Tomcat memory settings

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Tomcat memory settings

Bai, Youhuang
Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai




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Re: Tomcat memory settings

nathandunn

Bai,

Setting memory in tomcat will only affect it if you are using tomcat. 

./apollo run-local uses an embedded tomcat 8 server. 

To change the embedded memory setting (if you aren’t using tomcat) you can over-ride the default memory.  I’m not sure why Apollo is using your default memory.  I agree that that is strange. 

To over-ride that memory use:


You should only need to over-ride the “run" setting.    

Unless you have a fairly large user-base, however, the defaults listed should be more than sufficient.   If its just for you (or a small lab) if 768M *should* be sufficient, but it will be evident if not as you’ll see out-of-memory errors.

Let us know how this works. 

Cheers,

Nathan


On Jul 24, 2018, at 2:43 PM, Bai, Youhuang <[hidden email]> wrote:

Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai



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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答复: Tomcat memory settings

Bai, Youhuang
Hi Nathan

Thnaks. 
The reason I want to change the memory setting is that Apollo runs more than 2 hours in my Mac desktop (2.8Ghz i7, 16 GB Memory) and do not finish yet when I create the database with my jbroswe data (3 different annotation gff file, two bam file of the RNA seq data). My target genome have more than 300 scaffolds,  so I am wandering that how to get Apollo run quickly.

Bests,
Youhuang Bai



发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 16:58
收件人: Apollo List
主题: Re: [apollo] Tomcat memory settings


Bai,

Setting memory in tomcat will only affect it if you are using tomcat. 

./apollo run-local uses an embedded tomcat 8 server. 

To change the embedded memory setting (if you aren’t using tomcat) you can over-ride the default memory.  I’m not sure why Apollo is using your default memory.  I agree that that is strange. 

To over-ride that memory use:


You should only need to over-ride the “run" setting.    

Unless you have a fairly large user-base, however, the defaults listed should be more than sufficient.   If its just for you (or a small lab) if 768M *should* be sufficient, but it will be evident if not as you’ll see out-of-memory errors.

Let us know how this works. 

Cheers,

Nathan


On Jul 24, 2018, at 2:43 PM, Bai, Youhuang <[hidden email]> wrote:

Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai



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Re: 答复: Tomcat memory settings

nathandunn

I see.  Memory does help.  Some questions:

1 - You are saying that it is taken more than 2 hours to load a single organism with 300 scaffolds (I would expect it to take less than a minute.  5K takes about 3 minutes)?    Fixing the memory may help here. 

2 - How large is your largest scaffold (this is the only data that matters)? 

3 - Is the CPU running heavily during this process, if not, int might just be stuck? 

4 - Are you seeing any weird logs being produced by the server or from within the javascript client? 

5 - Can you load a limited set of your scaffolds to test to see if it might be a single bad scaffold? 

Nathan


On Jul 24, 2018, at 3:26 PM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

Thnaks. 
The reason I want to change the memory setting is that Apollo runs more than 2 hours in my Mac desktop (2.8Ghz i7, 16 GB Memory) and do not finish yet when I create the database with my jbroswe data (3 different annotation gff file, two bam file of the RNA seq data). My target genome have more than 300 scaffolds,  so I am wandering that how to get Apollo run quickly.

Bests,
Youhuang Bai



发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 16:58
收件人: Apollo List
主题: Re: [apollo] Tomcat memory settings


Bai,

Setting memory in tomcat will only affect it if you are using tomcat. 

./apollo run-local uses an embedded tomcat 8 server. 

To change the embedded memory setting (if you aren’t using tomcat) you can over-ride the default memory.  I’m not sure why Apollo is using your default memory.  I agree that that is strange. 

To over-ride that memory use:


You should only need to over-ride the “run" setting.    

Unless you have a fairly large user-base, however, the defaults listed should be more than sufficient.   If its just for you (or a small lab) if 768M *should* be sufficient, but it will be evident if not as you’ll see out-of-memory errors.

Let us know how this works. 

Cheers,

Nathan


On Jul 24, 2018, at 2:43 PM, Bai, Youhuang <[hidden email]> wrote:

Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai



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




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





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

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答复: 答复: Tomcat memory settings

Bai, Youhuang
Hi Nathan

The genome is small, about 30M. CPU is not running heavily. 
Here is the error info:

2018-07-25 10:18:19,437 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - Ping: Evaluating Saves

2018-07-25 10:18:19,438 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Evaluating saves: false

2018-07-25 10:18:19,445 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Saving with time diff: 60003

2018-07-25 10:18:19,458 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - permissions checked and alive

2018-07-25 10:18:21,645 [http-nio-8080-exec-6] DEBUG apollo.SecurityFilters  - apollo filter organism::addOrganism

2018-07-25 10:18:21,662 [http-nio-8080-exec-6] INFO  apollo.PermissionService  - Authenticating with usernamePasswordAuthenticatorService

| Error 2018-07-25 10:18:21,714 [http-nio-8080-exec-6] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.

2018-07-25 10:18:21,716 [http-nio-8080-exec-6] WARN  apollo.PermissionService  - Failed to authenticate user

2018-07-25 10:18:21,717 [http-nio-8080-exec-6] WARN  

apollo.SecurityFilters  - Authentication failed


Thanks


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 17:42
收件人: Apollo List
主题: Re: [apollo] 答复: Tomcat memory settings


I see.  Memory does help.  Some questions:

1 - You are saying that it is taken more than 2 hours to load a single organism with 300 scaffolds (I would expect it to take less than a minute.  5K takes about 3 minutes)?    Fixing the memory may help here. 

2 - How large is your largest scaffold (this is the only data that matters)? 

3 - Is the CPU running heavily during this process, if not, int might just be stuck? 

4 - Are you seeing any weird logs being produced by the server or from within the javascript client? 

5 - Can you load a limited set of your scaffolds to test to see if it might be a single bad scaffold? 

Nathan


On Jul 24, 2018, at 3:26 PM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

Thnaks. 
The reason I want to change the memory setting is that Apollo runs more than 2 hours in my Mac desktop (2.8Ghz i7, 16 GB Memory) and do not finish yet when I create the database with my jbroswe data (3 different annotation gff file, two bam file of the RNA seq data). My target genome have more than 300 scaffolds,  so I am wandering that how to get Apollo run quickly.

Bests,
Youhuang Bai



发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 16:58
收件人: Apollo List
主题: Re: [apollo] Tomcat memory settings


Bai,

Setting memory in tomcat will only affect it if you are using tomcat. 

./apollo run-local uses an embedded tomcat 8 server. 

To change the embedded memory setting (if you aren’t using tomcat) you can over-ride the default memory.  I’m not sure why Apollo is using your default memory.  I agree that that is strange. 

To over-ride that memory use:


You should only need to over-ride the “run" setting.    

Unless you have a fairly large user-base, however, the defaults listed should be more than sufficient.   If its just for you (or a small lab) if 768M *should* be sufficient, but it will be evident if not as you’ll see out-of-memory errors.

Let us know how this works. 

Cheers,

Nathan


On Jul 24, 2018, at 2:43 PM, Bai, Youhuang <[hidden email]> wrote:

Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai



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Re: 答复: 答复: Tomcat memory settings

nathandunn

Just to clarify, what do you see when you try to add an organism? 

Both in the javascript console in the browser and in the server? 

Nathan


On Jul 25, 2018, at 8:22 AM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

The genome is small, about 30M. CPU is not running heavily. 
Here is the error info:

2018-07-25 10:18:19,437 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - Ping: Evaluating Saves

2018-07-25 10:18:19,438 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Evaluating saves: false

2018-07-25 10:18:19,445 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Saving with time diff: 60003

2018-07-25 10:18:19,458 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - permissions checked and alive

2018-07-25 10:18:21,645 [http-nio-8080-exec-6] DEBUG apollo.SecurityFilters  - apollo filter organism::addOrganism

2018-07-25 10:18:21,662 [http-nio-8080-exec-6] INFO  apollo.PermissionService  - Authenticating with usernamePasswordAuthenticatorService

| Error 2018-07-25 10:18:21,714 [http-nio-8080-exec-6] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.

2018-07-25 10:18:21,716 [http-nio-8080-exec-6] WARN  apollo.PermissionService  - Failed to authenticate user

2018-07-25 10:18:21,717 [http-nio-8080-exec-6] WARN  

apollo.SecurityFilters  - Authentication failed


Thanks


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 17:42
收件人: Apollo List
主题: Re: [apollo] 答复: Tomcat memory settings


I see.  Memory does help.  Some questions:

1 - You are saying that it is taken more than 2 hours to load a single organism with 300 scaffolds (I would expect it to take less than a minute.  5K takes about 3 minutes)?    Fixing the memory may help here. 

2 - How large is your largest scaffold (this is the only data that matters)? 

3 - Is the CPU running heavily during this process, if not, int might just be stuck? 

4 - Are you seeing any weird logs being produced by the server or from within the javascript client? 

5 - Can you load a limited set of your scaffolds to test to see if it might be a single bad scaffold? 

Nathan


On Jul 24, 2018, at 3:26 PM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

Thnaks. 
The reason I want to change the memory setting is that Apollo runs more than 2 hours in my Mac desktop (2.8Ghz i7, 16 GB Memory) and do not finish yet when I create the database with my jbroswe data (3 different annotation gff file, two bam file of the RNA seq data). My target genome have more than 300 scaffolds,  so I am wandering that how to get Apollo run quickly.

Bests,
Youhuang Bai



发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 16:58
收件人: Apollo List
主题: Re: [apollo] Tomcat memory settings


Bai,

Setting memory in tomcat will only affect it if you are using tomcat. 

./apollo run-local uses an embedded tomcat 8 server. 

To change the embedded memory setting (if you aren’t using tomcat) you can over-ride the default memory.  I’m not sure why Apollo is using your default memory.  I agree that that is strange. 

To over-ride that memory use:


You should only need to over-ride the “run" setting.    

Unless you have a fairly large user-base, however, the defaults listed should be more than sufficient.   If its just for you (or a small lab) if 768M *should* be sufficient, but it will be evident if not as you’ll see out-of-memory errors.

Let us know how this works. 

Cheers,

Nathan


On Jul 24, 2018, at 2:43 PM, Bai, Youhuang <[hidden email]> wrote:

Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai



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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答复: 答复: 答复: Tomcat memory settings

Bai, Youhuang
I tried it ( Apollo 2.1.0 ) in two computers, the same error.

The web 
browser says "Processing..."

And the terminal shows that:

2018-07-25 10:18:19,437 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - Ping: Evaluating Saves

2018-07-25 10:18:19,438 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Evaluating saves: false

2018-07-25 10:18:19,445 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Saving with time diff: 60003

2018-07-25 10:18:19,458 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - permissions checked and alive

2018-07-25 10:18:21,645 [http-nio-8080-exec-6] DEBUG apollo.SecurityFilters  - apollo filter organism::addOrganism

2018-07-25 10:18:21,662 [http-nio-8080-exec-6] INFO  apollo.PermissionService  - Authenticating with usernamePasswordAuthenticatorService

| Error 2018-07-25 10:18:21,714 [http-nio-8080-exec-6] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.

2018-07-25 10:18:21,716 [http-nio-8080-exec-6] WARN  apollo.PermissionService  - Failed to authenticate user

2018-07-25 10:18:21,717 [http-nio-8080-exec-6] WARN  apollo.SecurityFilters  - Authentication failed


But I installed the Apollo 2.1.0.RC3 and I found it works on the Jbrowser data
Thanks

Youhuang

发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月25日 11:14
收件人: Apollo List
主题: Re: [apollo] 答复: 答复: Tomcat memory settings


Just to clarify, what do you see when you try to add an organism? 

Both in the javascript console in the browser and in the server? 

Nathan


On Jul 25, 2018, at 8:22 AM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

The genome is small, about 30M. CPU is not running heavily. 
Here is the error info:

2018-07-25 10:18:19,437 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - Ping: Evaluating Saves

2018-07-25 10:18:19,438 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Evaluating saves: false

2018-07-25 10:18:19,445 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Saving with time diff: 60003

2018-07-25 10:18:19,458 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - permissions checked and alive

2018-07-25 10:18:21,645 [http-nio-8080-exec-6] DEBUG apollo.SecurityFilters  - apollo filter organism::addOrganism

2018-07-25 10:18:21,662 [http-nio-8080-exec-6] INFO  apollo.PermissionService  - Authenticating with usernamePasswordAuthenticatorService

| Error 2018-07-25 10:18:21,714 [http-nio-8080-exec-6] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.

2018-07-25 10:18:21,716 [http-nio-8080-exec-6] WARN  apollo.PermissionService  - Failed to authenticate user

2018-07-25 10:18:21,717 [http-nio-8080-exec-6] WARN  

apollo.SecurityFilters  - Authentication failed


Thanks


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 17:42
收件人: Apollo List
主题: Re: [apollo] 答复: Tomcat memory settings


I see.  Memory does help.  Some questions:

1 - You are saying that it is taken more than 2 hours to load a single organism with 300 scaffolds (I would expect it to take less than a minute.  5K takes about 3 minutes)?    Fixing the memory may help here. 

2 - How large is your largest scaffold (this is the only data that matters)? 

3 - Is the CPU running heavily during this process, if not, int might just be stuck? 

4 - Are you seeing any weird logs being produced by the server or from within the javascript client? 

5 - Can you load a limited set of your scaffolds to test to see if it might be a single bad scaffold? 

Nathan


On Jul 24, 2018, at 3:26 PM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

Thnaks. 
The reason I want to change the memory setting is that Apollo runs more than 2 hours in my Mac desktop (2.8Ghz i7, 16 GB Memory) and do not finish yet when I create the database with my jbroswe data (3 different annotation gff file, two bam file of the RNA seq data). My target genome have more than 300 scaffolds,  so I am wandering that how to get Apollo run quickly.

Bests,
Youhuang Bai



发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 16:58
收件人: Apollo List
主题: Re: [apollo] Tomcat memory settings


Bai,

Setting memory in tomcat will only affect it if you are using tomcat. 

./apollo run-local uses an embedded tomcat 8 server. 

To change the embedded memory setting (if you aren’t using tomcat) you can over-ride the default memory.  I’m not sure why Apollo is using your default memory.  I agree that that is strange. 

To over-ride that memory use:


You should only need to over-ride the “run" setting.    

Unless you have a fairly large user-base, however, the defaults listed should be more than sufficient.   If its just for you (or a small lab) if 768M *should* be sufficient, but it will be evident if not as you’ll see out-of-memory errors.

Let us know how this works. 

Cheers,

Nathan


On Jul 24, 2018, at 2:43 PM, Bai, Youhuang <[hidden email]> wrote:

Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai



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Re: 答复: 答复: 答复: Tomcat memory settings

nathandunn

This is all normal output for Apollo for a logged-out user. 

My guess is that the re-installation fixed something, as RC3 wouldn’t have been much difference. 


Most likely you can achieve the same result by:

`./apollo clean-all` 

And 

`./apollo run-local` 

Which will force JBrowse to re-install totally.   Possibly something in the Apollo maintenance JBrowse branch was fixed.  

If it works with RC3, there is no reason to upgrade.

Cheers,

Nathan

On Jul 25, 2018, at 11:14 AM, Bai, Youhuang <[hidden email]> wrote:

I tried it ( Apollo 2.1.0 ) in two computers, the same error.

The web 
browser says "Processing..."

And the terminal shows that:

2018-07-25 10:18:19,437 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - Ping: Evaluating Saves

2018-07-25 10:18:19,438 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Evaluating saves: false

2018-07-25 10:18:19,445 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Saving with time diff: 60003

2018-07-25 10:18:19,458 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - permissions checked and alive

2018-07-25 10:18:21,645 [http-nio-8080-exec-6] DEBUG apollo.SecurityFilters  - apollo filter organism::addOrganism

2018-07-25 10:18:21,662 [http-nio-8080-exec-6] INFO  apollo.PermissionService  - Authenticating with usernamePasswordAuthenticatorService

| Error 2018-07-25 10:18:21,714 [http-nio-8080-exec-6] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.

2018-07-25 10:18:21,716 [http-nio-8080-exec-6] WARN  apollo.PermissionService  - Failed to authenticate user

2018-07-25 10:18:21,717 [http-nio-8080-exec-6] WARN  apollo.SecurityFilters  - Authentication failed


But I installed the Apollo 2.1.0.RC3 and I found it works on the Jbrowser data
Thanks

Youhuang

发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月25日 11:14
收件人: Apollo List
主题: Re: [apollo] 答复: 答复: Tomcat memory settings


Just to clarify, what do you see when you try to add an organism? 

Both in the javascript console in the browser and in the server? 

Nathan


On Jul 25, 2018, at 8:22 AM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

The genome is small, about 30M. CPU is not running heavily. 
Here is the error info:

2018-07-25 10:18:19,437 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - Ping: Evaluating Saves

2018-07-25 10:18:19,438 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Evaluating saves: false

2018-07-25 10:18:19,445 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Saving with time diff: 60003

2018-07-25 10:18:19,458 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - permissions checked and alive

2018-07-25 10:18:21,645 [http-nio-8080-exec-6] DEBUG apollo.SecurityFilters  - apollo filter organism::addOrganism

2018-07-25 10:18:21,662 [http-nio-8080-exec-6] INFO  apollo.PermissionService  - Authenticating with usernamePasswordAuthenticatorService

| Error 2018-07-25 10:18:21,714 [http-nio-8080-exec-6] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.

2018-07-25 10:18:21,716 [http-nio-8080-exec-6] WARN  apollo.PermissionService  - Failed to authenticate user

2018-07-25 10:18:21,717 [http-nio-8080-exec-6] WARN  

apollo.SecurityFilters  - Authentication failed


Thanks


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 17:42
收件人: Apollo List
主题: Re: [apollo] 答复: Tomcat memory settings


I see.  Memory does help.  Some questions:

1 - You are saying that it is taken more than 2 hours to load a single organism with 300 scaffolds (I would expect it to take less than a minute.  5K takes about 3 minutes)?    Fixing the memory may help here. 

2 - How large is your largest scaffold (this is the only data that matters)? 

3 - Is the CPU running heavily during this process, if not, int might just be stuck? 

4 - Are you seeing any weird logs being produced by the server or from within the javascript client? 

5 - Can you load a limited set of your scaffolds to test to see if it might be a single bad scaffold? 

Nathan


On Jul 24, 2018, at 3:26 PM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

Thnaks. 
The reason I want to change the memory setting is that Apollo runs more than 2 hours in my Mac desktop (2.8Ghz i7, 16 GB Memory) and do not finish yet when I create the database with my jbroswe data (3 different annotation gff file, two bam file of the RNA seq data). My target genome have more than 300 scaffolds,  so I am wandering that how to get Apollo run quickly.

Bests,
Youhuang Bai



发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 16:58
收件人: Apollo List
主题: Re: [apollo] Tomcat memory settings


Bai,

Setting memory in tomcat will only affect it if you are using tomcat. 

./apollo run-local uses an embedded tomcat 8 server. 

To change the embedded memory setting (if you aren’t using tomcat) you can over-ride the default memory.  I’m not sure why Apollo is using your default memory.  I agree that that is strange. 

To over-ride that memory use:


You should only need to over-ride the “run" setting.    

Unless you have a fairly large user-base, however, the defaults listed should be more than sufficient.   If its just for you (or a small lab) if 768M *should* be sufficient, but it will be evident if not as you’ll see out-of-memory errors.

Let us know how this works. 

Cheers,

Nathan


On Jul 24, 2018, at 2:43 PM, Bai, Youhuang <[hidden email]> wrote:

Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai



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答复: 答复: 答复: 答复: Tomcat memory settings

Bai, Youhuang
OK thanks

发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月25日 13:24
收件人: [hidden email]
主题: Re: [apollo] 答复: 答复: 答复: Tomcat memory settings


This is all normal output for Apollo for a logged-out user. 

My guess is that the re-installation fixed something, as RC3 wouldn’t have been much difference. 


Most likely you can achieve the same result by:

`./apollo clean-all` 

And 

`./apollo run-local` 

Which will force JBrowse to re-install totally.   Possibly something in the Apollo maintenance JBrowse branch was fixed.  

If it works with RC3, there is no reason to upgrade.

Cheers,

Nathan

On Jul 25, 2018, at 11:14 AM, Bai, Youhuang <[hidden email]> wrote:

I tried it ( Apollo 2.1.0 ) in two computers, the same error.

The web 
browser says "Processing..."

And the terminal shows that:

2018-07-25 10:18:19,437 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - Ping: Evaluating Saves

2018-07-25 10:18:19,438 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Evaluating saves: false

2018-07-25 10:18:19,445 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Saving with time diff: 60003

2018-07-25 10:18:19,458 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - permissions checked and alive

2018-07-25 10:18:21,645 [http-nio-8080-exec-6] DEBUG apollo.SecurityFilters  - apollo filter organism::addOrganism

2018-07-25 10:18:21,662 [http-nio-8080-exec-6] INFO  apollo.PermissionService  - Authenticating with usernamePasswordAuthenticatorService

| Error 2018-07-25 10:18:21,714 [http-nio-8080-exec-6] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.

2018-07-25 10:18:21,716 [http-nio-8080-exec-6] WARN  apollo.PermissionService  - Failed to authenticate user

2018-07-25 10:18:21,717 [http-nio-8080-exec-6] WARN  apollo.SecurityFilters  - Authentication failed


But I installed the Apollo 2.1.0.RC3 and I found it works on the Jbrowser data
Thanks

Youhuang

发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月25日 11:14
收件人: Apollo List
主题: Re: [apollo] 答复: 答复: Tomcat memory settings


Just to clarify, what do you see when you try to add an organism? 

Both in the javascript console in the browser and in the server? 

Nathan


On Jul 25, 2018, at 8:22 AM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

The genome is small, about 30M. CPU is not running heavily. 
Here is the error info:

2018-07-25 10:18:19,437 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - Ping: Evaluating Saves

2018-07-25 10:18:19,438 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Evaluating saves: false

2018-07-25 10:18:19,445 [http-nio-8080-exec-1] DEBUG apollo.PreferenceService  - Saving with time diff: 60003

2018-07-25 10:18:19,458 [http-nio-8080-exec-1] DEBUG apollo.AnnotatorController  - permissions checked and alive

2018-07-25 10:18:21,645 [http-nio-8080-exec-6] DEBUG apollo.SecurityFilters  - apollo filter organism::addOrganism

2018-07-25 10:18:21,662 [http-nio-8080-exec-6] INFO  apollo.PermissionService  - Authenticating with usernamePasswordAuthenticatorService

| Error 2018-07-25 10:18:21,714 [http-nio-8080-exec-6] ERROR authenticator.UsernamePasswordAuthenticatorService  - Problem authenticating: java.lang.IllegalArgumentException: Method argumet (authentication token) cannot be null.

2018-07-25 10:18:21,716 [http-nio-8080-exec-6] WARN  apollo.PermissionService  - Failed to authenticate user

2018-07-25 10:18:21,717 [http-nio-8080-exec-6] WARN  

apollo.SecurityFilters  - Authentication failed


Thanks


发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 17:42
收件人: Apollo List
主题: Re: [apollo] 答复: Tomcat memory settings


I see.  Memory does help.  Some questions:

1 - You are saying that it is taken more than 2 hours to load a single organism with 300 scaffolds (I would expect it to take less than a minute.  5K takes about 3 minutes)?    Fixing the memory may help here. 

2 - How large is your largest scaffold (this is the only data that matters)? 

3 - Is the CPU running heavily during this process, if not, int might just be stuck? 

4 - Are you seeing any weird logs being produced by the server or from within the javascript client? 

5 - Can you load a limited set of your scaffolds to test to see if it might be a single bad scaffold? 

Nathan


On Jul 24, 2018, at 3:26 PM, Bai, Youhuang <[hidden email]> wrote:

Hi Nathan

Thnaks. 
The reason I want to change the memory setting is that Apollo runs more than 2 hours in my Mac desktop (2.8Ghz i7, 16 GB Memory) and do not finish yet when I create the database with my jbroswe data (3 different annotation gff file, two bam file of the RNA seq data). My target genome have more than 300 scaffolds,  so I am wandering that how to get Apollo run quickly.

Bests,
Youhuang Bai



发件人: [hidden email] [[hidden email]] 代表 Nathan Dunn [[hidden email]]
发送时间: 2018年7月24日 16:58
收件人: Apollo List
主题: Re: [apollo] Tomcat memory settings


Bai,

Setting memory in tomcat will only affect it if you are using tomcat. 

./apollo run-local uses an embedded tomcat 8 server. 

To change the embedded memory setting (if you aren’t using tomcat) you can over-ride the default memory.  I’m not sure why Apollo is using your default memory.  I agree that that is strange. 

To over-ride that memory use:


You should only need to over-ride the “run" setting.    

Unless you have a fairly large user-base, however, the defaults listed should be more than sufficient.   If its just for you (or a small lab) if 768M *should* be sufficient, but it will be evident if not as you’ll see out-of-memory errors.

Let us know how this works. 

Cheers,

Nathan


On Jul 24, 2018, at 2:43 PM, Bai, Youhuang <[hidden email]> wrote:

Hi 

I have change the settings of CATALINA_OPTS as suggested by editing the setenv.sh script in $TOMCAT_BIN_DIR/setenv.sh, and I start only tomcat server without Apollo,  Java run with modified memory settings. 

But when I start to run Apollo: ./apollo run-local, the java use default memory setting again. I don't know how to change it in the Apollo.

Here I use ps -ef |grep java to comfirm it.

tomcat server without Apollo: 

  501 18506     1   0  2:32PM ttys000    0:12.07 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Djava.util.logging.config.file=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djdk.tls.ephemeralDHKeySize=2048 -Xmx12288m -Xms8192m -XX:ReservedCodeCacheSize=64m -XX:+UseG1GC -XX:+CMSClassUnloadingEnabled -Xloggc:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/logs/gc.log -XX:+PrintHeapAtGC -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -Dignore.endorsed.dirs= -classpath /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/bootstrap.jar:/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/bin/tomcat-juli.jar -Dcatalina.base=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Dcatalina.home=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat -Djava.io.tmpdir=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/opt/apache-tomcat/temp org.apache.catalina.startup.Bootstrap start

Apollo running:

  501 18621 18593   0  2:38PM ttys000    0:42.55 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -server -Xmx768M -Xms64M -Dfile.encoding=UTF-8 -Xdock:name=Grails -Xdock:icon=/Users/xiaozhuandai/.sdkman/candidates/grails/current/media/icons/grails.icns -classpath /Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.groovy/groovy-all/jars/groovy-all-2.4.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/dist/grails-bootstrap-2.5.5.jar:/System/Library/Java/Support -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/current -Dtools.jar=/Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar -Djava.net.preferIPv4Stack=true org.codehaus.groovy.grails.cli.support.GrailsStarter --main org.codehaus.groovy.grails.cli.GrailsScriptRunner --conf /Users/xiaozhuandai/.sdkman/candidates/grails/current/conf/groovy-starter.conf --classpath   -Dserver.port=8085 run-app

  501 18658 18621   0  2:39PM ttys000    3:00.80 /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/bin/java -Dfile.encoding=UTF-8 -Xmx2048M -Xms64M -Dgrails.fork.parent.process.port=49974 -Dgrails.fork.active=true -Dgrails.build.execution.context=/private/var/folders/3g/fj8bjhq94ssf1l4sjnl4xjrc0000gn/T/Apollo-2.1.07705185738681118749grails-execution-context -cp /Users/xiaozhuandai/Baiyouhuang/miniconda2/envs/biobai/lib/tools.jar:/Users/xiaozhuandai/.m2/repository/org/codehaus/groovy/groovy-all/2.4.4/groovy-all-2.4.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/jcl-over-slf4j/jars/jcl-over-slf4j-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/current/lib/org.codehaus.gant/gant_groovy1.8/jars/gant_groovy1.8-1.9.6.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.tomcat.embed/tomcat-embed-logging-log4j/jars/tomcat-embed-logging-log4j-7.0.70.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-plugin-log4j-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/log4j/log4j/jars/log4j-1.2.17.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/dist/grails-bootstrap-2.5.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-launcher/jars/ant-launcher-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-junit/jars/ant-junit-1.9.4.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/jline/jline/jars/jline-2.12.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.fusesource.jansi/jansi/jars/jansi-1.11.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant-trax/jars/ant-trax-1.7.1.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ivy/ivy/jars/ivy-2.3.0.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.slf4j/slf4j-api/jars/slf4j-api-1.7.5.jar:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.apache.ant/ant/jars/ant-1.9.4.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-el/8.0.33/tomcat-embed-el-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-jasper/8.0.33/tomcat-embed-jasper-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-logging-log4j/8.0.33/tomcat-embed-logging-log4j-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-websocket/8.0.33/tomcat-embed-websocket-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/apache/tomcat/embed/tomcat-embed-core/8.0.33/tomcat-embed-core-8.0.33.jar:/Users/xiaozhuandai/.m2/repository/org/eclipse/jdt/core/compiler/ecj/4.5/ecj-4.5.jar:/Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/target/work/plugins/tomcat-8.0.33/grails-plugin-tomcat-8.0.33.jar: -Dgrails.home=/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5 -javaagent:/Users/xiaozhuandai/.sdkman/candidates/grails/2.5.5/lib/org.springframework/springloaded/jars/springloaded-1.2.5.RELEASE.jar -Xverify:none -Dspringloaded.synchronize=true -Djdk.reflect.allowGetCallerClass=true -Dspringloaded=profile=grails;cacheDir=/Users/xiaozhuandai/.grails/2.5.5 org.grails.plugins.tomcat.fork.ForkedTomcatServer
  501 18756 18682   0  3:34PM ttys001    0:00.00 grep java

 Thanks.

Best, 
Youhuang Bai



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