tomcat starts it will unwrap the war file into a directory called “apollo”

I did what you suggested, now we have below files under /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/
ROOT        apollo.war    docs        examples    host-manager    manager

5. You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

I run ./apollo run-local 8082, it stop at
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo

But still I can not connect to http://localhost:8082/apollo. And I did not find the unwrap the war file into a directory called “apollo” under tomcat.




Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午3:22写道:



> On Jan 9, 2019, at 11:13 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Thank you very much. I am not not familiar with those things, but please see below that I get. Any ideas from the information below?
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> $ netstat -tan | grep 8084   
> tcp4       0      0  *.8084                 *.*                    LISTEN


This is good!

>
> 2 - Also, what do you see in the tomcat logs?
>
> Do you mean the log files below. It seems strange that there is no log file generated today.
>
> $ ls -l /usr/local/Cellar/tomcat/9.0.14/libexec/logs/
> total 56
> -rw-r-----  1 qwzhang  admin  8666 Jan  7 18:14 catalina.2019-01-07.log
> -rw-r-----  1 qwzhang  admin  8714 Jan  7 18:14 catalina.out
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 host-manager.2019-01-07.log
> -rw-r-----  1 qwzhang  admin   650 Jan  7 18:14 localhost.2019-01-07.log
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 localhost_access_log.2019-01-07.txt
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 manager.2019-01-07.log


In a separate terminal do:

tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out

This is give output if anything happens.

>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
> It shows Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server “localhost"

If you connect to http://localhost:8084/   do you see something?

Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

(Relevant to below)

> 4 - What is the name of war file you generated?
> Sorry I am not familiar with this. Would you please tell me where to find the war file?


Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.

This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

e.g.,:

cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war

When tomcat starts it will unwrap the war file into a directory called “apollo”

>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
> When I tried "./apollo run-local 8085" I get the following message. Maybe I already tried the port when I tested it.
> Running Grails application
> Error Server failed to start for port 8085: Address already in use (Bind failed) (Use --stacktrace to see the full trace)
> If I try "./apollo run-local 8083" and try to connect http://localhost:8084/apollo, still get the same information.
> Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server "localhost"
>

You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

But hopefully step 4 works.

Nathan

> Best
> Quanwei
>
> Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午1:22写道:
>
> A few questions:
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> 2 - Also, what do you see in the tomcat logs?
>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
>
> 4 - What is the name of war file you generated?
>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
>
>
> Nathan
>
> > On Jan 9, 2019, at 9:51 AM, Quanwei Zhang <[hidden email]> wrote:
> >
> > Dear Nathan:
> >
> > Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
> > Do you have any suggestion?
> >
> >
> > .....
> > BUILD SUCCESSFUL
> >
> > Total time: 57.359 secs
> >
> > This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> > | Compiling 7 source files
> >
> > | Compiling 7 source files.....
> > ***
> > Metrics servlet injected into web.xml
> > Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> > ***
> > | Running Grails application
> >
> > Configuring Shiro ...
> >
> > Shiro Configured
> > Starting Quartz Scheduler in QuartzFactoryBean
> > | Server running. Browse to http://localhost:8084/apollo
> >
> >
> > #Change in the BuildConfig.groovy file
> > //forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > grails.project.fork = [
> >         // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
> >         //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >
> >         compile: false,
> >         test   : false,
> >         run    : false,
> >         war    : false,
> >         console : false
> >         // configure settings for the test-app JVM, uses the daemon by default
> >         //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >         // configure settings for the run-app JVM
> >         //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the run-war JVM
> >         //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the Console UI JVM
> >         //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > ]
> >
> > if (System.getProperty("grails.debug")) {
> >     //grails.project.fork.war += [debug: true]
> >     grails.project.fork.run = false
> >     println "Using debug for run"
> > }
> >
> >
> > Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:
> >
> > Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though).
> >
> > A couple of things to try:
> >
> > 1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are. 
> >
> > 2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:
> >
> > https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L14
> >
> > And re-deploying it.
> >
> > Nathan
> >
> >
> >
> >
> >
> >> On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:
> >>
> >> Hi:
> >>
> >> I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.
> >>
> >> I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
> >> export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"
> >>
> >> I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.
> >>
> >> Node Version: 10
> >> Npm Version: 6
> >> Yarn Version: 1
> >> javac 1.8.0_191 found
> >> javac installed
> >> JDK 1.8 found: javac 1.8.0_191
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> No log file found in classpath.
> >> Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
> >> Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> :installJBrowseWebOnly
> >> JBrowse already exists
> >> From https://github.com/gmod/jbrowse
> >>  * tag                 1.15.4-release -> FETCH_HEAD
> >> Already up to date.
> >> yarn install v1.12.3
> >> [1/4] Resolving packages...
> >> success Already up-to-date.
> >> Done in 0.48s.
> >> yarn install v1.12.3
> >> info No lockfile found.
> >> [1/4] Resolving packages...
> >> [2/4] Fetching packages...
> >> [3/4] Linking dependencies...
> >> [4/4] Building fresh packages...
> >> success Saved lockfile.
> >> Done in 0.78s.
> >> Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> Evaluating plugin WebApollo=[included:true]
> >> Plugin jbrowse/plugins/WebApollo exists and appears valid.
> >> Evaluating plugin RegexSequenceSearch=[included:true]
> >> Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
> >> Evaluating plugin HideTrackLabels=[included:true]
> >> Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.
> >>
> >> > @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> >> > webpack
> >>
> >> clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
> >> jbrowse-glob-loader: building 203 JBrowse modules
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
> >> jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
> >> jbrowse-glob-loader: adding plugin module WebApollo/Permission
> >> jbrowse-glob-loader: adding plugin module WebApollo/main
> >> jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
> >> jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/EUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
> >> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
> >> jbrowse-glob-loader: adding plugin module DebugEvents/main
> >> jbrowse-glob-loader: adding plugin module CategoryUrl/main
> >> jbrowse-glob-loader: discovered a total of 247 modules
> >> jbrowse-glob-loader: skipping entry point module JBrowse/main
> >> Hash: 9eaefe2aad6bc3d71862
> >> Version: webpack 3.12.0
> >> Time: 9380ms
> >>                     Asset       Size         Chunks                    Chunk Names
> >>           0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]         
> >>               0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
> >>               2.bundle.js     145 kB              2  [emitted]         
> >>               3.bundle.js     531 kB              3  [emitted]  [big] 
> >>               4.bundle.js     398 kB              4  [emitted]  [big] 
> >>               5.bundle.js    1.68 kB              5  [emitted]         
> >>               6.bundle.js  920 bytes              6  [emitted]         
> >>     run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
> >>         browser.bundle.js     364 kB              8  [emitted]  [big]  browser
> >>            main.bundle.js     375 kB              9  [emitted]  [big]  main
> >>               1.bundle.js     456 kB              1  [emitted]  [big] 
> >>           1.bundle.js.map     611 kB              1  [emitted]         
> >>           2.bundle.js.map     200 kB              2  [emitted]         
> >>           3.bundle.js.map     691 kB              3  [emitted]         
> >>           4.bundle.js.map     504 kB              4  [emitted]         
> >>           5.bundle.js.map    1.87 kB              5  [emitted]         
> >>           6.bundle.js.map    1.13 kB              6  [emitted]         
> >> run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
> >>     browser.bundle.js.map     517 kB              8  [emitted]         browser
> >>        main.bundle.js.map     537 kB              9  [emitted]         main
> >>  dojo/resources/blank.gif   43 bytes                 [emitted]         
> >>  [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
> >>  [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
> >>  [373] ./src/JBrowse/main.js 13 kB {9} [built]
> >>  [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
> >>  [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
> >>  [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
> >>  [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
> >>  [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
> >>  [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
> >>  [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
> >>  [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
> >>  [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
> >>  [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
> >>  [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
> >>  [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
> >>     + 1485 hidden modules
> >> :javac
> >> :gwtc
> >>
> >> BUILD SUCCESSFUL
> >>
> >> Total time: 54.871 secs
> >>
> >> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> >> | Compiling 6 source files
> >>
> >> | Compiling 6 source files.....
> >> ***
> >> Metrics servlet injected into web.xml
> >> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> >> ***
> >> | Running Grails application
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> | Server running. Browse to http://localhost:8080/apollo
> >> Configuring Shiro ...
> >> Shiro Configured
> >> | Parent process shutdown. Exiting...
> >> | Error Forked Grails VM exited with error
> >>
> >> Best
> >> Quanwei
> >>
> >>
> >>
> >> 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.
> >
> >
> >
> >
> > 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.
>
>
>
>
> 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.





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: Error Forked Grails VM exited with error

nathandunn

I’m guessing you’re already running a tomcat on port 8080 as it looks like you’re getting a bind exception on port 8080 from the one installed with home-brew.   That’s why it didn’t unwrap the war file.  Tomcat from home-brew is either dead or running in a broken state. 

You’ll need to find that other tomcat and kill it and then restart the home-brew (or conversely, just use the original tomcat and remove the home-brew one). 

You can verify by typing:

ps -ef | grep catalina 

and

netstat -tan | grep LISTEN

To verify that something is already running.  

I’m not sure if the dockerized version would be any easier (depending on your familiarity): https://github.com/GMOD/docker-apollo


When using ./apollo run-local 8082 (or any number), are you leaving the terminal up when you check the web browser? 

Putting: http://localhost:8082/apollo or http://127.0.0.1:8082/apollo should work in a web browser if that is running in a terminal with no errors.  


Nathan



On Jan 9, 2019, at 1:02 PM, Quanwei Zhang <[hidden email]> wrote:

Thank you so much your patient and time. But I still can not get it work. Please see below for the information you asked

1. tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out
By the above command I get information like below. But is seems they are all old information (no information for today)
07-Jan-2019 18:14:50.418 SEVERE [main] org.apache.catalina.core.StandardServer.await Failed to create server shutdown socket on address [localhost] and port [8005] (base port [8005] and offset [0])
 java.net.BindException: Can't assign requested address (Bind failed)
        at java.net.PlainSocketImpl.socketBind(Native Method)
        at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
        at java.net.ServerSocket.bind(ServerSocket.java:375)
        at java.net.ServerSocket.<init>(ServerSocket.java:237)
        at org.apache.catalina.core.StandardServer.await(StandardServer.java:587)
        at org.apache.catalina.startup.Catalina.await(Catalina.java:725)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:671)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:350)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:492)

07-Jan-2019 18:14:50.419 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.429 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.430 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
07-Jan-2019 18:14:50.450 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.453 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]

2. If you connect to http://localhost:8084/   do you see something?

I can not see anything, just saying can not connect.

3. Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

$        ls /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
ROOT        docs        examples    host-manager    manager


4. Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.
This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
e.g.,:
cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war
When tomcat starts it will unwrap the war file into a directory called “apollo”

I did what you suggested, now we have below files under /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/
ROOT        apollo.war    docs        examples    host-manager    manager

5. You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

I run ./apollo run-local 8082, it stop at
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo

But still I can not connect to http://localhost:8082/apollo. And I did not find the unwrap the war file into a directory called “apollo” under tomcat.




Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午3:22写道:



> On Jan 9, 2019, at 11:13 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Thank you very much. I am not not familiar with those things, but please see below that I get. Any ideas from the information below?
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> $ netstat -tan | grep 8084   
> tcp4       0      0  *.8084                 *.*                    LISTEN


This is good!

>
> 2 - Also, what do you see in the tomcat logs?
>
> Do you mean the log files below. It seems strange that there is no log file generated today.
>
> $ ls -l /usr/local/Cellar/tomcat/9.0.14/libexec/logs/
> total 56
> -rw-r-----  1 qwzhang  admin  8666 Jan  7 18:14 catalina.2019-01-07.log
> -rw-r-----  1 qwzhang  admin  8714 Jan  7 18:14 catalina.out
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 host-manager.2019-01-07.log
> -rw-r-----  1 qwzhang  admin   650 Jan  7 18:14 localhost.2019-01-07.log
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 localhost_access_log.2019-01-07.txt
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 manager.2019-01-07.log


In a separate terminal do:

tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out

This is give output if anything happens.

>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
> It shows Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server “localhost"

If you connect to http://localhost:8084/   do you see something?

Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

(Relevant to below)

> 4 - What is the name of war file you generated?
> Sorry I am not familiar with this. Would you please tell me where to find the war file?


Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.

This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

e.g.,:

cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war

When tomcat starts it will unwrap the war file into a directory called “apollo”

>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
> When I tried "./apollo run-local 8085" I get the following message. Maybe I already tried the port when I tested it.
> Running Grails application
> Error Server failed to start for port 8085: Address already in use (Bind failed) (Use --stacktrace to see the full trace)
> If I try "./apollo run-local 8083" and try to connect http://localhost:8084/apollo, still get the same information.
> Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server "localhost"
>

You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

But hopefully step 4 works.

Nathan

> Best
> Quanwei
>
> Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午1:22写道:
>
> A few questions:
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> 2 - Also, what do you see in the tomcat logs?
>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
>
> 4 - What is the name of war file you generated?
>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
>
>
> Nathan
>
> > On Jan 9, 2019, at 9:51 AM, Quanwei Zhang <[hidden email]> wrote:
> >
> > Dear Nathan:
> >
> > Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
> > Do you have any suggestion?
> >
> >
> > .....
> > BUILD SUCCESSFUL
> >
> > Total time: 57.359 secs
> >
> > This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> > | Compiling 7 source files
> >
> > | Compiling 7 source files.....
> > ***
> > Metrics servlet injected into web.xml
> > Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> > ***
> > | Running Grails application
> >
> > Configuring Shiro ...
> >
> > Shiro Configured
> > Starting Quartz Scheduler in QuartzFactoryBean
> > | Server running. Browse to http://localhost:8084/apollo
> >
> >
> > #Change in the BuildConfig.groovy file
> > //forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > grails.project.fork = [
> >         // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
> >         //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >
> >         compile: false,
> >         test   : false,
> >         run    : false,
> >         war    : false,
> >         console : false
> >         // configure settings for the test-app JVM, uses the daemon by default
> >         //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >         // configure settings for the run-app JVM
> >         //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the run-war JVM
> >         //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the Console UI JVM
> >         //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > ]
> >
> > if (System.getProperty("grails.debug")) {
> >     //grails.project.fork.war += [debug: true]
> >     grails.project.fork.run = false
> >     println "Using debug for run"
> > }
> >
> >
> > Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:
> >
> > Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though).
> >
> > A couple of things to try:
> >
> > 1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are. 
> >
> > 2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:
> >
> > https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L14
> >
> > And re-deploying it.
> >
> > Nathan
> >
> >
> >
> >
> >
> >> On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:
> >>
> >> Hi:
> >>
> >> I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.
> >>
> >> I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
> >> export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"
> >>
> >> I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.
> >>
> >> Node Version: 10
> >> Npm Version: 6
> >> Yarn Version: 1
> >> javac 1.8.0_191 found
> >> javac installed
> >> JDK 1.8 found: javac 1.8.0_191
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> No log file found in classpath.
> >> Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
> >> Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> :installJBrowseWebOnly
> >> JBrowse already exists
> >> From https://github.com/gmod/jbrowse
> >>  * tag                 1.15.4-release -> FETCH_HEAD
> >> Already up to date.
> >> yarn install v1.12.3
> >> [1/4] Resolving packages...
> >> success Already up-to-date.
> >> Done in 0.48s.
> >> yarn install v1.12.3
> >> info No lockfile found.
> >> [1/4] Resolving packages...
> >> [2/4] Fetching packages...
> >> [3/4] Linking dependencies...
> >> [4/4] Building fresh packages...
> >> success Saved lockfile.
> >> Done in 0.78s.
> >> Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> Evaluating plugin WebApollo=[included:true]
> >> Plugin jbrowse/plugins/WebApollo exists and appears valid.
> >> Evaluating plugin RegexSequenceSearch=[included:true]
> >> Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
> >> Evaluating plugin HideTrackLabels=[included:true]
> >> Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.
> >>
> >> > @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> >> > webpack
> >>
> >> clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
> >> jbrowse-glob-loader: building 203 JBrowse modules
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
> >> jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
> >> jbrowse-glob-loader: adding plugin module WebApollo/Permission
> >> jbrowse-glob-loader: adding plugin module WebApollo/main
> >> jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
> >> jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/EUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
> >> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
> >> jbrowse-glob-loader: adding plugin module DebugEvents/main
> >> jbrowse-glob-loader: adding plugin module CategoryUrl/main
> >> jbrowse-glob-loader: discovered a total of 247 modules
> >> jbrowse-glob-loader: skipping entry point module JBrowse/main
> >> Hash: 9eaefe2aad6bc3d71862
> >> Version: webpack 3.12.0
> >> Time: 9380ms
> >>                     Asset       Size         Chunks                    Chunk Names
> >>           0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]         
> >>               0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
> >>               2.bundle.js     145 kB              2  [emitted]         
> >>               3.bundle.js     531 kB              3  [emitted]  [big] 
> >>               4.bundle.js     398 kB              4  [emitted]  [big] 
> >>               5.bundle.js    1.68 kB              5  [emitted]         
> >>               6.bundle.js  920 bytes              6  [emitted]         
> >>     run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
> >>         browser.bundle.js     364 kB              8  [emitted]  [big]  browser
> >>            main.bundle.js     375 kB              9  [emitted]  [big]  main
> >>               1.bundle.js     456 kB              1  [emitted]  [big] 
> >>           1.bundle.js.map     611 kB              1  [emitted]         
> >>           2.bundle.js.map     200 kB              2  [emitted]         
> >>           3.bundle.js.map     691 kB              3  [emitted]         
> >>           4.bundle.js.map     504 kB              4  [emitted]         
> >>           5.bundle.js.map    1.87 kB              5  [emitted]         
> >>           6.bundle.js.map    1.13 kB              6  [emitted]         
> >> run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
> >>     browser.bundle.js.map     517 kB              8  [emitted]         browser
> >>        main.bundle.js.map     537 kB              9  [emitted]         main
> >>  dojo/resources/blank.gif   43 bytes                 [emitted]         
> >>  [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
> >>  [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
> >>  [373] ./src/JBrowse/main.js 13 kB {9} [built]
> >>  [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
> >>  [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
> >>  [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
> >>  [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
> >>  [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
> >>  [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
> >>  [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
> >>  [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
> >>  [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
> >>  [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
> >>  [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
> >>  [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
> >>     + 1485 hidden modules
> >> :javac
> >> :gwtc
> >>
> >> BUILD SUCCESSFUL
> >>
> >> Total time: 54.871 secs
> >>
> >> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> >> | Compiling 6 source files
> >>
> >> | Compiling 6 source files.....
> >> ***
> >> Metrics servlet injected into web.xml
> >> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> >> ***
> >> | Running Grails application
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> | Server running. Browse to http://localhost:8080/apollo
> >> Configuring Shiro ...
> >> Shiro Configured
> >> | Parent process shutdown. Exiting...
> >> | Error Forked Grails VM exited with error
> >>
> >> Best
> >> Quanwei
> >>
> >>
> >>
> >> 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.
> >
> >
> >
> >
> > 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.
>
>
>
>
> 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.




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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Re: Error Forked Grails VM exited with error

Quanwei Zhang
Yes. leaving the terminal up.
I just tried http://127.0.0.1:8082/apollo, this seems works. But after register as an user  I get some error on the terminal. The attached file shows what I get from in the browser.

2019-01-09 16:44:28,424 [http-nio-8082-exec-5] WARN  apollo.PreferenceService  - No user present, so using the client token
| Error 2019-01-09 16:44:28,442 [http-nio-8082-exec-3] ERROR apollo.PermissionService  - Username not supplied so can not authenticate.
| Error 2019-01-09 16:44:28,462 [http-nio-8082-exec-3] ERROR apollo.PermissionService  - User null does not exist in the database.
| Error 2019-01-09 16:44:28,488 [http-nio-8082-exec-10] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-09 16:44:28,489 [http-nio-8082-exec-10] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2019-01-09 16:44:28,489 [http-nio-8082-exec-10] ERROR apollo.UserController  - Failed to authenticate
| Error 2019-01-09 16:44:28,599 [http-nio-8082-exec-6] ERROR apollo.PermissionService  - Username not supplied so can not authenticate.
| Error 2019-01-09 16:44:28,604 [http-nio-8082-exec-6] ERROR apollo.PermissionService  - User null does not exist in the database.
| Error 2019-01-09 16:46:13,566 [http-nio-8082-exec-10] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-09 16:46:13,766 [http-nio-8082-exec-7] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-09 16:46:13,804 [http-nio-8082-exec-6] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2019-01-09 16:47:18,249 [http-nio-8082-exec-10] WARN  apollo.AnnotatorController  - Permission exception: User does not have permission for any organisms.




Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午4:40写道:

I’m guessing you’re already running a tomcat on port 8080 as it looks like you’re getting a bind exception on port 8080 from the one installed with home-brew.   That’s why it didn’t unwrap the war file.  Tomcat from home-brew is either dead or running in a broken state. 

You’ll need to find that other tomcat and kill it and then restart the home-brew (or conversely, just use the original tomcat and remove the home-brew one). 

You can verify by typing:

ps -ef | grep catalina 

and

netstat -tan | grep LISTEN

To verify that something is already running.  

I’m not sure if the dockerized version would be any easier (depending on your familiarity): https://github.com/GMOD/docker-apollo


When using ./apollo run-local 8082 (or any number), are you leaving the terminal up when you check the web browser? 

Putting: http://localhost:8082/apollo or http://127.0.0.1:8082/apollo should work in a web browser if that is running in a terminal with no errors.  


Nathan



On Jan 9, 2019, at 1:02 PM, Quanwei Zhang <[hidden email]> wrote:

Thank you so much your patient and time. But I still can not get it work. Please see below for the information you asked

1. tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out
By the above command I get information like below. But is seems they are all old information (no information for today)
07-Jan-2019 18:14:50.418 SEVERE [main] org.apache.catalina.core.StandardServer.await Failed to create server shutdown socket on address [localhost] and port [8005] (base port [8005] and offset [0])
 java.net.BindException: Can't assign requested address (Bind failed)
        at java.net.PlainSocketImpl.socketBind(Native Method)
        at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
        at java.net.ServerSocket.bind(ServerSocket.java:375)
        at java.net.ServerSocket.<init>(ServerSocket.java:237)
        at org.apache.catalina.core.StandardServer.await(StandardServer.java:587)
        at org.apache.catalina.startup.Catalina.await(Catalina.java:725)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:671)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:350)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:492)

07-Jan-2019 18:14:50.419 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.429 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.430 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
07-Jan-2019 18:14:50.450 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.453 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]

2. If you connect to http://localhost:8084/   do you see something?

I can not see anything, just saying can not connect.

3. Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

$        ls /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
ROOT        docs        examples    host-manager    manager


4. Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.
This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
e.g.,:
cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war
When tomcat starts it will unwrap the war file into a directory called “apollo”

I did what you suggested, now we have below files under /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/
ROOT        apollo.war    docs        examples    host-manager    manager

5. You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

I run ./apollo run-local 8082, it stop at
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo

But still I can not connect to http://localhost:8082/apollo. And I did not find the unwrap the war file into a directory called “apollo” under tomcat.




Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午3:22写道:



> On Jan 9, 2019, at 11:13 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Thank you very much. I am not not familiar with those things, but please see below that I get. Any ideas from the information below?
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> $ netstat -tan | grep 8084   
> tcp4       0      0  *.8084                 *.*                    LISTEN


This is good!

>
> 2 - Also, what do you see in the tomcat logs?
>
> Do you mean the log files below. It seems strange that there is no log file generated today.
>
> $ ls -l /usr/local/Cellar/tomcat/9.0.14/libexec/logs/
> total 56
> -rw-r-----  1 qwzhang  admin  8666 Jan  7 18:14 catalina.2019-01-07.log
> -rw-r-----  1 qwzhang  admin  8714 Jan  7 18:14 catalina.out
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 host-manager.2019-01-07.log
> -rw-r-----  1 qwzhang  admin   650 Jan  7 18:14 localhost.2019-01-07.log
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 localhost_access_log.2019-01-07.txt
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 manager.2019-01-07.log


In a separate terminal do:

tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out

This is give output if anything happens.

>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
> It shows Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server “localhost"

If you connect to http://localhost:8084/   do you see something?

Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

(Relevant to below)

> 4 - What is the name of war file you generated?
> Sorry I am not familiar with this. Would you please tell me where to find the war file?


Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.

This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

e.g.,:

cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war

When tomcat starts it will unwrap the war file into a directory called “apollo”

>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
> When I tried "./apollo run-local 8085" I get the following message. Maybe I already tried the port when I tested it.
> Running Grails application
> Error Server failed to start for port 8085: Address already in use (Bind failed) (Use --stacktrace to see the full trace)
> If I try "./apollo run-local 8083" and try to connect http://localhost:8084/apollo, still get the same information.
> Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server "localhost"
>

You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

But hopefully step 4 works.

Nathan

> Best
> Quanwei
>
> Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午1:22写道:
>
> A few questions:
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> 2 - Also, what do you see in the tomcat logs?
>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
>
> 4 - What is the name of war file you generated?
>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
>
>
> Nathan
>
> > On Jan 9, 2019, at 9:51 AM, Quanwei Zhang <[hidden email]> wrote:
> >
> > Dear Nathan:
> >
> > Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
> > Do you have any suggestion?
> >
> >
> > .....
> > BUILD SUCCESSFUL
> >
> > Total time: 57.359 secs
> >
> > This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> > | Compiling 7 source files
> >
> > | Compiling 7 source files.....
> > ***
> > Metrics servlet injected into web.xml
> > Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> > ***
> > | Running Grails application
> >
> > Configuring Shiro ...
> >
> > Shiro Configured
> > Starting Quartz Scheduler in QuartzFactoryBean
> > | Server running. Browse to http://localhost:8084/apollo
> >
> >
> > #Change in the BuildConfig.groovy file
> > //forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > grails.project.fork = [
> >         // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
> >         //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >
> >         compile: false,
> >         test   : false,
> >         run    : false,
> >         war    : false,
> >         console : false
> >         // configure settings for the test-app JVM, uses the daemon by default
> >         //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >         // configure settings for the run-app JVM
> >         //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the run-war JVM
> >         //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the Console UI JVM
> >         //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > ]
> >
> > if (System.getProperty("grails.debug")) {
> >     //grails.project.fork.war += [debug: true]
> >     grails.project.fork.run = false
> >     println "Using debug for run"
> > }
> >
> >
> > Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:
> >
> > Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though).
> >
> > A couple of things to try:
> >
> > 1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are. 
> >
> > 2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:
> >
> > https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L14
> >
> > And re-deploying it.
> >
> > Nathan
> >
> >
> >
> >
> >
> >> On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:
> >>
> >> Hi:
> >>
> >> I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.
> >>
> >> I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
> >> export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"
> >>
> >> I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.
> >>
> >> Node Version: 10
> >> Npm Version: 6
> >> Yarn Version: 1
> >> javac 1.8.0_191 found
> >> javac installed
> >> JDK 1.8 found: javac 1.8.0_191
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> No log file found in classpath.
> >> Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
> >> Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> :installJBrowseWebOnly
> >> JBrowse already exists
> >> From https://github.com/gmod/jbrowse
> >>  * tag                 1.15.4-release -> FETCH_HEAD
> >> Already up to date.
> >> yarn install v1.12.3
> >> [1/4] Resolving packages...
> >> success Already up-to-date.
> >> Done in 0.48s.
> >> yarn install v1.12.3
> >> info No lockfile found.
> >> [1/4] Resolving packages...
> >> [2/4] Fetching packages...
> >> [3/4] Linking dependencies...
> >> [4/4] Building fresh packages...
> >> success Saved lockfile.
> >> Done in 0.78s.
> >> Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> Evaluating plugin WebApollo=[included:true]
> >> Plugin jbrowse/plugins/WebApollo exists and appears valid.
> >> Evaluating plugin RegexSequenceSearch=[included:true]
> >> Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
> >> Evaluating plugin HideTrackLabels=[included:true]
> >> Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.
> >>
> >> > @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> >> > webpack
> >>
> >> clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
> >> jbrowse-glob-loader: building 203 JBrowse modules
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
> >> jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
> >> jbrowse-glob-loader: adding plugin module WebApollo/Permission
> >> jbrowse-glob-loader: adding plugin module WebApollo/main
> >> jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
> >> jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/EUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
> >> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
> >> jbrowse-glob-loader: adding plugin module DebugEvents/main
> >> jbrowse-glob-loader: adding plugin module CategoryUrl/main
> >> jbrowse-glob-loader: discovered a total of 247 modules
> >> jbrowse-glob-loader: skipping entry point module JBrowse/main
> >> Hash: 9eaefe2aad6bc3d71862
> >> Version: webpack 3.12.0
> >> Time: 9380ms
> >>                     Asset       Size         Chunks                    Chunk Names
> >>           0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]         
> >>               0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
> >>               2.bundle.js     145 kB              2  [emitted]         
> >>               3.bundle.js     531 kB              3  [emitted]  [big] 
> >>               4.bundle.js     398 kB              4  [emitted]  [big] 
> >>               5.bundle.js    1.68 kB              5  [emitted]         
> >>               6.bundle.js  920 bytes              6  [emitted]         
> >>     run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
> >>         browser.bundle.js     364 kB              8  [emitted]  [big]  browser
> >>            main.bundle.js     375 kB              9  [emitted]  [big]  main
> >>               1.bundle.js     456 kB              1  [emitted]  [big] 
> >>           1.bundle.js.map     611 kB              1  [emitted]         
> >>           2.bundle.js.map     200 kB              2  [emitted]         
> >>           3.bundle.js.map     691 kB              3  [emitted]         
> >>           4.bundle.js.map     504 kB              4  [emitted]         
> >>           5.bundle.js.map    1.87 kB              5  [emitted]         
> >>           6.bundle.js.map    1.13 kB              6  [emitted]         
> >> run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
> >>     browser.bundle.js.map     517 kB              8  [emitted]         browser
> >>        main.bundle.js.map     537 kB              9  [emitted]         main
> >>  dojo/resources/blank.gif   43 bytes                 [emitted]         
> >>  [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
> >>  [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
> >>  [373] ./src/JBrowse/main.js 13 kB {9} [built]
> >>  [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
> >>  [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
> >>  [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
> >>  [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
> >>  [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
> >>  [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
> >>  [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
> >>  [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
> >>  [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
> >>  [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
> >>  [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
> >>  [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
> >>     + 1485 hidden modules
> >> :javac
> >> :gwtc
> >>
> >> BUILD SUCCESSFUL
> >>
> >> Total time: 54.871 secs
> >>
> >> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> >> | Compiling 6 source files
> >>
> >> | Compiling 6 source files.....
> >> ***
> >> Metrics servlet injected into web.xml
> >> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> >> ***
> >> | Running Grails application
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> | Server running. Browse to http://localhost:8080/apollo
> >> Configuring Shiro ...
> >> Shiro Configured
> >> | Parent process shutdown. Exiting...
> >> | Error Forked Grails VM exited with error
> >>
> >> Best
> >> Quanwei
> >>
> >>
> >>
> >> 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.
> >
> >
> >
> >
> > 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.
>
>
>
>
> 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.




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.





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: Error Forked Grails VM exited with error

nathandunn

Nope.  You are good.   Now you add some organisms and start annotating. 


If you want to run it on tomcat that is fine if you have other users to support, but if its just yourself on your laptop then run-local is fine. 

Just make sure that if you stop and start that your data has been retained (i.e., you won’t have to re-register).    The data, by default in dev mode is stored in AnnotationDatabase:devDb.h2.db

Nathan


On Jan 9, 2019, at 1:57 PM, Quanwei Zhang <[hidden email]> wrote:

Yes. leaving the terminal up.
I just tried http://127.0.0.1:8082/apollo, this seems works. But after register as an user  I get some error on the terminal. The attached file shows what I get from in the browser.

2019-01-09 16:44:28,424 [http-nio-8082-exec-5] WARN  apollo.PreferenceService  - No user present, so using the client token
| Error 2019-01-09 16:44:28,442 [http-nio-8082-exec-3] ERROR apollo.PermissionService  - Username not supplied so can not authenticate.
| Error 2019-01-09 16:44:28,462 [http-nio-8082-exec-3] ERROR apollo.PermissionService  - User null does not exist in the database.
| Error 2019-01-09 16:44:28,488 [http-nio-8082-exec-10] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-09 16:44:28,489 [http-nio-8082-exec-10] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2019-01-09 16:44:28,489 [http-nio-8082-exec-10] ERROR apollo.UserController  - Failed to authenticate
| Error 2019-01-09 16:44:28,599 [http-nio-8082-exec-6] ERROR apollo.PermissionService  - Username not supplied so can not authenticate.
| Error 2019-01-09 16:44:28,604 [http-nio-8082-exec-6] ERROR apollo.PermissionService  - User null does not exist in the database.
| Error 2019-01-09 16:46:13,566 [http-nio-8082-exec-10] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-09 16:46:13,766 [http-nio-8082-exec-7] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-09 16:46:13,804 [http-nio-8082-exec-6] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2019-01-09 16:47:18,249 [http-nio-8082-exec-10] WARN  apollo.AnnotatorController  - Permission exception: User does not have permission for any organisms.




Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午4:40写道:

I’m guessing you’re already running a tomcat on port 8080 as it looks like you’re getting a bind exception on port 8080 from the one installed with home-brew.   That’s why it didn’t unwrap the war file.  Tomcat from home-brew is either dead or running in a broken state. 

You’ll need to find that other tomcat and kill it and then restart the home-brew (or conversely, just use the original tomcat and remove the home-brew one). 

You can verify by typing:

ps -ef | grep catalina 

and

netstat -tan | grep LISTEN

To verify that something is already running.  

I’m not sure if the dockerized version would be any easier (depending on your familiarity): https://github.com/GMOD/docker-apollo


When using ./apollo run-local 8082 (or any number), are you leaving the terminal up when you check the web browser? 

Putting: http://localhost:8082/apollo or http://127.0.0.1:8082/apollo should work in a web browser if that is running in a terminal with no errors.  


Nathan



On Jan 9, 2019, at 1:02 PM, Quanwei Zhang <[hidden email]> wrote:

Thank you so much your patient and time. But I still can not get it work. Please see below for the information you asked

1. tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out
By the above command I get information like below. But is seems they are all old information (no information for today)
07-Jan-2019 18:14:50.418 SEVERE [main] org.apache.catalina.core.StandardServer.await Failed to create server shutdown socket on address [localhost] and port [8005] (base port [8005] and offset [0])
 java.net.BindException: Can't assign requested address (Bind failed)
        at java.net.PlainSocketImpl.socketBind(Native Method)
        at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
        at java.net.ServerSocket.bind(ServerSocket.java:375)
        at java.net.ServerSocket.<init>(ServerSocket.java:237)
        at org.apache.catalina.core.StandardServer.await(StandardServer.java:587)
        at org.apache.catalina.startup.Catalina.await(Catalina.java:725)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:671)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:350)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:492)

07-Jan-2019 18:14:50.419 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.429 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.430 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
07-Jan-2019 18:14:50.450 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.453 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]

2. If you connect to http://localhost:8084/   do you see something?

I can not see anything, just saying can not connect.

3. Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

$        ls /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
ROOT        docs        examples    host-manager    manager


4. Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.
This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
e.g.,:
cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war
When tomcat starts it will unwrap the war file into a directory called “apollo”

I did what you suggested, now we have below files under /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/
ROOT        apollo.war    docs        examples    host-manager    manager

5. You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

I run ./apollo run-local 8082, it stop at
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo

But still I can not connect to http://localhost:8082/apollo. And I did not find the unwrap the war file into a directory called “apollo” under tomcat.




Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午3:22写道:



> On Jan 9, 2019, at 11:13 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Thank you very much. I am not not familiar with those things, but please see below that I get. Any ideas from the information below?
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> $ netstat -tan | grep 8084   
> tcp4       0      0  *.8084                 *.*                    LISTEN


This is good!

>
> 2 - Also, what do you see in the tomcat logs?
>
> Do you mean the log files below. It seems strange that there is no log file generated today.
>
> $ ls -l /usr/local/Cellar/tomcat/9.0.14/libexec/logs/
> total 56
> -rw-r-----  1 qwzhang  admin  8666 Jan  7 18:14 catalina.2019-01-07.log
> -rw-r-----  1 qwzhang  admin  8714 Jan  7 18:14 catalina.out
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 host-manager.2019-01-07.log
> -rw-r-----  1 qwzhang  admin   650 Jan  7 18:14 localhost.2019-01-07.log
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 localhost_access_log.2019-01-07.txt
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 manager.2019-01-07.log


In a separate terminal do:

tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out

This is give output if anything happens.

>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
> It shows Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server “localhost"

If you connect to http://localhost:8084/   do you see something?

Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

(Relevant to below)

> 4 - What is the name of war file you generated?
> Sorry I am not familiar with this. Would you please tell me where to find the war file?


Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.

This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

e.g.,:

cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war

When tomcat starts it will unwrap the war file into a directory called “apollo”

>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
> When I tried "./apollo run-local 8085" I get the following message. Maybe I already tried the port when I tested it.
> Running Grails application
> Error Server failed to start for port 8085: Address already in use (Bind failed) (Use --stacktrace to see the full trace)
> If I try "./apollo run-local 8083" and try to connect http://localhost:8084/apollo, still get the same information.
> Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server "localhost"
>

You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

But hopefully step 4 works.

Nathan

> Best
> Quanwei
>
> Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午1:22写道:
>
> A few questions:
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> 2 - Also, what do you see in the tomcat logs?
>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
>
> 4 - What is the name of war file you generated?
>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
>
>
> Nathan
>
> > On Jan 9, 2019, at 9:51 AM, Quanwei Zhang <[hidden email]> wrote:
> >
> > Dear Nathan:
> >
> > Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
> > Do you have any suggestion?
> >
> >
> > .....
> > BUILD SUCCESSFUL
> >
> > Total time: 57.359 secs
> >
> > This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> > | Compiling 7 source files
> >
> > | Compiling 7 source files.....
> > ***
> > Metrics servlet injected into web.xml
> > Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> > ***
> > | Running Grails application
> >
> > Configuring Shiro ...
> >
> > Shiro Configured
> > Starting Quartz Scheduler in QuartzFactoryBean
> > | Server running. Browse to http://localhost:8084/apollo
> >
> >
> > #Change in the BuildConfig.groovy file
> > //forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > grails.project.fork = [
> >         // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
> >         //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >
> >         compile: false,
> >         test   : false,
> >         run    : false,
> >         war    : false,
> >         console : false
> >         // configure settings for the test-app JVM, uses the daemon by default
> >         //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >         // configure settings for the run-app JVM
> >         //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the run-war JVM
> >         //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the Console UI JVM
> >         //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > ]
> >
> > if (System.getProperty("grails.debug")) {
> >     //grails.project.fork.war += [debug: true]
> >     grails.project.fork.run = false
> >     println "Using debug for run"
> > }
> >
> >
> > Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:
> >
> > Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though).
> >
> > A couple of things to try:
> >
> > 1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are. 
> >
> > 2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:
> >
> > https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L14
> >
> > And re-deploying it.
> >
> > Nathan
> >
> >
> >
> >
> >
> >> On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:
> >>
> >> Hi:
> >>
> >> I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.
> >>
> >> I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
> >> export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"
> >>
> >> I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.
> >>
> >> Node Version: 10
> >> Npm Version: 6
> >> Yarn Version: 1
> >> javac 1.8.0_191 found
> >> javac installed
> >> JDK 1.8 found: javac 1.8.0_191
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> No log file found in classpath.
> >> Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
> >> Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> :installJBrowseWebOnly
> >> JBrowse already exists
> >> From https://github.com/gmod/jbrowse
> >>  * tag                 1.15.4-release -> FETCH_HEAD
> >> Already up to date.
> >> yarn install v1.12.3
> >> [1/4] Resolving packages...
> >> success Already up-to-date.
> >> Done in 0.48s.
> >> yarn install v1.12.3
> >> info No lockfile found.
> >> [1/4] Resolving packages...
> >> [2/4] Fetching packages...
> >> [3/4] Linking dependencies...
> >> [4/4] Building fresh packages...
> >> success Saved lockfile.
> >> Done in 0.78s.
> >> Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> Evaluating plugin WebApollo=[included:true]
> >> Plugin jbrowse/plugins/WebApollo exists and appears valid.
> >> Evaluating plugin RegexSequenceSearch=[included:true]
> >> Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
> >> Evaluating plugin HideTrackLabels=[included:true]
> >> Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.
> >>
> >> > @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> >> > webpack
> >>
> >> clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
> >> jbrowse-glob-loader: building 203 JBrowse modules
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
> >> jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
> >> jbrowse-glob-loader: adding plugin module WebApollo/Permission
> >> jbrowse-glob-loader: adding plugin module WebApollo/main
> >> jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
> >> jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/EUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
> >> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
> >> jbrowse-glob-loader: adding plugin module DebugEvents/main
> >> jbrowse-glob-loader: adding plugin module CategoryUrl/main
> >> jbrowse-glob-loader: discovered a total of 247 modules
> >> jbrowse-glob-loader: skipping entry point module JBrowse/main
> >> Hash: 9eaefe2aad6bc3d71862
> >> Version: webpack 3.12.0
> >> Time: 9380ms
> >>                     Asset       Size         Chunks                    Chunk Names
> >>           0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]         
> >>               0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
> >>               2.bundle.js     145 kB              2  [emitted]         
> >>               3.bundle.js     531 kB              3  [emitted]  [big] 
> >>               4.bundle.js     398 kB              4  [emitted]  [big] 
> >>               5.bundle.js    1.68 kB              5  [emitted]         
> >>               6.bundle.js  920 bytes              6  [emitted]         
> >>     run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
> >>         browser.bundle.js     364 kB              8  [emitted]  [big]  browser
> >>            main.bundle.js     375 kB              9  [emitted]  [big]  main
> >>               1.bundle.js     456 kB              1  [emitted]  [big] 
> >>           1.bundle.js.map     611 kB              1  [emitted]         
> >>           2.bundle.js.map     200 kB              2  [emitted]         
> >>           3.bundle.js.map     691 kB              3  [emitted]         
> >>           4.bundle.js.map     504 kB              4  [emitted]         
> >>           5.bundle.js.map    1.87 kB              5  [emitted]         
> >>           6.bundle.js.map    1.13 kB              6  [emitted]         
> >> run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
> >>     browser.bundle.js.map     517 kB              8  [emitted]         browser
> >>        main.bundle.js.map     537 kB              9  [emitted]         main
> >>  dojo/resources/blank.gif   43 bytes                 [emitted]         
> >>  [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
> >>  [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
> >>  [373] ./src/JBrowse/main.js 13 kB {9} [built]
> >>  [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
> >>  [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
> >>  [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
> >>  [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
> >>  [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
> >>  [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
> >>  [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
> >>  [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
> >>  [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
> >>  [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
> >>  [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
> >>  [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
> >>     + 1485 hidden modules
> >> :javac
> >> :gwtc
> >>
> >> BUILD SUCCESSFUL
> >>
> >> Total time: 54.871 secs
> >>
> >> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> >> | Compiling 6 source files
> >>
> >> | Compiling 6 source files.....
> >> ***
> >> Metrics servlet injected into web.xml
> >> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> >> ***
> >> | Running Grails application
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> | Server running. Browse to http://localhost:8080/apollo
> >> Configuring Shiro ...
> >> Shiro Configured
> >> | Parent process shutdown. Exiting...
> >> | Error Forked Grails VM exited with error
> >>
> >> Best
> >> Quanwei
> >>
> >>
> >>
> >> 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.
> >
> >
> >
> >
> > 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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Re: Error Forked Grails VM exited with error

Quanwei Zhang
I will try it. Hope it works. Now I just need to use it for myself.
Thank you very much for your suggestions and time.

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午5:09写道:

Nope.  You are good.   Now you add some organisms and start annotating. 


If you want to run it on tomcat that is fine if you have other users to support, but if its just yourself on your laptop then run-local is fine. 

Just make sure that if you stop and start that your data has been retained (i.e., you won’t have to re-register).    The data, by default in dev mode is stored in AnnotationDatabase:devDb.h2.db

Nathan


On Jan 9, 2019, at 1:57 PM, Quanwei Zhang <[hidden email]> wrote:

Yes. leaving the terminal up.
I just tried http://127.0.0.1:8082/apollo, this seems works. But after register as an user  I get some error on the terminal. The attached file shows what I get from in the browser.

2019-01-09 16:44:28,424 [http-nio-8082-exec-5] WARN  apollo.PreferenceService  - No user present, so using the client token
| Error 2019-01-09 16:44:28,442 [http-nio-8082-exec-3] ERROR apollo.PermissionService  - Username not supplied so can not authenticate.
| Error 2019-01-09 16:44:28,462 [http-nio-8082-exec-3] ERROR apollo.PermissionService  - User null does not exist in the database.
| Error 2019-01-09 16:44:28,488 [http-nio-8082-exec-10] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.
2019-01-09 16:44:28,489 [http-nio-8082-exec-10] WARN  apollo.PermissionService  - Failed to authenticate user
| Error 2019-01-09 16:44:28,489 [http-nio-8082-exec-10] ERROR apollo.UserController  - Failed to authenticate
| Error 2019-01-09 16:44:28,599 [http-nio-8082-exec-6] ERROR apollo.PermissionService  - Username not supplied so can not authenticate.
| Error 2019-01-09 16:44:28,604 [http-nio-8082-exec-6] ERROR apollo.PermissionService  - User null does not exist in the database.
| Error 2019-01-09 16:46:13,566 [http-nio-8082-exec-10] ERROR apollo.UserController  - org.bbop.apollo.PermissionException: User does not have permission for any organisms.
| Error 2019-01-09 16:46:13,766 [http-nio-8082-exec-7] ERROR apollo.UserController  - User does not have permission for any organisms.
| Error 2019-01-09 16:46:13,804 [http-nio-8082-exec-6] ERROR apollo.AnnotatorService  - Error: org.bbop.apollo.PermissionException: User does not have permission for any organisms.
2019-01-09 16:47:18,249 [http-nio-8082-exec-10] WARN  apollo.AnnotatorController  - Permission exception: User does not have permission for any organisms.




Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午4:40写道:

I’m guessing you’re already running a tomcat on port 8080 as it looks like you’re getting a bind exception on port 8080 from the one installed with home-brew.   That’s why it didn’t unwrap the war file.  Tomcat from home-brew is either dead or running in a broken state. 

You’ll need to find that other tomcat and kill it and then restart the home-brew (or conversely, just use the original tomcat and remove the home-brew one). 

You can verify by typing:

ps -ef | grep catalina 

and

netstat -tan | grep LISTEN

To verify that something is already running.  

I’m not sure if the dockerized version would be any easier (depending on your familiarity): https://github.com/GMOD/docker-apollo


When using ./apollo run-local 8082 (or any number), are you leaving the terminal up when you check the web browser? 

Putting: http://localhost:8082/apollo or http://127.0.0.1:8082/apollo should work in a web browser if that is running in a terminal with no errors.  


Nathan



On Jan 9, 2019, at 1:02 PM, Quanwei Zhang <[hidden email]> wrote:

Thank you so much your patient and time. But I still can not get it work. Please see below for the information you asked

1. tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out
By the above command I get information like below. But is seems they are all old information (no information for today)
07-Jan-2019 18:14:50.418 SEVERE [main] org.apache.catalina.core.StandardServer.await Failed to create server shutdown socket on address [localhost] and port [8005] (base port [8005] and offset [0])
 java.net.BindException: Can't assign requested address (Bind failed)
        at java.net.PlainSocketImpl.socketBind(Native Method)
        at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387)
        at java.net.ServerSocket.bind(ServerSocket.java:375)
        at java.net.ServerSocket.<init>(ServerSocket.java:237)
        at org.apache.catalina.core.StandardServer.await(StandardServer.java:587)
        at org.apache.catalina.startup.Catalina.await(Catalina.java:725)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:671)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:350)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:492)

07-Jan-2019 18:14:50.419 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.429 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.430 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
07-Jan-2019 18:14:50.450 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.453 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["ajp-nio-8009"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
07-Jan-2019 18:14:50.454 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["ajp-nio-8009"]

2. If you connect to http://localhost:8084/   do you see something?

I can not see anything, just saying can not connect.

3. Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

$        ls /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
ROOT        docs        examples    host-manager    manager


4. Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.
This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps
e.g.,:
cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war
When tomcat starts it will unwrap the war file into a directory called “apollo”

I did what you suggested, now we have below files under /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/
ROOT        apollo.war    docs        examples    host-manager    manager

5. You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

I run ./apollo run-local 8082, it stop at
Shiro Configured
Starting Quartz Scheduler in QuartzFactoryBean
| Server running. Browse to http://localhost:8082/apollo

But still I can not connect to http://localhost:8082/apollo. And I did not find the unwrap the war file into a directory called “apollo” under tomcat.




Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午3:22写道:



> On Jan 9, 2019, at 11:13 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Thank you very much. I am not not familiar with those things, but please see below that I get. Any ideas from the information below?
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> $ netstat -tan | grep 8084   
> tcp4       0      0  *.8084                 *.*                    LISTEN


This is good!

>
> 2 - Also, what do you see in the tomcat logs?
>
> Do you mean the log files below. It seems strange that there is no log file generated today.
>
> $ ls -l /usr/local/Cellar/tomcat/9.0.14/libexec/logs/
> total 56
> -rw-r-----  1 qwzhang  admin  8666 Jan  7 18:14 catalina.2019-01-07.log
> -rw-r-----  1 qwzhang  admin  8714 Jan  7 18:14 catalina.out
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 host-manager.2019-01-07.log
> -rw-r-----  1 qwzhang  admin   650 Jan  7 18:14 localhost.2019-01-07.log
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 localhost_access_log.2019-01-07.txt
> -rw-r-----  1 qwzhang  admin     0 Jan  7 18:14 manager.2019-01-07.log


In a separate terminal do:

tail -f /usr/local/Cellar/tomcat/9.0.14/libexec/logs/catalina.out

This is give output if anything happens.

>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
> It shows Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server “localhost"

If you connect to http://localhost:8084/   do you see something?

Also, what are the contents of this directory?

 /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

(Relevant to below)

> 4 - What is the name of war file you generated?
> Sorry I am not familiar with this. Would you please tell me where to find the war file?


Well, when you do ‘./apollo deploy’ it produces a file in your `targets` folder called apollo-2.2.0.war or something like that.

This is copied into your web-apps folder.   /usr/local/Cellar/tomcat/9.0.14/libexec/webapps

e.g.,:

cp apollo-directory/target/apollo-2.2.0.war /usr/local/Cellar/tomcat/9.0.14/libexec/webapps/apollo.war

When tomcat starts it will unwrap the war file into a directory called “apollo”

>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
> When I tried "./apollo run-local 8085" I get the following message. Maybe I already tried the port when I tested it.
> Running Grails application
> Error Server failed to start for port 8085: Address already in use (Bind failed) (Use --stacktrace to see the full trace)
> If I try "./apollo run-local 8083" and try to connect http://localhost:8084/apollo, still get the same information.
> Safari Can't open the page "localhost:8084/apollo" beacause Safari can't find the server "localhost"
>

You need an open port to test against.  ./apollo run-local <port-number>  should correspond to. http://localhost:<port-number>/apollo

But hopefully step 4 works.

Nathan

> Best
> Quanwei
>
> Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午1:22写道:
>
> A few questions:
>
> 1 - If you type:
>
>     netstat -tan | grep 8084   
>
> What do you see?
>
> 2 - Also, what do you see in the tomcat logs?
>
> 3 - If you go to the network developer tab of your browser for that page, what do you see?
>
> 4 - What is the name of war file you generated?
>
> 5 - What happens if you type: ./apollo run-local 8085 and try to connect to at http://localhost:8084/apollo
>
>
> Nathan
>
> > On Jan 9, 2019, at 9:51 AM, Quanwei Zhang <[hidden email]> wrote:
> >
> > Dear Nathan:
> >
> > Thank you for your suggestion. I adjusted the BuildConfig.groovy file (shown below in blue). This time it just stopped at "Server running. Browse to http://localhost:8084/apollo". And I can not access "http://localhost:8084/apollo".
> > Do you have any suggestion?
> >
> >
> > .....
> > BUILD SUCCESSFUL
> >
> > Total time: 57.359 secs
> >
> > This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> > | Compiling 7 source files
> >
> > | Compiling 7 source files.....
> > ***
> > Metrics servlet injected into web.xml
> > Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> > ***
> > | Running Grails application
> >
> > Configuring Shiro ...
> >
> > Shiro Configured
> > Starting Quartz Scheduler in QuartzFactoryBean
> > | Server running. Browse to http://localhost:8084/apollo
> >
> >
> > #Change in the BuildConfig.groovy file
> > //forkConfig = [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > grails.project.fork = [
> >         // configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
> >         //compile: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >
> >         compile: false,
> >         test   : false,
> >         run    : false,
> >         war    : false,
> >         console : false
> >         // configure settings for the test-app JVM, uses the daemon by default
> >         //test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
> >         // configure settings for the run-app JVM
> >         //run    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the run-war JVM
> >         //war    : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
> >         // configure settings for the Console UI JVM
> >         //console : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
> > ]
> >
> > if (System.getProperty("grails.debug")) {
> >     //grails.project.fork.war += [debug: true]
> >     grails.project.fork.run = false
> >     println "Using debug for run"
> > }
> >
> >
> > Nathan Dunn <[hidden email]> 于2019年1月9日周三 下午12:11写道:
> >
> > Well, the good news is that its picking up your options correctly and everything seems to be processed correctly, but somehow the error is getting buried when it forks the process in tomcat (I have not seen this before, though).
> >
> > A couple of things to try:
> >
> > 1 - mirror your production and development settings (and feel free to share important parts of that) and run `./apollo run-local` and see if you can connect that way and see what the log files are. 
> >
> > 2 -  Per recommendation here:  https://stackoverflow.com/a/34747384/1739366 you can set it up not to fork at all, by setting all of these to false:
> >
> > https://github.com/GMOD/Apollo/blob/master/grails-app/conf/BuildConfig.groovy#L14
> >
> > And re-deploying it.
> >
> > Nathan
> >
> >
> >
> >
> >
> >> On Jan 9, 2019, at 8:25 AM, Quanwei Zhang <[hidden email]> wrote:
> >>
> >> Hi:
> >>
> >> I am trying to set up Apollo on my Mac (with macOS Hihg Sierra, 16GB memory). But I got the following errors. I tried to make changes of  -Xms -Xmx, but did not solve the problem.
> >>
> >> I did not find the setenv.sh file under tomcat. So I created the file under /usr/local/Cellar/tomcat/9.0.14/libexec/bin/setenv.sh and added the following information in the file.
> >> export CATALINA_OPTS="-Xmx2048m -Xms256m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:$CATALINA_HOME/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps"
> >>
> >> I have also tried to change VM sizes as arguments of grails.project.fork values inside BuildConfig.groovy but no luck. Do you have any suggestions.
> >>
> >> Node Version: 10
> >> Npm Version: 6
> >> Yarn Version: 1
> >> javac 1.8.0_191 found
> >> javac installed
> >> JDK 1.8 found: javac 1.8.0_191
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> No log file found in classpath.
> >> Final JBrowse settings [git:[url:https://github.com/gmod/jbrowse, branch:1.15.4-release, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]]
> >> Final plugins [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> :installJBrowseWebOnly
> >> JBrowse already exists
> >> From https://github.com/gmod/jbrowse
> >>  * tag                 1.15.4-release -> FETCH_HEAD
> >> Already up to date.
> >> yarn install v1.12.3
> >> [1/4] Resolving packages...
> >> success Already up-to-date.
> >> Done in 0.48s.
> >> yarn install v1.12.3
> >> info No lockfile found.
> >> [1/4] Resolving packages...
> >> [2/4] Fetching packages...
> >> [3/4] Linking dependencies...
> >> [4/4] Building fresh packages...
> >> success Saved lockfile.
> >> Done in 0.78s.
> >> Installing JBrowse plugins  [WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true]]
> >> Evaluating plugin WebApollo=[included:true]
> >> Plugin jbrowse/plugins/WebApollo exists and appears valid.
> >> Evaluating plugin RegexSequenceSearch=[included:true]
> >> Plugin jbrowse/plugins/RegexSequenceSearch exists and appears valid.
> >> Evaluating plugin HideTrackLabels=[included:true]
> >> Plugin jbrowse/plugins/HideTrackLabels exists and appears valid.
> >>
> >> > @gmod/jbrowse@1.15.4 build /Users/qwzhang/Documents/tools/Apollo/jbrowse
> >> > webpack
> >>
> >> clean-webpack-plugin: /Users/qwzhang/Documents/tools/Apollo/jbrowse/dist has been removed.
> >> jbrowse-glob-loader: building 203 JBrowse modules
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Hierarchical
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/TrackList/Faceted
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloCanvasFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/WebApolloAlignments2
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/SequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableResultFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLVariants
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableHTMLFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableBLASTFeatures
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/DraggableAlignments
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Track/AnnotSequenceTrack
> >> jbrowse-glob-loader: adding plugin module WebApollo/View/Dialog/Help
> >> jbrowse-glob-loader: adding plugin module WebApollo/TrackConfigTransformer
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ScratchPad
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/PseudoNCList
> >> jbrowse-glob-loader: adding plugin module WebApollo/Store/SeqFeature/ApolloGFF3
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceSearch
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceOntologyUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/SequenceFeatureDialog
> >> jbrowse-glob-loader: adding plugin module WebApollo/Permission
> >> jbrowse-glob-loader: adding plugin module WebApollo/main
> >> jbrowse-glob-loader: adding plugin module WebApollo/JSONUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/InformationEditor
> >> jbrowse-glob-loader: adding plugin module WebApollo/FormatUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureSelectionManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/FeatureEdgeMatchManager
> >> jbrowse-glob-loader: adding plugin module WebApollo/EUtils
> >> jbrowse-glob-loader: adding plugin module WebApollo/BioFeatureUtils
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/View/SearchSeqDialog
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/Store/SeqFeature/RegexSearch
> >> jbrowse-glob-loader: adding plugin module RegexSequenceSearch/main
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatHTMLFeatures/main
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/Track/NeatFeatures
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Segments
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/ProcessedTranscript
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Gene
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/View/FeatureGlyph/Box
> >> jbrowse-glob-loader: adding plugin module NeatCanvasFeatures/main
> >> jbrowse-glob-loader: adding plugin module HideTrackLabels/main
> >> jbrowse-glob-loader: adding plugin module DebugEvents/main
> >> jbrowse-glob-loader: adding plugin module CategoryUrl/main
> >> jbrowse-glob-loader: discovered a total of 247 modules
> >> jbrowse-glob-loader: skipping entry point module JBrowse/main
> >> Hash: 9eaefe2aad6bc3d71862
> >> Version: webpack 3.12.0
> >> Time: 9380ms
> >>                     Asset       Size         Chunks                    Chunk Names
> >>           0.bundle.js.map    11.3 MB  0, 1, 2, 3, 4  [emitted]         
> >>               0.bundle.js    8.16 MB  0, 1, 2, 3, 4  [emitted]  [big] 
> >>               2.bundle.js     145 kB              2  [emitted]         
> >>               3.bundle.js     531 kB              3  [emitted]  [big] 
> >>               4.bundle.js     398 kB              4  [emitted]  [big] 
> >>               5.bundle.js    1.68 kB              5  [emitted]         
> >>               6.bundle.js  920 bytes              6  [emitted]         
> >>     run_jasmine.bundle.js     571 kB              7  [emitted]  [big]  run_jasmine
> >>         browser.bundle.js     364 kB              8  [emitted]  [big]  browser
> >>            main.bundle.js     375 kB              9  [emitted]  [big]  main
> >>               1.bundle.js     456 kB              1  [emitted]  [big] 
> >>           1.bundle.js.map     611 kB              1  [emitted]         
> >>           2.bundle.js.map     200 kB              2  [emitted]         
> >>           3.bundle.js.map     691 kB              3  [emitted]         
> >>           4.bundle.js.map     504 kB              4  [emitted]         
> >>           5.bundle.js.map    1.87 kB              5  [emitted]         
> >>           6.bundle.js.map    1.13 kB              6  [emitted]         
> >> run_jasmine.bundle.js.map     854 kB              7  [emitted]         run_jasmine
> >>     browser.bundle.js.map     517 kB              8  [emitted]         browser
> >>        main.bundle.js.map     537 kB              9  [emitted]         main
> >>  dojo/resources/blank.gif   43 bytes                 [emitted]         
> >>  [129] ./build/dojo-webpack-plugin-loader/dojo/dojo.js 70.7 kB {7} {8} {9} [built]
> >>  [337] ./src/JBrowse/standalone.js 140 bytes {0} {8} [built]
> >>  [373] ./src/JBrowse/main.js 13 kB {9} [built]
> >>  [374] ./tests/js_tests/main.js 1.58 kB {7} [built]
> >>  [386] ./tests/js_tests/spec/TabixIndex.spec.js 1.34 kB {7} [built]
> >>  [602] ./plugins/RegexSequenceSearch/js/Store/SeqFeature/RegexSearch.js 4.73 kB {0} [built]
> >>  [603] ./plugins/RegexSequenceSearch/js/main.js 2.29 kB {0} [built]
> >>  [604] ./plugins/NeatHTMLFeatures/js/View/Track/NeatFeatures.js 9.36 kB {0} [built]
> >>  [605] ./plugins/NeatHTMLFeatures/js/main.js 515 bytes {0} [built]
> >>  [606] ./plugins/NeatCanvasFeatures/js/View/Track/NeatFeatures.js 663 bytes {0} [built]
> >>  [607] ./plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js 647 bytes {0} [built]
> >>  [608] ./plugins/NeatCanvasFeatures/js/main.js 251 bytes {0} [built]
> >>  [609] ./plugins/HideTrackLabels/js/main.js 4.41 kB {0} [built]
> >>  [610] ./plugins/DebugEvents/js/main.js 6.21 kB {0} [built]
> >>  [611] ./plugins/CategoryUrl/js/main.js 4.48 kB {0} [built]
> >>     + 1485 hidden modules
> >> :javac
> >> :gwtc
> >>
> >> BUILD SUCCESSFUL
> >>
> >> Total time: 54.871 secs
> >>
> >> This build could be faster, please consider using the Gradle Daemon: https://docs.gradle.org/2.11/userguide/gradle_daemon.html
> >> | Compiling 6 source files
> >>
> >> | Compiling 6 source files.....
> >> ***
> >> Metrics servlet injected into web.xml
> >> Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
> >> ***
> >> | Running Grails application
> >> Picked up JAVA_TOOL_OPTIONS: -Xms256M -Xmx1024M
> >> | Server running. Browse to http://localhost:8080/apollo
> >> Configuring Shiro ...
> >> Shiro Configured
> >> | Parent process shutdown. Exiting...
> >> | Error Forked Grails VM exited with error
> >>
> >> Best
> >> Quanwei
> >>
> >>
> >>
> >> 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.
> >
> >
> >
> >
> > 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.
>
>
>
>
> 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.




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.

<apollo.pdf>


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.





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.