Elasticsearch in Docker Container - "failed to write in data directory" after simple restart

Question

some weeks ago I created an elk stack (elasticsearch, logstash, kibana) to handle the load of logfiles better.

It all worked perfectly. Today I invoked some new Patterns into logstash and for some reason, I restarted via docker-compose down && docker-compose up -d.

Now elasticsearch doesn't start up anymore.

root@xyz:/srv/elk# docker-compose logs elasticsearch
Attaching to elk_elasticsearch_1
elasticsearch_1  | [2017-07-01T07:34:36,859][INFO ][o.e.n.Node               ] [lw-e01] initializing ...
elasticsearch_1  | [2017-07-01T07:34:36,999][INFO ][o.e.e.NodeEnvironment    ] [lw-e01] using [1] data paths, mounts [[/usr/share/elasticsearch/data (/dev/mapper/HDD-ELK)]], net usable_space [19.1gb], net total_space [49gb], spins? [possibly], types [ext4]
elasticsearch_1  | [2017-07-01T07:34:36,999][INFO ][o.e.e.NodeEnvironment    ] [lw-e01] heap size [3.9gb], compressed ordinary object pointers [true]
elasticsearch_1  | [2017-07-01T07:34:37,635][WARN ][o.e.b.ElasticsearchUncaughtExceptionHandler] [lw-e01] uncaught exception in thread [main]
elasticsearch_1  | org.elasticsearch.bootstrap.StartupException: java.lang.IllegalStateException: Failed to created node environment
elasticsearch_1  |      at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:127) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Elasticsearch.execute(Elasticsearch.java:114) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.cli.EnvironmentAwareCommand.execute(EnvironmentAwareCommand.java:67) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.cli.Command.mainWithoutErrorHandling(Command.java:122) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.cli.Command.main(Command.java:88) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:91) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Elasticsearch.main(Elasticsearch.java:84) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  | Caused by: java.lang.IllegalStateException: Failed to created node environment
elasticsearch_1  |      at org.elasticsearch.node.Node.<init>(Node.java:265) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.node.Node.<init>(Node.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap$6.<init>(Bootstrap.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:360) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:123) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      ... 6 more
elasticsearch_1  | Caused by: java.io.IOException: failed to write in data directory [/usr/share/elasticsearch/data/nodes/0/indices/a94kXbSER2CE97qdPhgVLA/_state] write permission is required
elasticsearch_1  |      at org.elasticsearch.env.NodeEnvironment.tryWriteTempFile(NodeEnvironment.java:1075) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.env.NodeEnvironment.assertCanWrite(NodeEnvironment.java:1047) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.env.NodeEnvironment.<init>(NodeEnvironment.java:277) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.node.Node.<init>(Node.java:262) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.node.Node.<init>(Node.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap$6.<init>(Bootstrap.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:360) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:123) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      ... 6 more
elasticsearch_1  | Caused by: java.nio.file.FileAlreadyExistsException: /usr/share/elasticsearch/data/nodes/0/indices/a94kXbSER2CE97qdPhgVLA/_state/.es_temp_file
elasticsearch_1  |      at sun.nio.fs.UnixException.translateToIOException(UnixException.java:88) ~[?:?]
elasticsearch_1  |      at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102) ~[?:?]
elasticsearch_1  |      at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107) ~[?:?]
elasticsearch_1  |      at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214) ~[?:?]
elasticsearch_1  |      at java.nio.file.Files.newByteChannel(Files.java:361) ~[?:1.8.0_131]
elasticsearch_1  |      at java.nio.file.Files.createFile(Files.java:632) ~[?:1.8.0_131]
elasticsearch_1  |      at org.elasticsearch.env.NodeEnvironment.tryWriteTempFile(NodeEnvironment.java:1072) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.env.NodeEnvironment.assertCanWrite(NodeEnvironment.java:1047) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.env.NodeEnvironment.<init>(NodeEnvironment.java:277) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.node.Node.<init>(Node.java:262) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.node.Node.<init>(Node.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap$6.<init>(Bootstrap.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap.setup(Bootstrap.java:242) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Bootstrap.init(Bootstrap.java:360) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      at org.elasticsearch.bootstrap.Elasticsearch.init(Elasticsearch.java:123) ~[elasticsearch-5.4.0.jar:5.4.0]
elasticsearch_1  |      ... 6 more

OK it Looks like a simple permissions, Problem, but also after a chown -R 1000.1000 elasticsearch/it crashes (AND set other ownerships).

The Setup: I Setup a Server with an LVM for the docker-compose Project. In the docker-compose.yml I described the three Services.

version: '3'

services:
  elasticsearch:
    image: my/elasticsearch/image:5.4.0
    volumes:
      - ./elasticsearch/data:/usr/share/elasticsearch/data
      - ./elasticsearch/config:/usr/share/elasticsearch/config
      - /etc/localtime:/etc/localtime:ro
    environment:
      ES_JAVA_OPTS: "-Xmx4g -Xms1g"
    ulimits:
      memlock:
        soft: -1
        hard: -1
    networks:
      - nginx_net

  logstash:
    image: my/logstash/image:5.4.0
    command: ["logstash", "-f", "/etc/logstash.conf"]
    volumes:
      - ./logstash.conf:/etc/logstash.conf:ro
      - ./logstash.yml:/etc/logstash/logstash.yml:ro
      - ./GeoDb/GeoLite2-City.mmdb:/GeoLite2-City.mmdb:ro
      - ./patterns:/etc/logstash/patterns:ro
      - /etc/localtime:/etc/localtime:ro
    ports:
      - "5044:5044"
    environment:
      LS_JAVA_OPTS: "-Xmx1g -Xms512m"
    depends_on:
      - elasticsearch
    networks:
      - nginx_net

  kibana:
    image: my/kibana/image:5.4.0
    volumes:
      - ./kibana/config/:/usr/share/kibana/config
      - ./kibana/config/kibana.yml:/etc/kibana/kibana.yml
      - /etc/localtime:/etc/localtime:ro
    depends_on:
      - elasticsearch
    networks:
      - nginx_net

networks:
  nginx_net:
    external: true

As you can see, I do not use the official Images directly, I install (at the Moment) XPack too, all three Images looking like this

FROM elasticsearch:5.4.0

RUN bin/elasticsearch-plugin install x-pack --batch

The scond thing I do different is I didn't use named volumes. That's because I like to have one folder containing the whole Project, also better for my LVM Management.

root@xyz:/srv/elk# ls -l
insgesamt 43488
-rw-r--r-- 1 root root     1514 Jul  1 09:34 docker-compose.yml
drwxr-xr-x 4 1000 1000     4096 Mai 18 17:43 elasticsearch
drwxr-xr-x 3 root root     4096 Mai 21 12:49 GeoDb
-rw-r--r-- 1 root root 25398754 Mai 21 12:49 GeoLite2-City.tar.gz
-rw-r--r-- 1 root root 19074950 Mai 21 12:03 GeoLiteCity.dat
drwxr-xr-x 3 root root     4096 Mai 14 16:20 kibana
-rw-r--r-- 1 root root     5523 Jul  1 09:02 logstash.conf
-rw-r--r-- 1 root root     4708 Jun  3 11:25 logstash.yml
drwx------ 2 root root    16384 Mai 17 23:40 lost+found
drwxr-xr-x 2 root root     4096 Jun  7 22:08 patterns
-rwxr-xr-x 1 root root      168 Mai 21 12:49 update-geoip.sh
root@xyz:/srv/elk# du -hs elasticsearch/
28G     elasticsearch/

I read about plugins like local-persist to use named volumes but also specify the DIR to save the files to. But also I read, that docker recommends to not use plugins in production.

I would be pretty happy for any idea / link.

OK simple rm elasticsearch/data/nodes/0/indices/a94kXbSER2CE97qdPhgVLA/_state/.es_temp_file in main Folder of docker-compose Project helped me start EL again... — lippoliv
– lippoliv, Commented Jul 1, 2017 at 19:07
Something wonky with permissions. The Elastic images expect specific permissions on the data directory — xeraa
– xeraa, Commented Jul 2, 2017 at 7:56

lippoliv · Accepted Answer · 2017-07-03 06:17:51Z

3

OK simple: run (in my case) rm elasticsearch/data/nodes/0/indices/a94kXbSER2CE97qdPhgVLA/_s‌tate/.es_temp_file in main Folder of docker-compose Project helped me start EL again...

To figure out the exactly path look at the java.nio.file.FileAlreadyExistsException

answered Jul 3, 2017 at 6:17

lippoliv

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codenamev · Accepted Answer · 2017-10-04 20:14:18Z

0

The above answer didn't work for me. It ended up being a memory issue with Docker. Boosting Docker's memory allotment resolved it.

answered Oct 4, 2017 at 20:14

codenamev

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