Issue with atlas-run - Web Application Stopped Error

[Shubham Sharma]

I am running this command in my atlas project:
/opt/atlassian-plugin-sdk/bin/atlas-run -Datlassian.plugins.enable.wait=true -Djira.webserver.host=0.0.0.0

and after this url http://<VM-IP>:2990 getting this result:

/var/atlassian/application-data/jira/log/atlassian-jira.log, in this path of log i am getting this:

2025-02-11 12:22:57,151+0530 versioning-stats-0 INFO [c.a.jira.versioning.EntityVersioningManagerWithStats] [JIRA-STATS] [VERSIONING] snapshot stats: {"requestMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"5":0,"10":0,"50":0,"100":0,"200":0}},"requestCount":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0}},"requestPercent":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"3":0,"5":0,"10":0,"20":0,"30":0}},"incrementIssueVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"incrementCommentVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"incrementWorklogVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"incrementRelatedCommentVersionsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"incrementRelatedWorklogVersionsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"markIssueDeletedAndIncrementVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"markCommentDeletedAndIncrementVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"markWorklogDeletedAndIncrementVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"getIssueVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"getCommentVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"getWorklogVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"getRelatedCommentVersionsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"getRelatedWorklogVersionsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"getLocalVersionsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"5":0,"10":0,"50":0,"100":0,"500":0,"1000":0}},"markEntityDeletedAndIncrementVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"cleanAllDeletedEntityVersionsOlderThanMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"findEntityVersionsUpdatedInRangeMillis":{"count":90,"min":0,"max":171,"sum":248,"avg":2,"distributionCounter":{}},"getLatestEntityUpdateTimeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}}} 2025-02-11 12:22:57,269+0530 periodic-de-index-fixer-0 INFO [c.a.j.index.ha.TotalAndSnapshotIndexRepairStats] [JIRA-STATS] [INDEX-FIXER] index repair total stats: {"processedDeindexOperations":{"count":300,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"processedReindexOperations":{"count":300,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"durationIsLongerThanRetentionPeriod":{"count":300,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"indexRecoveryMillis":{"count":300,"min":0,"max":175,"sum":1448,"avg":4,"distributionCounter":{}},"errors":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}}} 2025-02-11 12:22:57,270+0530 periodic-de-index-fixer-0 INFO [c.a.j.index.ha.TotalAndSnapshotIndexRepairStats] [JIRA-STATS] [INDEX-FIXER] index repair snapshot stats: {"processedDeindexOperations":{"count":30,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"processedReindexOperations":{"count":30,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"durationIsLongerThanRetentionPeriod":{"count":30,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"indexRecoveryMillis":{"count":30,"min":1,"max":175,"sum":300,"avg":10,"distributionCounter":{}},"errors":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}}} 2025-02-11 12:23:41,851+0530 index-writer-stats-ISSUE-2-0 INFO [c.a.jira.index.WriterWithStats] [JIRA-STATS] [index-writer-stats] ISSUE : total stats: {"addDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"deleteDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentConditionallyMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"updateDocumentsWithVersionMillis":{"count":1,"min":2391,"max":2391,"sum":2391,"avg":2391,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":1,"10000":0,"30000":0,"60000":0}},"updateDocumentsWithVersionSize":{"count":1,"min":1,"max":1,"sum":1,"avg":1,"distributionCounter":{"1":1,"10":0,"100":0,"1000":0,"10000":0}},"replaceDocumentsWithVersionMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"10":0,"100":0,"500":0,"1000":0,"5000":0,"10000":0,"30000":0,"60000":0}},"replaceDocumentsWithVersionSize":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{"1":0,"10":0,"100":0,"1000":0,"10000":0}},"optimizeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"closeMillis":{"count":0,"min":0,"max":0,"sum":0,"avg":0,"distributionCounter":{}},"commitMillis":{"count":1,"min":857,"max":857,"sum":857,"avg":857,"distributionCounter":{}}}, index writer version cache stats: {"put":1,"get":1,"getFound":0,"clear":0,"clearSizeExceeded":0}, index writer searcher stats: {"createNew":1,"reuse":0}

AND in atlas terminal output, i am seeing this error

[INFO] [talledLocalContainer] Feb 11, 2025 12:25:48 PM org.apache.catalina.loader.WebappClassLoaderBase checkStateForResourceLoading [INFO] [talledLocalContainer] INFO: Illegal access: this web application instance has been stopped already. Could not load [com.google.gson.GsonBuilder]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access. [INFO] [talledLocalContainer] java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load [com.google.gson.GsonBuilder]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access. [INFO] [talledLocalContainer] at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1349) [INFO] [talledLocalContainer] at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1337) [INFO] [talledLocalContainer] at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1174) [INFO] [talledLocalContainer] at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1141) [INFO] [talledLocalContainer] at com.atlassian.jira.util.stats.GsonStatsSerializer.buildGson(GsonStatsSerializer.java:43) [INFO] [talledLocalContainer] at com.atlassian.jira.util.stats.GsonStatsSerializer.serialize(GsonStatsSerializer.java:25) [INFO] [talledLocalContainer] at com.atlassian.jira.util.stats.JiraStats.log(JiraStats.java:468) [INFO] [talledLocalContainer] at com.atlassian.jira.util.stats.JiraStats.printAndReset(JiraStats.java:418) [INFO] [talledLocalContainer] at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [INFO] [talledLocalContainer] at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308) [INFO] [talledLocalContainer] at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180) [INFO] [talledLocalContainer] at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294) [INFO] [talledLocalContainer] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [INFO] [talledLocalContainer] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [INFO] [talledLocalContainer] at java.lang.Thread.run(Thread.java:750) [INFO] [talledLocalContainer] [INFO] [talledLocalContainer] Feb 11, 2025 12:25:49 PM org.apache.catalina.loader.WebappClassLoaderBase checkStateForResourceLoading [INFO] [talledLocalContainer] INFO: Illegal access: this web application instance has been stopped already. Could not load [com.atlassian.jira.util.stats.LongStats]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access. [INFO] [talledLocalContainer] java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load [com.atlassian.jira.util.stats.LongStats]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access. [INFO] [talledLocalContainer] at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1349) [INFO] [talledLocalContainer] at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1337) [INFO] [talledLocalContainer] at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1174) [INFO] [talledLocalContainer] at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1141) [INFO] [talledLocalContainer] at com.atlassian.jira.util.stats.MutableLongStats.get(MutableLongStats.java:58) [INFO] [talledLocalContainer] at com.atlassian.jira.mention.stats.data.UserSearchServiceStatsData.getTotalMeasuredOperationsForStatsOverheadInMillis(UserSearchServiceStatsData.java:34) [INFO] [talledLocalContainer] at com.atlassian.jira.util.stats.JiraStats.log(JiraStats.java:456) [INFO] [talledLocalContainer] at com.atlassian.jira.util.stats.JiraStats.printAndReset(JiraStats.java:418) [INFO] [talledLocalContainer] at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [INFO] [talledLocalContainer] at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308) [INFO] [talledLocalContainer] at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180) [INFO] [talledLocalContainer] at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294) [INFO] [talledLocalContainer] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [INFO] [talledLocalContainer] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [INFO] [talledLocalContainer] at java.lang.Thread.run(Thread.java:750) [INFO] [talledLocalContainer]

It seems that the web application instance is being stopped, leading to IllegalStateException errors. Could you please help me understand the cause of this issue and suggest a resolution?

Version:
ATLAS Version: 9.1.1
ATLAS Home: /opt/atlassian-plugin-sdk ATLAS Scripts: /opt/atlassian-plugin-sdk/bin
ATLAS Maven Home: /opt/atlassian-plugin-sdk/apache-maven-3.9.8 AMPS Version: 9.1.1

Executing: /opt/atlassian-plugin-sdk/apache-maven-3.9.8/bin/mvn --version -gs /opt/atlassian-plugin-sdk/apache-maven-3.9.8/conf/settings.xml Apache Maven 3.9.8 (36645f6c9b5079805ea5009217e36f2cffd34256)
Maven home: /opt/atlassian-plugin-sdk/apache-maven-3.9.8
Java version: 1.8.0_442, vendor: Private Build, runtime: /usr/lib/jvm/java-8-openjdk-amd64/jre
Default locale: en_IN, platform encoding: UTF-8 OS name: "linux", version: "6.8.0-52-generic", arch: "amd64", family: "unix"

[Tuncay Senturk]

Hi @Shubham Sharma 

It is very difficult to find the root cause, but it is best to clear the problems in the logs, as the devil is in the logs.

For instance, one of the errors in the log "Could not load [com.google.gson.GsonBuilder]" suggests a dependency issue, with Gson. Have you already had a dependency with Gson (directly or indirectly)?

If not you can add the dependency and see how it goes

<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.8.9</version> 
<scope>provided</scope> 
</dependency>

By the way, I'd suggest Atlassian Developer Community as you may find more answers there.

I hope it helps

[Shubham Sharma]

Nope Still not working
getting this in chrome

HTTP Status 404 – Not Found

---

Type Status Report

Description The origin server did not find a current representation for the target resource or is not willing to disclose that one exists.

---

Apache Tomcat/9.0.84

[Tuncay Senturk]

Okay, what about the logs? Did you notice that the error related to gson has disappeared? I just want to rule that out before moving on to the other error logs in your log file.