Using Persistent Host Volume for ElasticSearch with Docker-Compose

Question

Running Elasticsearch using the below docker-compose.yml is throwing an error

Java.nio.file.AccessDeniedException: /usr/share/elasticsearch/data/nodes

It appears that this is due to trying to mount /usr/share/elasticsearch/data in the Docker container to ./data/elasticsearch/data on the host.

Tried setting user: "1000:1000" after identifying the following info, but still getting the same error.

the owner/group of /usr/share/elasticsearch/data/nodes to be elasticsearch:elasticsearch
the owner/group of /usr/share/elasticsearch/data to be elasticsearch:root
uid=1000(elasticsearch) gid=1000(elasticsearch) groups=1000(elasticsearch)

Question: Is it possible to mount it to the host volume ./data/elasticsearch/data, and not by using an anonymous or named volume?

Using docker-compose 1.24.0, docker 19.03.6-rc1, Ubuntu 18.04.3.

docker-compose.yml

version: '3'
services:

  elasticsearch:
    image: docker.elastic.co/elasticsearch/elasticsearch-oss:6.8.2
    user: "1000:1000"
    volumes:
      - ./data/elasticsearch:/usr/share/elasticsearch/data
    environment:
      - http.host=0.0.0.0
      - transport.host=localhost
      - network.host=0.0.0.0
      - "ES_JAVA_OPTS=-Xms512m -Xmx512m"
    ulimits:
      memlock:
        soft: -1
        hard: -1
    deploy:
      resources:
        limits:
          memory: 1g
    networks:
      - graylog

networks:
  graylog:
    driver: bridge

Elasticsearch Full Error from docker logs

elasticsearch_1  | OpenJDK 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated in version 9.0 and will likely be removed in a future release.
elasticsearch_1  | [2020-01-31T23:51:11,119][WARN ][o.e.b.ElasticsearchUncaughtExceptionHandler] [unknown] uncaught exception in thread [main]
elasticsearch_1  | org.elasticsearch.bootstrap.StartupException: java.lang.IllegalStateException: Failed to create node environment
elasticsearch_1  |  at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:163) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Elasticsearch.execute(Elasticsearch.java:150) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:86) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:124) ~[elasticsearch-cli-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.cli.Command.main(Command.java:90) ~[elasticsearch-cli-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:116) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:93) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  | Caused by: java.lang.IllegalStateException: Failed to create node environment
elasticsearch_1  |  at org.elasticsearch.node.Node.<init>(Node.java:299) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.node.Node.<init>(Node.java:266) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Bootstrap$5.<init>(Bootstrap.java:212) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:212) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:333) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:159) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  ... 6 more
elasticsearch_1  | Caused by: java.nio.file.AccessDeniedException: /usr/share/elasticsearch/data/nodes
elasticsearch_1  |  at sun.nio.fs.UnixException.translateToIOException(UnixException.java:90) ~[?:?]
elasticsearch_1  |  at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) ~[?:?]
elasticsearch_1  |  at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116) ~[?:?]
elasticsearch_1  |  at sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:389) ~[?:?]
elasticsearch_1  |  at java.nio.file.Files.createDirectory(Files.java:692) ~[?:?]
elasticsearch_1  |  at java.nio.file.Files.createAndCheckIsDirectory(Files.java:799) ~[?:?]
elasticsearch_1  |  at java.nio.file.Files.createDirectories(Files.java:785) ~[?:?]
elasticsearch_1  |  at org.elasticsearch.env.NodeEnvironment.lambda$new$0(NodeEnvironment.java:273) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.env.NodeEnvironment$NodeLock.<init>(NodeEnvironment.java:206) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.env.NodeEnvironment.<init>(NodeEnvironment.java:270) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.node.Node.<init>(Node.java:296) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.node.Node.<init>(Node.java:266) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Bootstrap$5.<init>(Bootstrap.java:212) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:212) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:333) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:159) ~[elasticsearch-6.8.2.jar:6.8.2]
elasticsearch_1  |  ... 6 more

Zeitounator · Accepted Answer · 2020-02-01 00:58:02Z

After launching the container on its own and inspecting it, I saw the data dir was owned by 1000:root. So I simply reproduced this on the directory to bind and elastic started without any problems:

$ cd /tmp
$ mkdir -p so_test_elastic/data
$ cd so_test_elastic
$ sudo chown 1000:root data
$ docker run -it --rm --name es -v $(pwd)/data:/usr/share/elasticsearch/data docker.elastic.co/elasticsearch/elasticsearch-oss:6.8.2
OpenJDK 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated in version 9.0 and will likely be removed in a future release.
[2020-02-01T00:55:31,776][INFO ][o.e.e.NodeEnvironment    ] [C1_TRq-] using [1] data paths, mounts [[/usr/share/elasticsearch/data (/dev/sda2)]], net usable_space [253.6gb], net total_space [862gb], types [btrfs]
[2020-02-01T00:55:31,778][INFO ][o.e.e.NodeEnvironment    ] [C1_TRq-] heap size [989.8mb], compressed ordinary object pointers [true]
[2020-02-01T00:55:31,779][INFO ][o.e.n.Node               ] [C1_TRq-] node name derived from node ID [C1_TRq-6TruEDL9vDOdP9Q]; set [node.name] to override
[2020-02-01T00:55:31,779][INFO ][o.e.n.Node               ] [C1_TRq-] version[6.8.2], pid[1], build[oss/docker/b506955/2019-07-24T15:24:41.545295Z], OS[Linux/4.15.0-76-generic/amd64], JVM[Oracle Corporation/OpenJDK 64-Bit Server VM/12.0.1/12.0.1+12]
[2020-02-01T00:55:31,779][INFO ][o.e.n.Node               ] [C1_TRq-] JVM arguments [-Xms1g, -Xmx1g, -XX:+UseConcMarkSweepGC, -XX:CMSInitiatingOccupancyFraction=75, -XX:+UseCMSInitiatingOccupancyOnly, -Des.networkaddress.cache.ttl=60, -Des.networkaddress.cache.negative.ttl=10, -XX:+AlwaysPreTouch, -Xss1m, -Djava.awt.headless=true, -Dfile.encoding=UTF-8, -Djna.nosys=true, -XX:-OmitStackTraceInFastThrow, -Dio.netty.noUnsafe=true, -Dio.netty.noKeySetOptimization=true, -Dio.netty.recycler.maxCapacityPerThread=0, -Dlog4j.shutdownHookEnabled=false, -Dlog4j2.disable.jmx=true, -Djava.io.tmpdir=/tmp/elasticsearch-6545090589525108799, -XX:+HeapDumpOnOutOfMemoryError, -XX:HeapDumpPath=data, -XX:ErrorFile=logs/hs_err_pid%p.log, -Xlog:gc*,gc+age=trace,safepoint:file=logs/gc.log:utctime,pid,tags:filecount=32,filesize=64m, -Djava.locale.providers=COMPAT, -XX:UseAVX=2, -Des.cgroups.hierarchy.override=/, -Des.path.home=/usr/share/elasticsearch, -Des.path.conf=/usr/share/elasticsearch/config, -Des.distribution.flavor=oss, -Des.distribution.type=docker]
[2020-02-01T00:55:32,367][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [aggs-matrix-stats]
[2020-02-01T00:55:32,367][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [analysis-common]
[2020-02-01T00:55:32,367][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [ingest-common]
[2020-02-01T00:55:32,367][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [ingest-geoip]
[2020-02-01T00:55:32,367][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [ingest-user-agent]
[2020-02-01T00:55:32,367][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [lang-expression]
[2020-02-01T00:55:32,367][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [lang-mustache]
[2020-02-01T00:55:32,367][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [lang-painless]
[2020-02-01T00:55:32,368][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [mapper-extras]
[2020-02-01T00:55:32,368][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [parent-join]
[2020-02-01T00:55:32,368][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [percolator]
[2020-02-01T00:55:32,368][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [rank-eval]
[2020-02-01T00:55:32,368][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [reindex]
[2020-02-01T00:55:32,368][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [repository-url]
[2020-02-01T00:55:32,368][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [transport-netty4]
[2020-02-01T00:55:32,368][INFO ][o.e.p.PluginsService     ] [C1_TRq-] loaded module [tribe]
[2020-02-01T00:55:32,369][INFO ][o.e.p.PluginsService     ] [C1_TRq-] no plugins loaded
[2020-02-01T00:55:34,347][INFO ][o.e.d.DiscoveryModule    ] [C1_TRq-] using discovery type [zen] and host providers [settings]
[2020-02-01T00:55:34,628][INFO ][o.e.n.Node               ] [C1_TRq-] initialized
[2020-02-01T00:55:34,628][INFO ][o.e.n.Node               ] [C1_TRq-] starting ...
[2020-02-01T00:55:34,718][INFO ][o.e.t.TransportService   ] [C1_TRq-] publish_address {172.17.0.2:9300}, bound_addresses {0.0.0.0:9300}
[2020-02-01T00:55:34,725][INFO ][o.e.b.BootstrapChecks    ] [C1_TRq-] bound or publishing to a non-loopback address, enforcing bootstrap checks
[2020-02-01T00:55:37,765][INFO ][o.e.c.s.MasterService    ] [C1_TRq-] zen-disco-elected-as-master ([0] nodes joined), reason: new_master {C1_TRq-}{C1_TRq-6TruEDL9vDOdP9Q}{qio5SYagRraILpZj5QfRiQ}{172.17.0.2}{172.17.0.2:9300}
[2020-02-01T00:55:37,767][INFO ][o.e.c.s.ClusterApplierService] [C1_TRq-] new_master {C1_TRq-}{C1_TRq-6TruEDL9vDOdP9Q}{qio5SYagRraILpZj5QfRiQ}{172.17.0.2}{172.17.0.2:9300}, reason: apply cluster state (from master [master {C1_TRq-}{C1_TRq-6TruEDL9vDOdP9Q}{qio5SYagRraILpZj5QfRiQ}{172.17.0.2}{172.17.0.2:9300} committed version [1] source [zen-disco-elected-as-master ([0] nodes joined)]])
[2020-02-01T00:55:37,786][INFO ][o.e.h.n.Netty4HttpServerTransport] [C1_TRq-] publish_address {172.17.0.2:9200}, bound_addresses {0.0.0.0:9200}
[2020-02-01T00:55:37,786][INFO ][o.e.n.Node               ] [C1_TRq-] started
[2020-02-01T00:55:37,828][INFO ][o.e.g.GatewayService     ] [C1_TRq-] recovered [0] indices into cluster_state

Is it possible to have a solution where the user only run the command docker-compose up without having to execute other commands such as chmod or chown?
@Nyxynyx using a docker volume instead of a bind mounted directory should help.

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