D4Science Infrastructure

dataminer2-p-d4s.d4science.org is updated already, as I wrote yesterday. You only need to start the tomcat instance to be able to test it.

The following keys should be placed in the tomcat/webapps/wps/ecocfg/PARALLEL_PROCESSING/ folder to make all algorithms run

FARM.gcubekey
d4science.research-infrastructures.eu.gcubekey
gCubeApps.gcubekey

I remember this was in the previous production installation script.

The script is there, a tag was missing and it was excluded from the upgrade tasks list.
Now it's fixed and the keys are in place.

dataminer2-p-d4s.d4science.org works correctly! dataminer1-p has been shutdown, so that dataminer2 responds to dataminer.d4science.org (and works).
Thus, the dataminer.d4science.org service is working now for all the algorithms. That's good news.

Once dataminer1-p will have been installed I will repeat tests on it.

The tomcat on dataminer1-p-d4s doesn't start or does not respond (no logging and no answers from the applications). Maybe something went wrong when you re-installed the environment?

It seems to be an issue with the javaassist lib of tomcat. Did you meet this error previously?

2016-02-18 14:20:22,579 [localhost-startStop-1] INFO  org.apache.catalina.startup.HostConfig- Deploying web application archive /home/gcube/tomcat/webapps/common-smartgears-probe.war
2016-02-18 14:20:23,677 [localhost-startStop-1] ERROR org.apache.catalina.startup.ContextConfig- Unable to process Jar entry [javassist/ByteArrayClassPath.class] from Jar [jar:file:/home/gcube/tomcat/lib/javassist-3.19.0-GA.jar!/] for annotations
java.io.EOFException
        at java.io.DataInputStream.readUnsignedShort(DataInputStream.java:340)
        at org.apache.tomcat.util.bcel.classfile.Utility.swallowMethodParameters(Utility.java:797)
        at org.apache.tomcat.util.bcel.classfile.Attribute.readAttribute(Attribute.java:171)
        at org.apache.tomcat.util.bcel.classfile.FieldOrMethod.<init>(FieldOrMethod.java:57)
        at org.apache.tomcat.util.bcel.classfile.Method.<init>(Method.java:71)
        at org.apache.tomcat.util.bcel.classfile.ClassParser.readMethods(ClassParser.java:267)
        at org.apache.tomcat.util.bcel.classfile.ClassParser.parse(ClassParser.java:127)
        at org.apache.catalina.startup.ContextConfig.processAnnotationsStream(ContextConfig.java:2058)
        at org.apache.catalina.startup.ContextConfig.processAnnotationsJar(ContextConfig.java:1934)
        at org.apache.catalina.startup.ContextConfig.processAnnotationsUrl(ContextConfig.java:1900)
        at org.apache.catalina.startup.ContextConfig.processAnnotations(ContextConfig.java:1885)
        at org.apache.catalina.startup.ContextConfig.webConfig(ContextConfig.java:1317)
        at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:876)
        at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:374)
        at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
        at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5378)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:649)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1083)
        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1880)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
        at java.util.concurrent.FutureTask.run(FutureTask.java:262)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)
2016-02-18 14:20:23,683 [localhost-startStop-1] ERROR org.apache.catalina.startup.ContextConfig- Unable to process Jar entry [javassist/CannotCompileException.class] from Jar [jar:file:/home/gcube/tomcat/lib/javassist-3.19.0-GA.jar!/] for annotations
java.io.EOFException
        at java.io.DataInputStream.readUnsignedShort(DataInputStream.java:340)
        at org.apache.tomcat.util.bcel.classfile.Utility.swallowMethodParameters(Utility.java:796)
        at org.apache.tomcat.util.bcel.classfile.Attribute.readAttribute(Attribute.java:171)
        at org.apache.tomcat.util.bcel.classfile.FieldOrMethod.<init>(FieldOrMethod.java:57)
        at org.apache.tomcat.util.bcel.classfile.Method.<init>(Method.java:71)
        at org.apache.tomcat.util.bcel.classfile.ClassParser.readMethods(ClassParser.java:267)
        at org.apache.tomcat.util.bcel.classfile.ClassParser.parse(ClassParser.java:127)
        at org.apache.catalina.startup.ContextConfig.processAnnotationsStream(ContextConfig.java:2058)
        at org.apache.catalina.startup.ContextConfig.processAnnotationsJar(ContextConfig.java:1934)
        at org.apache.catalina.startup.ContextConfig.processAnnotationsUrl(ContextConfig.java:1900)
        at org.apache.catalina.startup.ContextConfig.processAnnotations(ContextConfig.java:1885)
        at org.apache.catalina.startup.ContextConfig.webConfig(ContextConfig.java:1317)
        at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:876)

This one happens on all the dataminer installation when tomcat starts. I told you on skype the other day about it. It seems harmless.

The problem was instead that /home/gcube/Smartgears/state/ghn.xml was corrupted. Removing the 'state' directory solves the problem. It happens regularly when the container is restarted more than once and there's a small amount of time from one restart and the other. I opened a bug about it some days ago: https://support.d4science.org/issues/2176

I just removed /home/gcube/Smartgears/state, you can start the server at any time now.

I also imported into the pom.xml used by the playbook the dependencies that you sent me:

<dependency>
           <groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-external-algorithms</artifactId>
<version>[1.1.5-SNAPSHOT,2.0.0-SNAPSHOT)</version>
           <exclusions>
               <exclusion>
                   <artifactId>slf4j-api</artifactId>
                   <groupId>org.slf4j</groupId>
               </exclusion>
               <exclusion>
<artifactId>common-utils-encryption</artifactId>
                   <groupId>org.gcube.core</groupId>
               </exclusion>
               <exclusion>
<artifactId>common-encryption</artifactId>
                   <groupId>org.gcube.core</groupId>
               </exclusion>
               <exclusion>
<artifactId>accounting-lib</artifactId>
<groupId>org.gcube.accounting</groupId>
               </exclusion>
           </exclusions>
       </dependency>