Sage-Bionetworks / sage-monorepo

Where OpenChallenges, Schematic, and other Sage open source apps are built
https://sage-bionetworks.github.io/sage-monorepo/
Apache License 2.0
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[Bug] Elasticsearch experiences Bulk write of deprecation logs encountered some failures #2081

Closed tschaffter closed 12 months ago

tschaffter commented 12 months ago

Is there an existing issue for this?

What product(s) are you seeing the problem on?

OpenChallenges

Current behavior

  1. openchallenges-build-images
  2. nx serve-detach openchallenges-organization-service

The three ES instances fail to start. The 2nd and 3rd nodes fail because the first node fails. The logs of the first node end with:

{"type": "server", "timestamp": "2023-09-05T01:10:35,197Z", "level": "ERROR", "component": "o.e.x.d.l.DeprecationIndexingComponent", "cluster.name": "openchallenges-elasticsearch", "node.name": "openchallenges-elasticsearch", "message": "Bulk write of deprecation logs encountered some failures: [[aAnjYooBlfoVQw1-QYdS UnavailableShardsException[[.ds-.logs-deprecation.elasticsearch-default-2023.09.05-000001][0] primary shard is not active Timeout: [1m], request: [BulkShardRequest [[.ds-.logs-deprecation.elasticsearch-default-2023.09.05-000001][0]] containing [index {[.logs-deprecation.elasticsearch-default][_doc][aAnjYooBlfoVQw1-QYdS], source[{\"event.dataset\": \"deprecation.elasticsearch\", \"@timestamp\": \"2023-09-05T01:09:33,754Z\", \"log.level\": \"CRITICAL\", \"log.logger\": \"org.elasticsearch.deprecation.xpack.security.support.SecurityStatusChangeListener\", \"elasticsearch.cluster.name\": \"openchallenges-elasticsearch\", \"elasticsearch.cluster.uuid\": \"\", \"elasticsearch.node.id\": \"\", \"elasticsearch.node.name\": \"openchallenges-elasticsearch\", \"trace.id\": \"\", \"message\": \"The default behavior of disabling security on basic licenses is deprecated. In a later version of Elasticsearch, the value of [xpack.security.enabled] will default to \\\"true\\\" , regardless of the license level. See https://www.elastic.co/guide/en/elasticsearch/reference/7.17/security-minimal-setup.html to enable security, or explicitly disable security by setting [xpack.security.enabled] to false in elasticsearch.yml\", \"data_stream.type\": \"logs\", \"data_stream.dataset\": \"deprecation.elasticsearch\", \"data_stream.namespace\": \"default\", \"ecs.version\": \"1.7\", \"elasticsearch.event.category\": \"security\", \"event.code\": \"security_implicitly_disabled\", \"elasticsearch.http.request.x_opaque_id\": \"\" }\n]}]]]]]", "cluster.uuid": "wZ2xG9a6SgaKDagsEcmNQg", "node.id": "ZtDSIXS0SUik_RGVJUdPWA"  }

Expected behavior

No response

Anything else?

Experienced when working on #2079

Commit ID

No response

Are you developing inside the dev container?

Code of Conduct

tschaffter commented 12 months ago

There is almost no space left on the EC2 instance:

vscode@7047b27f8ebb:/workspaces/sage-monorepo$ df -h
Filesystem      Size  Used Avail Use% Mounted on
overlay          80G   74G  6.1G  93% /

Removing all Docker artifacts in the dev container does not free as much as expected:

vscode@7047b27f8ebb:/workspaces/sage-monorepo$ df -h
Filesystem      Size  Used Avail Use% Mounted on
overlay          80G   58G   23G  72% /

Removing all the images on the host saves 23G:

[ec2-user@ip-10-41-30-105 sage-monorepo]$ df -h
Filesystem      Size  Used Avail Use% Mounted on
devtmpfs         16G     0   16G   0% /dev
tmpfs            16G     0   16G   0% /dev/shm
tmpfs            16G  596K   16G   1% /run
tmpfs            16G     0   16G   0% /sys/fs/cgroup
/dev/nvme0n1p1   80G   37G   44G  46% /
tmpfs           3.2G     0  3.2G   0% /run/user/1000
tschaffter commented 12 months ago

Conclusion

After making some space, the OC stack started successfully, including the Elasticsearch nodes.