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I am trying to deploy cBioPortal on a VPS server using Docker.
SSD 200GB
3Core
memory 2GB
Debian12 amd64
Then I get the following message and it will not proceed permanently.
I confirmed that cBioPortal works fine on my local macOS and Ubuntu Desktop. So I tried to deploy cBioPortal on the VPS server as well. I can operate the terminal, but I am not a IT engineer and I don't know how web apps work or how to deploy them.
I would appreciate it if you could tell me where to start checking.
I understand that Discussions is not a support center, but is run by volunteers. Thank you very much.
[+] Running 47/13
✔ cbioportal-session-database 9 layers [⣿⣿⣿⣿⣿⣿⣿⣿⣿] 0B/0B Pulled 40.7s
✔ cbioportal-database 11 layers [⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿] 0B/0B Pulled 51.0s
✔ cbioportal 18 layers [⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿] 0B/0B Pulled 113.5s
✔ cbioportal-session 5 layers [⣿⣿⣿⣿⣿] 0B/0B Pulled 90.2s
[+] Running 7/6
✔ Network cbioportal-docker-compose_cbio-net Created 0.1s
✔ Volume "cbioportal-docker-compose_cbioportal_mysql_data" Created 0.0s
✔ Volume "cbioportal-docker-compose_cbioportal_mongo_data" Created 0.0s
✔ Container cbioportal-database-container Created 0.7s
✔ Container cbioportal-session-database-container Created 0.7s
✔ Container cbioportal-session-container Created 0.1s
✔ Container cbioportal-container Created 0.0s
Attaching to cbioportal-container, cbioportal-database-container, cbioportal-session-container, cbioportal-session-database-container
cbioportal-database-container | 2023-10-11 00:44:25+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.43-1.el7 started.
cbioportal-session-database-container | 2023-10-11T00:44:26.191+0000 I CONTROL [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none'
cbioportal-session-database-container | 2023-10-11T00:44:26.198+0000 W ASIO [main] No TransportLayer configured during NetworkInterface startup
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] MongoDB starting : pid=1 port=27017 dbpath=/data/db 64-bit host=ece0968527e0
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] db version v4.2.24
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] git version: 5e4ec1d24431fcdd28b579a024c5c801b8cde4e2
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.1.1 11 Sep 2018
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] allocator: tcmalloc
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] modules: none
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] build environment:
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] distmod: ubuntu1804
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] distarch: x86_64
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] target_arch: x86_64
cbioportal-session-database-container | 2023-10-11T00:44:26.201+0000 I CONTROL [initandlisten] options: { net: { bindIp: "*" } }
cbioportal-session-database-container | 2023-10-11T00:44:26.203+0000 I STORAGE [initandlisten]
cbioportal-session-database-container | 2023-10-11T00:44:26.203+0000 I STORAGE [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
cbioportal-session-database-container | 2023-10-11T00:44:26.203+0000 I STORAGE [initandlisten] ** See http://dochub.mongodb.org/core/prodnotes-filesystem
cbioportal-session-database-container | 2023-10-11T00:44:26.203+0000 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=471M,cache_overflow=(file_max=0M),session_max=33000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000,close_scan_interval=10,close_handle_minimum=250),statistics_log=(wait=0),verbose=[recovery_progress,checkpoint_progress],
cbioportal-database-container | 2023-10-11 00:44:26+00:00 [Note] [Entrypoint]: Switching to dedicated user 'mysql'
cbioportal-database-container | 2023-10-11 00:44:26+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.43-1.el7 started.
cbioportal-container | Using database config:
cbioportal-database-container | 2023-10-11 00:44:26+00:00 [Note] [Entrypoint]: Initializing database files
cbioportal-database-container | 2023-10-11T00:44:26.847499Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
cbioportal-session-database-container | 2023-10-11T00:44:27.444+0000 I STORAGE [initandlisten] WiredTiger message [1696985067:444498][1:0x7fe61b2fcb00], txn-recover: Set global recovery timestamp: (0, 0)
cbioportal-session-database-container | 2023-10-11T00:44:27.494+0000 I RECOVERY [initandlisten] WiredTiger recoveryTimestamp. Ts: Timestamp(0, 0)
cbioportal-session-database-container | 2023-10-11T00:44:27.645+0000 I STORAGE [initandlisten] Timestamp monitor starting
cbioportal-database-container | 2023-10-11T00:44:27.662661Z 0 [Warning] InnoDB: New log files created, LSN=45790
cbioportal-session-database-container | 2023-10-11T00:44:27.662+0000 I CONTROL [initandlisten]
cbioportal-session-database-container | 2023-10-11T00:44:27.662+0000 I CONTROL [initandlisten] ** WARNING: Access control is not enabled for the database.
cbioportal-session-database-container | 2023-10-11T00:44:27.662+0000 I CONTROL [initandlisten] ** Read and write access to data and configuration is unrestricted.
cbioportal-session-database-container | 2023-10-11T00:44:27.662+0000 I CONTROL [initandlisten]
cbioportal-session-database-container | 2023-10-11T00:44:27.663+0000 I CONTROL [initandlisten]
cbioportal-session-database-container | 2023-10-11T00:44:27.663+0000 I CONTROL [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/enabled is 'always'.
cbioportal-session-database-container | 2023-10-11T00:44:27.663+0000 I CONTROL [initandlisten] ** We suggest setting it to 'never'
cbioportal-session-database-container | 2023-10-11T00:44:27.663+0000 I CONTROL [initandlisten]
cbioportal-session-database-container | 2023-10-11T00:44:27.673+0000 I STORAGE [initandlisten] createCollection: admin.system.version with provided UUID: d38a4e1b-10a9-42e8-83a5-12aae11325f8 and options: { uuid: UUID("d38a4e1b-10a9-42e8-83a5-12aae11325f8") }
cbioportal-session-database-container | 2023-10-11T00:44:27.683+0000 I INDEX [initandlisten] index build: done building index _id_ on ns admin.system.version
cbioportal-session-database-container | 2023-10-11T00:44:27.684+0000 I COMMAND [initandlisten] setting featureCompatibilityVersion to 4.2
cbioportal-session-database-container | 2023-10-11T00:44:27.688+0000 I STORAGE [initandlisten] Flow Control is enabled on this deployment.
cbioportal-session-database-container | 2023-10-11T00:44:27.692+0000 I STORAGE [initandlisten] createCollection: local.startup_log with generated UUID: 5340bfe2-af6f-4272-87d0-e63b33a4c00e and options: { capped: true, size: 10485760 }
cbioportal-session-database-container | 2023-10-11T00:44:27.743+0000 I INDEX [initandlisten] index build: done building index _id_ on ns local.startup_log
cbioportal-session-database-container | 2023-10-11T00:44:27.744+0000 I FTDC [initandlisten] Initializing full-time diagnostic data capture with directory '/data/db/diagnostic.data'
cbioportal-session-database-container | 2023-10-11T00:44:27.754+0000 I NETWORK [listener] Listening on /tmp/mongodb-27017.sock
cbioportal-session-database-container | 2023-10-11T00:44:27.755+0000 I NETWORK [listener] Listening on 0.0.0.0
cbioportal-session-database-container | 2023-10-11T00:44:27.755+0000 I NETWORK [listener] waiting for connections on port 27017
cbioportal-session-database-container | 2023-10-11T00:44:27.765+0000 I CONTROL [LogicalSessionCacheReap] Sessions collection is not set up; waiting until next sessions reap interval: config.system.sessions does not exist
cbioportal-session-database-container | 2023-10-11T00:44:27.766+0000 I STORAGE [LogicalSessionCacheRefresh] createCollection: config.system.sessions with provided UUID: c21d4d93-f7ab-4dab-b2d3-dd500603b93e and options: { uuid: UUID("c21d4d93-f7ab-4dab-b2d3-dd500603b93e") }
cbioportal-database-container | 2023-10-11T00:44:27.789030Z 0 [Warning] InnoDB: Creating foreign key constraint system tables.
cbioportal-session-database-container | 2023-10-11T00:44:27.788+0000 I INDEX [LogicalSessionCacheRefresh] index build: done building index _id_ on ns config.system.sessions
cbioportal-session-database-container | 2023-10-11T00:44:27.802+0000 I INDEX [LogicalSessionCacheRefresh] index build: starting on config.system.sessions properties: { v: 2, key: { lastUse: 1 }, name: "lsidTTLIndex", ns: "config.system.sessions", expireAfterSeconds: 1800 } using method: Hybrid
cbioportal-session-database-container | 2023-10-11T00:44:27.802+0000 I INDEX [LogicalSessionCacheRefresh] build may temporarily use up to 200 megabytes of RAM
cbioportal-session-database-container | 2023-10-11T00:44:27.802+0000 I INDEX [LogicalSessionCacheRefresh] index build: collection scan done. scanned 0 total records in 0 seconds
cbioportal-session-database-container | 2023-10-11T00:44:27.803+0000 I INDEX [LogicalSessionCacheRefresh] index build: inserted 0 keys from external sorter into index in 0 seconds
cbioportal-session-database-container | 2023-10-11T00:44:27.805+0000 I INDEX [LogicalSessionCacheRefresh] index build: done building index lsidTTLIndex on ns config.system.sessions
cbioportal-database-container | 2023-10-11T00:44:27.861132Z 0 [Warning] No existing UUID has been found, so we assume that this is the first time that this server has been started. Generating a new UUID: 551849e3-67cf-11ee-85c0-0242ac120003.
cbioportal-database-container | 2023-10-11T00:44:27.863223Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
cbioportal-database-container | 2023-10-11T00:44:27.998633Z 0 [Warning] A deprecated TLS version TLSv1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container | 2023-10-11T00:44:27.998658Z 0 [Warning] A deprecated TLS version TLSv1.1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container | 2023-10-11T00:44:28.000009Z 0 [Warning] CA certificate ca.pem is self signed.
cbioportal-database-container | 2023-10-11T00:44:28.080000Z 1 [Warning] root@localhost is created with an empty password ! Please consider switching off the --initialize-insecure option.
cbioportal-session-container |
cbioportal-session-container | . ____ _ __ _ _
cbioportal-session-container | /\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \
cbioportal-session-container | ( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
cbioportal-session-container | \\/ ___)| |_)| | | | | || (_| | ) ) ) )
cbioportal-session-container | ' |____| .__|_| |_|_| |_\__, | / / / /
cbioportal-session-container | =========|_|==============|___/=/_/_/_/
cbioportal-session-container | :: Spring Boot :: (v2.7.6)
cbioportal-session-container |
cbioportal-session-container | 2023-10-11 00:44:28.492 INFO 7 --- [ main] o.c.session_service.SessionService : Starting SessionService v0.5.0 using Java 11.0.18 on 2d902b35dece with PID 7 (/app.war started by root in /)
cbioportal-session-container | 2023-10-11 00:44:28.500 INFO 7 --- [ main] o.c.session_service.SessionService : No active profile set, falling back to 1 default profile: "default"
cbioportal-session-container | 2023-10-11 00:44:30.088 INFO 7 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data MongoDB repositories in DEFAULT mode.
cbioportal-session-container | 2023-10-11 00:44:30.165 INFO 7 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 70 ms. Found 1 MongoDB repository interfaces.
cbioportal-database-container | 2023-10-11 00:44:30+00:00 [Note] [Entrypoint]: Database files initialized
cbioportal-database-container | 2023-10-11 00:44:30+00:00 [Note] [Entrypoint]: Starting temporary server
cbioportal-database-container | 2023-10-11 00:44:30+00:00 [Note] [Entrypoint]: Waiting for server startup
cbioportal-session-container | 2023-10-11 00:44:30.965 INFO 7 --- [ main] o.s.b.w.embedded.tomcat.TomcatWebServer : Tomcat initialized with port(s): 5000 (http)
cbioportal-session-container | 2023-10-11 00:44:30.983 INFO 7 --- [ main] o.apache.catalina.core.StandardService : Starting service [Tomcat]
cbioportal-session-container | 2023-10-11 00:44:30.984 INFO 7 --- [ main] org.apache.catalina.core.StandardEngine : Starting Servlet engine: [Apache Tomcat/9.0.69]
cbioportal-database-container | 2023-10-11T00:44:31.187466Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
cbioportal-database-container | 2023-10-11T00:44:31.193227Z 0 [Note] mysqld (mysqld 5.7.43) starting as process 127 ...
cbioportal-database-container | 2023-10-11T00:44:31.201872Z 0 [Note] InnoDB: PUNCH HOLE support available
cbioportal-database-container | 2023-10-11T00:44:31.201924Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
cbioportal-database-container | 2023-10-11T00:44:31.201929Z 0 [Note] InnoDB: Uses event mutexes
cbioportal-database-container | 2023-10-11T00:44:31.201933Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
cbioportal-database-container | 2023-10-11T00:44:31.201946Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.13
cbioportal-database-container | 2023-10-11T00:44:31.201951Z 0 [Note] InnoDB: Using Linux native AIO
cbioportal-database-container | 2023-10-11T00:44:31.202996Z 0 [Note] InnoDB: Number of pools: 1
cbioportal-database-container | 2023-10-11T00:44:31.203552Z 0 [Note] InnoDB: Using CPU crc32 instructions
cbioportal-session-container | 2023-10-11 00:44:31.204 INFO 7 --- [ main] o.a.c.c.C.[Tomcat].[localhost].[/] : Initializing Spring embedded WebApplicationContext
cbioportal-session-container | 2023-10-11 00:44:31.204 INFO 7 --- [ main] w.s.c.ServletWebServerApplicationContext : Root WebApplicationContext: initialization completed in 2585 ms
cbioportal-database-container | 2023-10-11T00:44:31.218976Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
cbioportal-database-container | 2023-10-11T00:44:31.239923Z 0 [Note] InnoDB: Completed initialization of buffer pool
cbioportal-database-container | 2023-10-11T00:44:31.246036Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
cbioportal-database-container | 2023-10-11T00:44:31.263341Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
cbioportal-database-container | 2023-10-11T00:44:31.280367Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
cbioportal-database-container | 2023-10-11T00:44:31.280445Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
cbioportal-database-container | 2023-10-11T00:44:31.318198Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
cbioportal-database-container | 2023-10-11T00:44:31.319877Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
cbioportal-database-container | 2023-10-11T00:44:31.319910Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
cbioportal-database-container | 2023-10-11T00:44:31.320912Z 0 [Note] InnoDB: 5.7.43 started; log sequence number 2766921
cbioportal-database-container | 2023-10-11T00:44:31.321874Z 0 [Note] Plugin 'FEDERATED' is disabled.
cbioportal-database-container | 2023-10-11T00:44:31.322310Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
cbioportal-database-container | 2023-10-11T00:44:31.331229Z 0 [Note] InnoDB: Buffer pool(s) load completed at 231011 0:44:31
cbioportal-database-container | 2023-10-11T00:44:31.338096Z 0 [Note] Found ca.pem, server-cert.pem and server-key.pem in data directory. Trying to enable SSL support using them.
cbioportal-database-container | 2023-10-11T00:44:31.338130Z 0 [Note] Skipping generation of SSL certificates as certificate files are present in data directory.
cbioportal-database-container | 2023-10-11T00:44:31.338139Z 0 [Warning] A deprecated TLS version TLSv1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container | 2023-10-11T00:44:31.338143Z 0 [Warning] A deprecated TLS version TLSv1.1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container | 2023-10-11T00:44:31.339400Z 0 [Warning] CA certificate ca.pem is self signed.
cbioportal-database-container | 2023-10-11T00:44:31.339633Z 0 [Note] Skipping generation of RSA key pair as key files are present in data directory.
cbioportal-database-container | 2023-10-11T00:44:31.342721Z 0 [Warning] Insecure configuration for --pid-file: Location '/var/run/mysqld' in the path is accessible to all OS users. Consider choosing a different directory.
cbioportal-database-container | 2023-10-11T00:44:31.357682Z 0 [Note] Event Scheduler: Loaded 0 events
cbioportal-database-container | 2023-10-11T00:44:31.358195Z 0 [Note] mysqld: ready for connections.
cbioportal-database-container | Version: '5.7.43' socket: '/var/run/mysqld/mysqld.sock' port: 0 MySQL Community Server (GPL)
cbioportal-session-container | 2023-10-11 00:44:31.684 INFO 7 --- [ main] org.mongodb.driver.client : MongoClient with metadata {"driver": {"name": "mongo-java-driver|sync|spring-boot", "version": "4.6.1"}, "os": {"type": "Linux", "name": "Linux", "architecture": "amd64", "version": "6.1.0-13-amd64"}, "platform": "Java/Eclipse Adoptium/11.0.18+10"} created with settings MongoClientSettings{readPreference=primary, writeConcern=WriteConcern{w=null, wTimeout=null ms, journal=null}, retryWrites=true, retryReads=true, readConcern=ReadConcern{level=null}, credential=null, streamFactoryFactory=null, commandListeners=[], codecRegistry=ProvidersCodecRegistry{codecProviders=[ValueCodecProvider{}, BsonValueCodecProvider{}, DBRefCodecProvider{}, DBObjectCodecProvider{}, DocumentCodecProvider{}, IterableCodecProvider{}, MapCodecProvider{}, GeoJsonCodecProvider{}, GridFSFileCodecProvider{}, Jsr310CodecProvider{}, JsonObjectCodecProvider{}, BsonCodecProvider{}, EnumCodecProvider{}, com.mongodb.Jep395RecordCodecProvider@5c42d2b7]}, clusterSettings={hosts=[cbioportal-session-database:27017], srvServiceName=mongodb, mode=SINGLE, requiredClusterType=UNKNOWN, requiredReplicaSetName='null', serverSelector='null', clusterListeners='[]', serverSelectionTimeout='30000 ms', localThreshold='30000 ms'}, socketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=0, receiveBufferSize=0, sendBufferSize=0}, heartbeatSocketSettings=SocketSettings{connectTimeoutMS=10000, readTimeoutMS=10000, receiveBufferSize=0, sendBufferSize=0}, connectionPoolSettings=ConnectionPoolSettings{maxSize=100, minSize=0, maxWaitTimeMS=120000, maxConnectionLifeTimeMS=0, maxConnectionIdleTimeMS=0, maintenanceInitialDelayMS=0, maintenanceFrequencyMS=60000, connectionPoolListeners=[], maxConnecting=2}, serverSettings=ServerSettings{heartbeatFrequencyMS=10000, minHeartbeatFrequencyMS=500, serverListeners='[]', serverMonitorListeners='[]'}, sslSettings=SslSettings{enabled=false, invalidHostNameAllowed=false, context=null}, applicationName='null', compressorList=[], uuidRepresentation=JAVA_LEGACY, serverApi=null, autoEncryptionSettings=null, contextProvider=null}
cbioportal-session-database-container | 2023-10-11T00:44:31.691+0000 I NETWORK [listener] connection accepted from 172.18.0.4:35938 #1 (1 connection now open)
cbioportal-session-database-container | 2023-10-11T00:44:31.691+0000 I NETWORK [listener] connection accepted from 172.18.0.4:35940 #2 (2 connections now open)
cbioportal-session-database-container | 2023-10-11T00:44:31.703+0000 I NETWORK [conn2] received client metadata from 172.18.0.4:35940 conn2: { driver: { name: "mongo-java-driver|sync|spring-boot", version: "4.6.1" }, os: { type: "Linux", name: "Linux", architecture: "amd64", version: "6.1.0-13-amd64" }, platform: "Java/Eclipse Adoptium/11.0.18+10" }
cbioportal-session-database-container | 2023-10-11T00:44:31.703+0000 I NETWORK [conn1] received client metadata from 172.18.0.4:35938 conn1: { driver: { name: "mongo-java-driver|sync|spring-boot", version: "4.6.1" }, os: { type: "Linux", name: "Linux", architecture: "amd64", version: "6.1.0-13-amd64" }, platform: "Java/Eclipse Adoptium/11.0.18+10" }
cbioportal-session-container | 2023-10-11 00:44:31.721 INFO 7 --- [-database:27017] org.mongodb.driver.connection : Opened connection [connectionId{localValue:2, serverValue:2}] to cbioportal-session-database:27017
cbioportal-session-container | 2023-10-11 00:44:31.721 INFO 7 --- [-database:27017] org.mongodb.driver.connection : Opened connection [connectionId{localValue:1, serverValue:1}] to cbioportal-session-database:27017
cbioportal-session-container | 2023-10-11 00:44:31.723 INFO 7 --- [-database:27017] org.mongodb.driver.cluster : Monitor thread successfully connected to server with description ServerDescription{address=cbioportal-session-database:27017, type=STANDALONE, state=CONNECTED, ok=true, minWireVersion=0, maxWireVersion=8, maxDocumentSize=16777216, logicalSessionTimeoutMinutes=30, roundTripTimeNanos=27959730}
cbioportal-database-container | 2023-10-11 00:44:31+00:00 [Note] [Entrypoint]: Temporary server started.
cbioportal-database-container | '/var/lib/mysql/mysql.sock' -> '/var/run/mysqld/mysqld.sock'
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-database-container | 2023-10-11T00:44:32.005944Z 3 [Note] InnoDB: Stopping purge
cbioportal-database-container | 2023-10-11T00:44:32.016635Z 3 [Note] InnoDB: Resuming purge
cbioportal-database-container | 2023-10-11T00:44:32.018384Z 3 [Note] InnoDB: Stopping purge
cbioportal-database-container | 2023-10-11T00:44:32.021742Z 3 [Note] InnoDB: Resuming purge
cbioportal-database-container | 2023-10-11T00:44:32.023203Z 3 [Note] InnoDB: Stopping purge
cbioportal-database-container | 2023-10-11T00:44:32.026728Z 3 [Note] InnoDB: Resuming purge
cbioportal-database-container | 2023-10-11T00:44:32.028340Z 3 [Note] InnoDB: Stopping purge
cbioportal-database-container | 2023-10-11T00:44:32.031598Z 3 [Note] InnoDB: Resuming purge
cbioportal-database-container | Warning: Unable to load '/usr/share/zoneinfo/iso3166.tab' as time zone. Skipping it.
cbioportal-database-container | Warning: Unable to load '/usr/share/zoneinfo/leapseconds' as time zone. Skipping it.
cbioportal-session-container | 2023-10-11 00:44:32.824 WARN 7 --- [ main] .s.s.UserDetailsServiceAutoConfiguration :
cbioportal-session-container |
cbioportal-session-container | Using generated security password: 5c785644-625b-4c2c-81a8-ecf64f3d5558
cbioportal-session-container |
cbioportal-session-container | This generated password is for development use only. Your security configuration must be updated before running your application in production.
cbioportal-session-container |
cbioportal-session-container | 2023-10-11 00:44:33.032 INFO 7 --- [ main] o.s.s.web.DefaultSecurityFilterChain : Will secure any request with [org.springframework.security.web.session.DisableEncodeUrlFilter@54e81b21, org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter@38d5b107, org.springframework.security.web.context.SecurityContextPersistenceFilter@117632cf, org.springframework.security.web.header.HeaderWriterFilter@772485dd, org.springframework.security.web.authentication.logout.LogoutFilter@2e27d72f, org.springframework.security.web.savedrequest.RequestCacheAwareFilter@d71adc2, org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter@1c65121, org.springframework.security.web.authentication.AnonymousAuthenticationFilter@6650813a, org.springframework.security.web.session.SessionManagementFilter@51bde877, org.springframework.security.web.access.ExceptionTranslationFilter@49bd54f7, org.springframework.security.web.access.intercept.FilterSecurityInterceptor@315ba14a]
cbioportal-session-container | 2023-10-11 00:44:33.078 INFO 7 --- [ main] pertySourcedRequestMappingHandlerMapping : Mapped URL path [/v2/api-docs] onto method [springfox.documentation.swagger2.web.Swagger2Controller#getDocumentation(String, HttpServletRequest)]
cbioportal-session-container | 2023-10-11 00:44:33.576 INFO 7 --- [ main] o.s.b.w.embedded.tomcat.TomcatWebServer : Tomcat started on port(s): 5000 (http) with context path ''
cbioportal-session-container | 2023-10-11 00:44:33.578 INFO 7 --- [ main] d.s.w.p.DocumentationPluginsBootstrapper : Context refreshed
cbioportal-session-container | 2023-10-11 00:44:33.614 INFO 7 --- [ main] d.s.w.p.DocumentationPluginsBootstrapper : Found 1 custom documentation plugin(s)
cbioportal-session-container | 2023-10-11 00:44:33.677 INFO 7 --- [ main] s.d.s.w.s.ApiListingReferenceScanner : Scanning for api listing references
cbioportal-session-container | 2023-10-11 00:44:33.959 INFO 7 --- [ main] o.c.session_service.SessionService : Started SessionService in 6.377 seconds (JVM running for 7.769)
cbioportal-database-container | Warning: Unable to load '/usr/share/zoneinfo/tzdata.zi' as time zone. Skipping it.
cbioportal-database-container | Warning: Unable to load '/usr/share/zoneinfo/zone.tab' as time zone. Skipping it.
cbioportal-database-container | Warning: Unable to load '/usr/share/zoneinfo/zone1970.tab' as time zone. Skipping it.
cbioportal-database-container | 2023-10-11 00:44:34+00:00 [Note] [Entrypoint]: Creating database cbioportal
cbioportal-database-container | 2023-10-11 00:44:34+00:00 [Note] [Entrypoint]: Creating user cbio_user
cbioportal-database-container | 2023-10-11 00:44:34+00:00 [Note] [Entrypoint]: Giving user cbio_user access to schema cbioportal
cbioportal-database-container |
cbioportal-database-container | 2023-10-11 00:44:34+00:00 [Note] [Entrypoint]: /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-initdb.d/cgds.sql
cbioportal-database-container |
cbioportal-database-container |
cbioportal-database-container | 2023-10-11 00:44:35+00:00 [Note] [Entrypoint]: /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-initdb.d/seed.sql.gz
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
After a while, the following message may appear.
cbioportal-database-container |
cbioportal-database-container |
cbioportal-database-container | 2023-10-11 00:51:27+00:00 [Note] [Entrypoint]: Stopping temporary server
cbioportal-database-container | 2023-10-11T00:51:27.836123Z 0 [Note] Giving 0 client threads a chance to die gracefully
cbioportal-database-container | 2023-10-11T00:51:27.836282Z 0 [Note] Shutting down slave threads
cbioportal-database-container | 2023-10-11T00:51:27.836345Z 0 [Note] Forcefully disconnecting 0 remaining clients
cbioportal-database-container | 2023-10-11T00:51:27.836415Z 0 [Note] Event Scheduler: Purging the queue. 0 events
cbioportal-database-container | 2023-10-11T00:51:27.836987Z 0 [Note] Binlog end
cbioportal-database-container | 2023-10-11T00:51:27.840173Z 0 [Note] Shutting down plugin 'ngram'
cbioportal-database-container | 2023-10-11T00:51:27.840787Z 0 [Note] Shutting down plugin 'partition'
cbioportal-database-container | 2023-10-11T00:51:27.840805Z 0 [Note] Shutting down plugin 'BLACKHOLE'
cbioportal-database-container | 2023-10-11T00:51:27.840814Z 0 [Note] Shutting down plugin 'ARCHIVE'
cbioportal-database-container | 2023-10-11T00:51:27.840817Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
cbioportal-database-container | 2023-10-11T00:51:27.841158Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
cbioportal-database-container | 2023-10-11T00:51:27.841189Z 0 [Note] Shutting down plugin 'MyISAM'
cbioportal-database-container | 2023-10-11T00:51:27.841349Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
cbioportal-database-container | 2023-10-11T00:51:27.841558Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
cbioportal-database-container | 2023-10-11T00:51:27.841572Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
cbioportal-database-container | 2023-10-11T00:51:27.841575Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
cbioportal-database-container | 2023-10-11T00:51:27.841578Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
cbioportal-database-container | 2023-10-11T00:51:27.841580Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
cbioportal-database-container | 2023-10-11T00:51:27.841583Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
cbioportal-database-container | 2023-10-11T00:51:27.841585Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
cbioportal-database-container | 2023-10-11T00:51:27.841587Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
cbioportal-database-container | 2023-10-11T00:51:27.841590Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
cbioportal-database-container | 2023-10-11T00:51:27.841592Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
cbioportal-database-container | 2023-10-11T00:51:27.841594Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
cbioportal-database-container | 2023-10-11T00:51:27.841597Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
cbioportal-database-container | 2023-10-11T00:51:27.841599Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
cbioportal-database-container | 2023-10-11T00:51:27.841601Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
cbioportal-database-container | 2023-10-11T00:51:27.841604Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
cbioportal-database-container | 2023-10-11T00:51:27.841606Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
cbioportal-database-container | 2023-10-11T00:51:27.841608Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
cbioportal-database-container | 2023-10-11T00:51:27.841611Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
cbioportal-database-container | 2023-10-11T00:51:27.841619Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
cbioportal-database-container | 2023-10-11T00:51:27.841621Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
cbioportal-database-container | 2023-10-11T00:51:27.841624Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
cbioportal-database-container | 2023-10-11T00:51:27.841626Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
cbioportal-database-container | 2023-10-11T00:51:27.841628Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
cbioportal-database-container | 2023-10-11T00:51:27.841631Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
cbioportal-database-container | 2023-10-11T00:51:27.841633Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
cbioportal-database-container | 2023-10-11T00:51:27.841635Z 0 [Note] Shutting down plugin 'INNODB_CMP'
cbioportal-database-container | 2023-10-11T00:51:27.841638Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
cbioportal-database-container | 2023-10-11T00:51:27.841640Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
cbioportal-database-container | 2023-10-11T00:51:27.841644Z 0 [Note] Shutting down plugin 'INNODB_TRX'
cbioportal-database-container | 2023-10-11T00:51:27.841646Z 0 [Note] Shutting down plugin 'InnoDB'
cbioportal-database-container | 2023-10-11T00:51:27.842360Z 0 [Note] InnoDB: FTS optimize thread exiting.
cbioportal-database-container | 2023-10-11T00:51:27.843017Z 0 [Note] InnoDB: Starting shutdown...
cbioportal-database-container | 2023-10-11T00:51:27.943442Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
cbioportal-database-container | 2023-10-11T00:51:27.945496Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 231011 0:51:27
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-database-container | 2023-10-11T00:51:30.576784Z 0 [Note] InnoDB: Shutdown completed; log sequence number 760142832
cbioportal-database-container | 2023-10-11T00:51:30.578019Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
cbioportal-database-container | 2023-10-11T00:51:30.578318Z 0 [Note] Shutting down plugin 'MEMORY'
cbioportal-database-container | 2023-10-11T00:51:30.578344Z 0 [Note] Shutting down plugin 'CSV'
cbioportal-database-container | 2023-10-11T00:51:30.578351Z 0 [Note] Shutting down plugin 'sha256_password'
cbioportal-database-container | 2023-10-11T00:51:30.578354Z 0 [Note] Shutting down plugin 'mysql_native_password'
cbioportal-database-container | 2023-10-11T00:51:30.579007Z 0 [Note] Shutting down plugin 'binlog'
cbioportal-database-container | 2023-10-11T00:51:30.581329Z 0 [Note] mysqld: Shutdown complete
cbioportal-database-container |
cbioportal-database-container | 2023-10-11 00:51:30+00:00 [Note] [Entrypoint]: Temporary server stopped
cbioportal-database-container |
cbioportal-database-container | 2023-10-11 00:51:30+00:00 [Note] [Entrypoint]: MySQL init process done. Ready for start up.
cbioportal-database-container |
cbioportal-database-container | 2023-10-11T00:51:31.146605Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
cbioportal-database-container | 2023-10-11T00:51:31.149536Z 0 [Note] mysqld (mysqld 5.7.43) starting as process 1 ...
cbioportal-database-container | 2023-10-11T00:51:31.156142Z 0 [Note] InnoDB: PUNCH HOLE support available
cbioportal-database-container | 2023-10-11T00:51:31.156186Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
cbioportal-database-container | 2023-10-11T00:51:31.156191Z 0 [Note] InnoDB: Uses event mutexes
cbioportal-database-container | 2023-10-11T00:51:31.156194Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
cbioportal-database-container | 2023-10-11T00:51:31.156198Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.13
cbioportal-database-container | 2023-10-11T00:51:31.156202Z 0 [Note] InnoDB: Using Linux native AIO
cbioportal-database-container | 2023-10-11T00:51:31.157263Z 0 [Note] InnoDB: Number of pools: 1
cbioportal-database-container | 2023-10-11T00:51:31.157728Z 0 [Note] InnoDB: Using CPU crc32 instructions
cbioportal-database-container | 2023-10-11T00:51:31.161747Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
cbioportal-database-container | 2023-10-11T00:51:31.182503Z 0 [Note] InnoDB: Completed initialization of buffer pool
cbioportal-database-container | 2023-10-11T00:51:31.189594Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
cbioportal-database-container | 2023-10-11T00:51:31.205889Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
cbioportal-database-container | 2023-10-11T00:51:31.222619Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
cbioportal-database-container | 2023-10-11T00:51:31.222687Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
cbioportal-database-container | 2023-10-11T00:51:31.258014Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
cbioportal-database-container | 2023-10-11T00:51:31.260283Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
cbioportal-database-container | 2023-10-11T00:51:31.260304Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
cbioportal-database-container | 2023-10-11T00:51:31.262586Z 0 [Note] InnoDB: 5.7.43 started; log sequence number 760142832
cbioportal-database-container | 2023-10-11T00:51:31.263122Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
cbioportal-database-container | 2023-10-11T00:51:31.263490Z 0 [Note] Plugin 'FEDERATED' is disabled.
cbioportal-database-container | 2023-10-11T00:51:31.281918Z 0 [Note] Found ca.pem, server-cert.pem and server-key.pem in data directory. Trying to enable SSL support using them.
cbioportal-database-container | 2023-10-11T00:51:31.281945Z 0 [Note] Skipping generation of SSL certificates as certificate files are present in data directory.
cbioportal-database-container | 2023-10-11T00:51:31.281951Z 0 [Warning] A deprecated TLS version TLSv1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container | 2023-10-11T00:51:31.281954Z 0 [Warning] A deprecated TLS version TLSv1.1 is enabled. Please use TLSv1.2 or higher.
cbioportal-database-container | 2023-10-11T00:51:31.283383Z 0 [Warning] CA certificate ca.pem is self signed.
cbioportal-database-container | 2023-10-11T00:51:31.283569Z 0 [Note] Skipping generation of RSA key pair as key files are present in data directory.
cbioportal-database-container | 2023-10-11T00:51:31.284286Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
cbioportal-database-container | 2023-10-11T00:51:31.284598Z 0 [Note] IPv6 is available.
cbioportal-database-container | 2023-10-11T00:51:31.285326Z 0 [Note] - '::' resolves to '::';
cbioportal-database-container | 2023-10-11T00:51:31.285399Z 0 [Note] Server socket created on IP: '::'.
cbioportal-database-container | 2023-10-11T00:51:31.288137Z 0 [Warning] Insecure configuration for --pid-file: Location '/var/run/mysqld' in the path is accessible to all OS users. Consider choosing a different directory.
cbioportal-database-container | 2023-10-11T00:51:31.325092Z 0 [Note] Event Scheduler: Loaded 0 events
cbioportal-database-container | 2023-10-11T00:51:31.326625Z 0 [Note] mysqld: ready for connections.
cbioportal-database-container | Version: '5.7.43' socket: '/var/run/mysqld/mysqld.sock' port: 3306 MySQL Community Server (GPL)
cbioportal-database-container | 2023-10-11T00:51:32.285466Z 0 [Note] InnoDB: Buffer pool(s) load completed at 231011 0:51:32
And finally, the following message keeps appearing
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
cbioportal-container | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
cbioportal-container | mysqladmin ping -s -h -P3306 -u -p
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Hi cBioPortal developers.
I am trying to deploy cBioPortal on a VPS server using Docker.
Then I get the following message and it will not proceed permanently.
I confirmed that cBioPortal works fine on my local macOS and Ubuntu Desktop. So I tried to deploy cBioPortal on the VPS server as well. I can operate the terminal, but I am not a IT engineer and I don't know how web apps work or how to deploy them.
I would appreciate it if you could tell me where to start checking.
I understand that Discussions is not a support center, but is run by volunteers. Thank you very much.
After a while, the following message may appear.
And finally, the following message keeps appearing
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