Timeout error on Docker on Ubuntu -- "Waiting for Elasticsearch to be up"

[cimar]

The datashare.sh script successfully installs everything but then never successfully connects to elasticsearch. It eventually yields a timeout error but then keeps trying. Ubuntu 20.04.3 LTS (focal)

sudo ./datashare.sh
datashare_elasticsearch_1 is up-to-date
datashare_redis_1 is up-to-date
binding data directory to 
binding NER models directory to /root/.local/share/datashare/dist
2021-10-25 19:00:08,983 [main] INFO  Main - Running datashare web server
2021-10-25 19:00:08,991 [main] WARN  PropertiesProvider - no null file found, using default values
2021-10-25 19:00:09,003 [main] INFO  PropertiesProvider - adding properties from env vars {mountedDataDir=/root/Datashare}
2021-10-25 19:00:09,003 [main] INFO  PropertiesProvider - properties set to {mountedDataDir=/root/Datashare}
2021-10-25 19:00:09,004 [main] INFO  PropertiesProvider - merged properties (without override) with {parserParallelism=1, cors=no-cors, dataDir=/home/datashare/data, parallelism=4, scrollSlices=1, elasticsearchDataPath=/home/datashare/es, elasticsearchAddress=http://elasticsearch:9200, protectedUriPrefix=/api/, redisPoolSize=1, mode=LOCAL, clusterName=datashare, nlpParallelism=1, busType=redis, defaultProject=local-datashare, scrollSize=1000, ocr=true, messageBusAddress=redis://redis:6379, dataSourceUrl=jdbc:sqlite:/home/datashare/dist/database.sqlite, defaultUserName=local, extensionsDir=/home/datashare/extensions, tcpListenPort=8080, queueName=extract:queue, pluginsDir=/home/datashare/plugins, redisAddress=redis://redis:6379, queueType=redis, browserOpenLink=false, sessionTtlSeconds=43200}
2021-10-25 19:00:09,862 [Thread-0] INFO  ExtensionLoader - read directory /home/datashare/extensions and found jars (executable): []
2021-10-25 19:00:09,884 [Thread-0] INFO  HikariDataSource - HikariPool-1 - Starting...
2021-10-25 19:00:09,967 [Thread-0] INFO  HikariDataSource - HikariPool-1 - Start completed.
2021-10-25 19:00:10,028 [Thread-0] INFO  HikariDataSource - HikariPool-2 - Starting...
2021-10-25 19:00:10,032 [Thread-0] INFO  HikariDataSource - HikariPool-2 - Start completed.
2021-10-25 19:00:10,035 [Thread-0] INFO  HikariDataSource - HikariPool-3 - Starting...
2021-10-25 19:00:10,036 [Thread-0] INFO  HikariDataSource - HikariPool-3 - Start completed.
2021-10-25 19:00:10,050 [Thread-0] INFO  HikariDataSource - HikariPool-4 - Starting...
2021-10-25 19:00:10,052 [Thread-0] INFO  HikariDataSource - HikariPool-4 - Start completed.
2021-10-25 19:00:14,883 [Thread-0] INFO  JdbcExecutor - SELECT COUNT(*) FROM DATABASECHANGELOGLOCK
2021-10-25 19:00:14,889 [Thread-0] INFO  JdbcExecutor - SELECT COUNT(*) FROM DATABASECHANGELOGLOCK
2021-10-25 19:00:14,892 [Thread-0] INFO  JdbcExecutor - SELECT LOCKED FROM DATABASECHANGELOGLOCK WHERE ID=1
2021-10-25 19:00:14,939 [Thread-0] INFO  StandardLockService - Successfully acquired change log lock
2021-10-25 19:00:16,377 [Thread-0] INFO  JdbcExecutor - SELECT MD5SUM FROM DATABASECHANGELOG WHERE MD5SUM IS NOT NULL
2021-10-25 19:00:16,379 [Thread-0] INFO  JdbcExecutor - SELECT COUNT(*) FROM DATABASECHANGELOG
2021-10-25 19:00:16,379 [Thread-0] INFO  StandardChangeLogHistoryService - Reading from DATABASECHANGELOG
2021-10-25 19:00:16,384 [Thread-0] INFO  JdbcExecutor - SELECT * FROM DATABASECHANGELOG ORDER BY DATEEXECUTED ASC, ORDEREXECUTED ASC
2021-10-25 19:00:16,494 [Thread-0] INFO  StandardLockService - Successfully released change log lock
2021-10-25 19:00:16,494 [Thread-0] INFO  HikariDataSource - HikariPool-4 - Shutdown initiated...
2021-10-25 19:00:16,500 [Thread-0] INFO  HikariDataSource - HikariPool-4 - Shutdown completed.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/home/datashare/lib/datashare-dist-9.20.3-all.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2021-10-25 19:00:16,803 [Thread-0] INFO  Indexer - indexer defined with cfg{indexJoinField='join', docTypeField='type', shards=1, replicas=1}
2021-10-25 19:00:16,898 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch: System error
2021-10-25 19:00:17,248 [redisson-netty-2-5] INFO  MasterConnectionPool - 1 connections initialized for redis/172.18.0.3:6379
2021-10-25 19:00:17,248 [redisson-netty-2-6] INFO  MasterPubSubConnectionPool - 1 connections initialized for redis/172.18.0.3:6379
2021-10-25 19:00:17,319 [Thread-0] INFO  ExtensionLoader - read directory /home/datashare/extensions and found jars (executable): []
2021-10-25 19:00:17,901 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:17,917 [Thread-0] INFO  Fluent - Production mode
2021-10-25 19:00:17,956 [Thread-0] INFO  Fluent - Server started on port 8080
2021-10-25 19:00:18,904 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:19,907 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:20,910 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:21,913 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:22,918 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:23,921 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:24,924 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:25,926 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:26,954 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch: System error
2021-10-25 19:00:27,957 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:28,958 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:29,963 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:30,965 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:31,970 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:32,973 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:33,976 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:34,979 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:35,982 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:37,018 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch: System error
2021-10-25 19:00:38,027 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:39,030 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:40,033 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:41,034 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:42,037 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:43,040 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:44,043 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:45,046 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:46,048 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.io.IOException: elasticsearch
2021-10-25 19:00:47,051 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Connection refused
2021-10-25 19:00:48,053 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Connection refused
2021-10-25 19:00:49,055 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Connection refused
2021-10-25 19:00:50,059 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Connection refused
2021-10-25 19:00:51,062 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Connection refused
2021-10-25 19:00:52,064 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Connection refused
2021-10-25 19:00:58,070 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Timeout connecting to [elasticsearch/172.18.0.4:9200]
2021-10-25 19:01:04,076 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Timeout connecting to [elasticsearch/172.18.0.4:9200]
2021-10-25 19:01:10,081 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Timeout connecting to [elasticsearch/172.18.0.4:9200]
2021-10-25 19:01:16,087 [pool-4-thread-1] INFO  IndexWaiterFilter - Ping failed. Waiting for Elasticsearch to be up java.net.ConnectException: Timeout connecting to [elasticsearch/172.18.0.4:9200]

[mvanzalu]

Hello @cimar do you still have the issue on the latest version ?

[github-actions[bot]]

This issue is stale because it has been open for 40 days with no activity.

[github-actions[bot]]

This issue was closed because it has been inactive for 20 days since being marked as stale.