Elasticsearch timeout issues

Hi,

I am repeatedly facing timeout issues while visualizing data ki Kibana.

Here are the logs I saw when the timeout used to occur:

[2018-05-31T09:05:08,785][DEBUG][o.e.a.a.c.n.s.TransportNodesStatsAction] [GXT24Jx] failed to execute on node [GXT24JxFR2u09ohBu50mBg]
org.elasticsearch.transport.ReceiveTimeoutTransportException: [GXT24Jx][10.30.197.90:9300][cluster:monitor/nodes/stats[n]] request_id [16296211] timed out after [15602ms]
        at org.elasticsearch.transport.TransportService$TimeoutHandler.run(TransportService.java:982) [elasticsearch-6.2.4.jar:6.2.4]
        at org.elasticsearch.common.util.concurrent.ThreadContext$ContextPreservingRunnable.run(ThreadContext.java:573) [elasticsearch-6.2.4.jar:6.2.4]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_151]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_151]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_151]
[2018-05-31T09:05:11,684][WARN ][o.e.m.j.JvmGcMonitorService] [GXT24Jx] [gc][417220] overhead, spent [2.7s] collecting in the last [2.9s]
[2018-05-31T09:05:11,714][ERROR][o.e.x.w.t.s.ExecutableScriptTransform] [GXT24Jx] failed to execute [script] transform for [MS4pzhrVTKa3P7BrRUfwGA_elasticsearch_cluster_status_62e53d8c-2691-4d55-856f-a41271e5c2a4-2018-05-31T09:05:08.779Z]org.elasticsearch.script.ScriptException: runtime error
        at org.elasticsearch.painless.PainlessScript.convertToScriptException(PainlessScript.java:101) ~[?:?]
        at org.elasticsearch.painless.PainlessScript$Script.execute(ctx.vars.email_recipient = (ctx.payload.kibana_settings.hits.total > 0) ? ctx.payload.kibana_settings.hits.hits[0]._source.kibana_settings.xpack.default_admin_email : null;ctx.vars.is_new = ctx.vars.fails_check && !ctx.vars.not_resolved;ctx.vars.is_resolve ...:1070) ~[?:?]
        at org.elasticsearch.painless.ScriptImpl.run(ScriptImpl.java:105) ~[?:?]
        at org.elasticsearch.xpack.watcher.transform.script.ExecutableScriptTransform.doExecute(ExecutableScriptTransform.java:69) ~[x-pack-watcher-6.2.4.jar:6.2.4]
        at org.elasticsearch.xpack.watcher.transform.script.ExecutableScriptTransform.execute(ExecutableScriptTransform.java:53) ~[x-pack-watcher-6.2.4.jar:6.2.4]
        at org.elasticsearch.xpack.watcher.transform.script.ExecutableScriptTransform.execute(ExecutableScriptTransform.java:38) ~[x-pack-watcher-6.2.4.jar:6.2.4]
        at org.elasticsearch.xpack.watcher.execution.ExecutionService.executeInner(ExecutionService.java:476) ~[x-pack-watcher-6.2.4.jar:6.2.4]
        at org.elasticsearch.xpack.watcher.execution.ExecutionService.execute(ExecutionService.java:317) ~[x-pack-watcher-6.2.4.jar:6.2.4]
        at org.elasticsearch.xpack.watcher.execution.ExecutionService.lambda$executeAsync$6(ExecutionService.java:421) ~[x-pack-watcher-6.2.4.jar:6.2.4]
        at org.elasticsearch.xpack.watcher.execution.ExecutionService$WatchExecutionTask.run(ExecutionService.java:575) [x-pack-watcher-6.2.4.jar:6.2.4]
        at org.elasticsearch.common.util.concurrent.ThreadContext$ContextPreservingRunnable.run(ThreadContext.java:573) [elasticsearch-6.2.4.jar:6.2.4]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_151]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_151]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_151]
Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
        at java.util.ArrayList.rangeCheck(ArrayList.java:657) ~[?:1.8.0_151]
        at java.util.ArrayList.get(ArrayList.java:433) ~[?:1.8.0_151]
        at org.elasticsearch.painless.PainlessScript$Script.execute(ctx.vars.email_recipient = (ctx.payload.kibana_settings.hits.total > 0) ? ctx.payload.kibana_settings.hits.hits[0]._source.kibana_settings.xpack.default_admin_email : null;ctx.vars.is_new = ctx.vars.fails_check && !ctx.vars.not_resolved;ctx.vars.is_resolve ...:347) ~[?:?]
        ... 12 more

Here are the specs of ELK stack.
No. of ES nodes = 1
Amount to data ingested daily - few GBs only.
CPU cores = 4
CPU utilization, iowait and memory utilization are normal when the timeout occurs.

What version of the Elastic Stack?
What the heap size?
What is the viz query that is being ran, how many indices does it touch?

Elastic stack version - 6.2.4
Heap size - 1G
No. of indices it touches - It varies depending on visualization. But it gets timed out even when viewing the indices from settings in Kibana.

I guess heap size might need to be increased.

Please do start with the increase in heap size and then visualise in Kibana and feedback any issues remaining.

Looks like that was the issue. Changed heap size to 4G and everything is working just fine.

Thanks for the pointers.

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