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Answered
Anyone Faced An Issue With Elasticsearch Before

Anyone faced an issue with elasticsearch before

h8q2wwsd3o-algo-1-vnnpg | 2025-05-19 11:41:21,688 - clearml.log - WARNING - failed logging task to backend (1 lines, <500/100: events.add_batch/v1.0 (General data error: err=1 document(s) failed to index., extra_info=[events-log-d1bd92a3b039400cbafc60a7a5b1e52b][0] primary shard is not active Timeout: [1m], request: [BulkShardRequest [[events-log-d1bd92a3b039400cbafc60a7a5b1e52b][0]] containing [index {[events-log-d1bd92a3b039400cbafc60a7a5b1e52b][f3abecd0f46f4bd289e0ac39662fd850], source[{"timestamp":1747654820464,"type":"log","task":"fd3d00d99d88427bbc576cba53db062d","level":"info","worker":"b1193fbdd662","msg":"Starting the training.\nClearML Monitor: GPU monitoring failed getting GPU reading, switching off GPU monitoring","model_event":false,"@timestamp":"2025-05-19T11:40:21.919Z","metric":"","variant":""}]}] and a refresh])>)

8q2wwsd3o-algo-1-vnnpg | 2025-05-19 11:48:20,538 - urllib3.connectionpool - WARNING - Retrying (Retry(total=234, connect=234, read=240, redirect=240, status=240)) after connection broken by 'ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x794c188c8460>, 'Connection to "" timed out. (connect timeout=10.0)')': /v2.23/events.add_batch

I'm self-hosting clearml server on ec2 (t3.large).

  
  
Posted 3 months ago
Votes Newest

Answers 51


Looks like elastic is failing to access a shard. Do you have visibility into machine utilization? How much RAM is elastic consuming?

Also, is this the entire error repeating or is there more context?

  
  
Posted 3 months ago

It's the entire error repeating.
And, this happens at the end of the script.

I'm using the recommended instance (t3.large).

  
  
Posted 3 months ago

@<1523701070390366208:profile|CostlyOstrich36>
I've updated the instance type to t3a.large.
The issue persisted.

  
  
Posted 3 months ago

Hi @<1835488771542355968:profile|PerplexedShells66> , please inspect your Elasticsearch logs. Any errors or warnings there?

  
  
Posted 3 months ago

I need to ssh the instance, right?
I'll check it out.

  
  
Posted 3 months ago

Yes

  
  
Posted 3 months ago

One of the most likely reasons for this issue would be insufficient free disk space for Elasticsearch. This may happen if less than 10% of free space is left on ES storage location. But there may be also other reasons

  
  
Posted 3 months ago

ok. Currently the ebs is 15 GB, is there a recommended size?

  
  
Posted 3 months ago

It depends on your usage. ES has some default watermarks that are activated when the amount of used space is above 85% and 90% (can be overwritten) of the storage. At some point it may transfer the index to a "readonly" state.

  
  
Posted 3 months ago

I don't store anything on clearml server; everything is being stored in S3 and referenced by ClearML.

  
  
Posted 3 months ago

Then possibly it is another reason. Need to search for in the ES logs

  
  
Posted 3 months ago

While on the host you can run some ES commands to check the shards health and allocations. For example this:

curl -XGET "localhost:9200/_cluster/allocation/explain?pretty"

It may give more clues to the problem

  
  
Posted 3 months ago

ok, I'm recreating the ec2 isntance to generate ssh key pair, then I'll check the elasticsearch logs.

  
  
Posted 3 months ago

it's behaving very strangely.

I'm trying to provision the instance, but something is off.
It's as if some functionalities are missing.
image

  
  
Posted 3 months ago

I tried deleting all the underlying resources: ec2 & ebs, and recreating it again.

  
  
Posted 3 months ago

@<1722061389024989184:profile|ResponsiveKoala38> I'm looking at the logs now (used "docker logs clearml-elastic").

The status seemed to had transitioned, but the it's not clear the error.

{"@timestamp":"2025-05-20T08:36:18.412Z", "log.level": "INFO", "message":"setting file [/usr/share/elasticsearch/config/operator/settings.json] not found, initializing [file_settings] as empty", "ecs.version": "1.2.0","service.name":"ES_ECS","event.dataset":"elasticsearch.server","process.thread.name":"elasticsearch[file-watcher[/usr/share/elasticsearch/config/operator/settings.json]]","log.logger":"org.elasticsearch.reservedstate.service.FileSettingsService","elasticsearch.cluster.uuid":"lvIPB_h3RiWqbCvCA-1dbw","elasticsearch.node.id":"wEMvgjW3SUSt8Y8ls7aEyw","elasticsearch.node.name":"clearml","elasticsearch.cluster.name":"clearml"}
{"@timestamp":"2025-05-20T08:36:19.068Z", "log.level": "INFO", "message":"Node [{clearml}{wEMvgjW3SUSt8Y8ls7aEyw}] is selected as the current health node.", "ecs.version": "1.2.0","service.name":"ES_ECS","event.dataset":"elasticsearch.server","process.thread.name":"elasticsearch[clearml][management][T#1]","log.logger":"org.elasticsearch.health.node.selection.HealthNodeTaskExecutor","elasticsearch.cluster.uuid":"lvIPB_h3RiWqbCvCA-1dbw","elasticsearch.node.id":"wEMvgjW3SUSt8Y8ls7aEyw","elasticsearch.node.name":"clearml","elasticsearch.cluster.name":"clearml"}
{"@timestamp":"2025-05-20T08:36:19.360Z", "log.level": "INFO",  "current.health":"GREEN","message":"Cluster health status changed from [RED] to [GREEN] (reason: [shards started [[events-plot-][0]]]).","previous.health":"RED","reason":"shards started [[events-plot-][0]]" , "ecs.version": "1.2.0","service.name":"ES_ECS","event.dataset":"elasticsearch.server","process.thread.name":"elasticsearch[clearml][masterService#updateTask][T#1]","log.logger":"org.elasticsearch.cluster.routing.allocation.AllocationService","elasticsearch.cluster.uuid":"lvIPB_h3RiWqbCvCA-1dbw","elasticsearch.node.id":"wEMvgjW3SUSt8Y8ls7aEyw","elasticsearch.node.name":"clearml","elasticsearch.cluster.name":"clearml"}
{"@timestamp":"2025-05-20T08:36:48.250Z", "log.level": "INFO", "message":"[queue_metrics_d1bd92a3b039400cbafc60a7a5b1e52b_2025-05] creating index, cause [auto(bulk api)], templates [queue_metrics], shards [1]/[0]", "ecs.version": "1.2.0","service.name":"ES_ECS","event.dataset":"elasticsearch.server","process.thread.name":"elasticsearch[clearml][masterService#updateTask][T#1]","log.logger":"org.elasticsearch.cluster.metadata.MetadataCreateIndexService","elasticsearch.cluster.uuid":"lvIPB_h3RiWqbCvCA-1dbw","elasticsearch.node.id":"wEMvgjW3SUSt8Y8ls7aEyw","elasticsearch.node.name":"clearml","elasticsearch.cluster.name":"clearml"}
{"@timestamp":"2025-05-20T08:36:48.489Z", "log.level": "INFO",  "current.health":"GREEN","message":"Cluster health status changed from [YELLOW] to [GREEN] (reason: [shards started [[queue_metrics_d1bd92a3b039400cbafc60a7a5b1e52b_2025-05][0]]]).","previous.health":"YELLOW","reason":"shards started [[queue_metrics_d1bd92a3b039400cbafc60a7a5b1e52b_2025-05][0]]" , "ecs.version": "1.2.0","service.name":"ES_ECS","event.dataset":"elasticsearch.server","process.thread.name":"elasticsearch[clearml][masterService#updateTask][T#1]","log.logger":"org.elasticsearch.cluster.routing.allocation.AllocationService","elasticsearch.cluster.uuid":"lvIPB_h3RiWqbCvCA-1dbw","elasticsearch.node.id":"wEMvgjW3SUSt8Y8ls7aEyw","elasticsearch.node.name":"clearml","elasticsearch.cluster.name":"clearml"}
{"@timestamp":"2025-05-20T09:25:56.852Z", "log.level": "INFO", "message":"[events-log-d1bd92a3b039400cbafc60a7a5b1e52b] creating index, cause [auto(bulk api)], templates [events_log], shards [1]/[0]", "ecs.version": "1.2.0","service.name":"ES_ECS","event.dataset":"elasticsearch.server","process.thread.name":"elasticsearch[clearml][masterService#updateTask][T#11]","log.logger":"org.elasticsearch.cluster.metadata.MetadataCreateIndexService","elasticsearch.cluster.uuid":"lvIPB_h3RiWqbCvCA-1dbw","elasticsearch.node.id":"wEMvgjW3SUSt8Y8ls7aEyw","elasticsearch.node.name":"clearml","elasticsearch.cluster.name":"clearml"}
{"@timestamp":"2025-05-20T09:25:56.964Z", "log.level": "INFO",  "current.health":"GREEN","message":"Cluster health status changed from [YELLOW] to [GREEN] (reason: [shards started [[events-log-d1bd92a3b039400cbafc60a7a5b1e52b][0]]]).","previous.health":"YELLOW","reason":"shards started [[events-log-d1bd92a3b039400cbafc60a7a5b1e52b][0]]" , "ecs.version": "1.2.0","service.name":"ES_ECS","event.dataset":"elasticsearch.server","process.thread.name":"elasticsearch[clearml][masterService#updateTask][T#11]","log.logger":"org.elasticsearch.cluster.routing.allocation.AllocationService","elasticsearch.cluster.uuid":"lvIPB_h3RiWqbCvCA-1dbw","elasticsearch.node.id":"wEMvgjW3SUSt8Y8ls7aEyw","elasticsearch.node.name":"clearml","elasticsearch.cluster.name":"clearml"}
  
  
Posted 3 months ago

curl -XGET "localhost:9200/_cluster/allocation/explain?pretty"
curl: (7) Failed to connect to localhost port 9200 after 0 ms: Couldn't connect to server

  
  
Posted 3 months ago

I do not see any issues in the log. Do you still get errors in the task due to the failure in events.add_batch?

  
  
Posted 3 months ago

On what host did you run the curl command?

  
  
Posted 3 months ago

ecc2, after I ssh-ed the instance.

  
  
Posted 3 months ago

Probably the 9200 port is not mapped from the ES container in the docker compose
The easiest would be to perform "sudo docker exec -it clearml-elastic /bin/bash" and then run the curl command from inside the ES docker

  
  
Posted 3 months ago

{
  "error" : {
    "root_cause" : [
      {
        "type" : "illegal_argument_exception",
        "reason" : "No shard was specified in the request which means the response should explain a randomly-chosen unassigned shard, but there are no unassigned shards in this cluster. To explain the allocation of an assigned shard you must specify the target shard in the request. See 
 for more information."
      }
    ],
    "type" : "illegal_argument_exception",
    "reason" : "No shard was specified in the request which means the response should explain a randomly-chosen unassigned shard, but there are no unassigned shards in this cluster. To explain the allocation of an assigned shard you must specify the target shard in the request. See 
 for more information."
  },
  "status" : 400
}

this means that elasticsearch server hasn't started, right?

  
  
Posted 3 months ago

No, it says that it does not detect any problematic shards. Given that output and the absence of the errors in the logs I would expect that you will not get the error anymore

  
  
Posted 3 months ago

Did you try to run your job again?

  
  
Posted 3 months ago

I have been rerunning it since yesterday. The error persists.

I can try one more time though.

  
  
Posted 3 months ago

I would try it again.

  
  
Posted 3 months ago

Alright, it's running...

  
  
Posted 3 months ago

@<1722061389024989184:profile|ResponsiveKoala38> It's not resolved.

  
  
Posted 3 months ago

In ES container please run "curl -XGET localhost:9200/_cat/indices"

  
  
Posted 3 months ago

What is the status that you get for the "events-log-d1bd92a3b039400cbafc60a7a5b1e52b" index?

  
  
Posted 3 months ago