Installation of distro with docker compose fails

[catweis]

Describe the bug I tried to install the Distro-version from GitHub with docker compose. But it exists with some error code, I do not understand. For testing, I have used a clean and new linux system, twice.

To Reproduce

1. I have downloaded the Distro from GitHub
2. I started the installation with docker-compose -f dh_caMicroscope.yml up
3. There is the following error:

Creating network "distro_default" with the default driver Pulling mongo (mongo:4.2-bionic)... 4.2-bionic: Pulling from library/mongo 456d651ccb27: Pull complete 0d873b46166f: Pull complete b700537f311e: Pull complete 8ba0f53e4854: Pull complete 80b58c92c83f: Pull complete f4ed2f74d01b: Pull complete 0a2bd86063a1: Pull complete 9d3479b42a1a: Pull complete 59e7441cc47f: Pull complete Digest: sha256:b9633e6eb4ff0b96ab48a14e0b3792bb185a5daa3ea4c83b69e0bec2a8f5379a Status: Downloaded newer image for mongo:4.2-bionic Pulling back (camicroscope/caracal:latest)... latest: Pulling from camicroscope/caracal fa1690ae9228: Pull complete 2e799f213a71: Pull complete 83086ca62414: Pull complete 83fd155f6c91: Pull complete 71f84117b593: Pull complete 3b0d74d5e595: Pull complete 2663b58c5f3c: Pull complete cfd4e70f8767: Pull complete f1649ad9b855: Pull complete a6f29a811e51: Pull complete dbf6e08966fb: Pull complete Digest: sha256:d32d2ad6e51e3069a706c8112f1d03d2d7aa0431c4db1dd4a2a3ded59f303b5f Status: Downloaded newer image for camicroscope/caracal:latest Pulling iip (camicroscope/iipimage:latest)... latest: Pulling from camicroscope/iipimage d519e2592276: Pulling fs layer d22d2dfcfa9c: Pulling fs layer b3afe92c540b: Pulling fs layer f132eb32600c: Pulling fs layer 656eed345341: Pulling fs layer d997a5b00862: Pulling fs layer ce1a16d57185: Pulling fs layer e9dccd3e9305: Pulling fs layer aa944791aaff: Pulling fs layer cbda0eed89e4: Pulling fs layer f3ac8c6696a1: Pull complete 6d5c0609bf72: Pull complete 7f3f4e19709b: Pull complete ad5706679bdd: Pull complete 29cab59db9cd: Pull complete 1b62486b3399: Pull complete 0e1c109062c2: Pull complete be6e5f2ea5d3: Pull complete d1c79b973fac: Pull complete 7af66d892f09: Pull complete 914f9ce178a0: Pull complete 8f2e3273d3d0: Pull complete 35ee6dcf95b0: Pull complete ffe2fd0e000f: Pull complete 94b64151fccc: Pull complete 7efeff70c246: Pull complete d976816aa311: Pull complete 72fd4d475a96: Pull complete 51b3ffa03cab: Pull complete 1014c1f41d2c: Pull complete ba761b93afcc: Pull complete d9454aad60f1: Pull complete 2d9dbc6fd99e: Pull complete 8e9a76dca507: Pull complete 3c4055694229: Pull complete 2f2c1aefbd04: Pull complete ae8b2a79ed36: Pull complete 4fd8460f80d9: Pull complete e537ba43b279: Pull complete Digest: sha256:0d4bdc55e5fd77f992ab1d1bb44c570b9d587255a3ca955c050caad37dcc979c Status: Downloaded newer image for camicroscope/iipimage:latest Pulling loader (camicroscope/slideloader:latest)... latest: Pulling from camicroscope/slideloader 092586df9206: Pull complete ef599477fae0: Pull complete 4530c6472b5d: Pull complete d34d61487075: Pull complete 87fc2710b63f: Pull complete f142141aaad3: Pull complete 12eb19f5f2be: Pull complete d34466b69a2a: Pull complete fd8a0746ef83: Pull complete b9b92267804c: Pull complete 1bb86f6ffd2d: Pull complete 513a8c6698db: Pull complete 307b5b83655c: Pull complete ef7f501267da: Pull complete 63f5bed8872f: Pull complete 85e39ac47182: Pull complete bee7e3f8cb13: Pull complete 1739564bb1c5: Pull complete ce80f8bd8fa7: Pull complete 07501b932e7b: Pull complete 8f2046c0eea2: Pull complete 8c0e32917d16: Pull complete aa0a77d81757: Pull complete Digest: sha256:0b42150b5be5b4d070c6eeade5c58db98a4e677f1376c03704f39b4b72b98b4e Status: Downloaded newer image for camicroscope/slideloader:latest Creating ca-load ... done Creating ca-iip ... done Creating ca-mongo ... done Creating ca-back ... done Creating ca-idx ... done Attaching to ca-iip, ca-mongo, ca-load, ca-back, ca-idx ca-idx | /usr/local/bin/docker-entrypoint.sh: line 418: /config/run_idx.sh: No such file or directory ca-load | [2023-02-19 11:49:49 +0000] [7] [INFO] Starting gunicorn 20.0.4 ca-load | [2023-02-19 11:49:49 +0000] [7] [INFO] Listening at: http://0.0.0.0:4000 (7) ca-load | [2023-02-19 11:49:49 +0000] [7] [INFO] Using worker: sync ca-load | [2023-02-19 11:49:49 +0000] [10] [INFO] Booting worker with pid: 10 ca-load | [2023-02-19 11:49:49 +0000] [11] [INFO] Booting worker with pid: 11 ca-load | [2023-02-19 11:49:49 +0000] [12] [INFO] Booting worker with pid: 12 ca-load | [2023-02-19 11:49:49 +0000] [13] [INFO] Booting worker with pid: 13 ca-mongo | 2023-02-19T11:49:48.860+0000 I CONTROL [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none' ca-mongo | 2023-02-19T11:49:48.864+0000 W ASIO [main] No TransportLayer configured during NetworkInterface startup ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] MongoDB starting : pid=1 port=27017 dbpath=/data/db 64-bit host=1db79c011754 ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] db version v4.2.23 ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] git version: f4e6602d3a4c5b22e9d8bcf0722d0afd0ec01ea2 ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.1.1 11 Sep 2018 ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] allocator: tcmalloc ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] modules: none ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] build environment: ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] distmod: ubuntu1804 ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] distarch: x86_64 ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] target_arch: x86_64 ca-mongo | 2023-02-19T11:49:48.864+0000 I CONTROL [initandlisten] options: { net: { bindIp: "*" } } ca-mongo | 2023-02-19T11:49:48.865+0000 I STORAGE [initandlisten] ca-mongo | 2023-02-19T11:49:48.865+0000 I STORAGE [initandlisten] WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine ca-mongo | 2023-02-19T11:49:48.865+0000 I STORAGE [initandlisten] See http://dochub.mongodb.org/core/prodnotes-filesystem ca-mongo | 2023-02-19T11:49:48.866+0000 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=3468M,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], ca-mongo | 2023-02-19T11:49:49.896+0000 I STORAGE [initandlisten] WiredTiger message [1676807389:896650][1:0x7f147a9cbb00], txn-recover: Set global recovery timestamp: (0, 0) ca-mongo | 2023-02-19T11:49:49.941+0000 I RECOVERY [initandlisten] WiredTiger recoveryTimestamp. Ts: Timestamp(0, 0) ca-mongo | 2023-02-19T11:49:50.082+0000 I STORAGE [initandlisten] Timestamp monitor starting ca-mongo | 2023-02-19T11:49:50.189+0000 I CONTROL [initandlisten] ca-mongo | 2023-02-19T11:49:50.189+0000 I CONTROL [initandlisten] WARNING: Access control is not enabled for the database. ca-mongo | 2023-02-19T11:49:50.189+0000 I CONTROL [initandlisten] Read and write access to data and configuration is unrestricted. ca-mongo | 2023-02-19T11:49:50.189+0000 I CONTROL [initandlisten] ca-mongo | 2023-02-19T11:49:50.196+0000 I STORAGE [initandlisten] createCollection: admin.system.version with provided UUID: 06888b0d-15ff-4337-8a61-ee26f8b4dd0b and options: { uuid: UUID("06888b0d-15ff-4337-8a61-ee26f8b4dd0b") } ca-mongo | 2023-02-19T11:49:50.263+0000 I INDEX [initandlisten] index build: done building index id on ns admin.system.version ca-mongo | 2023-02-19T11:49:50.263+0000 I COMMAND [initandlisten] setting featureCompatibilityVersion to 4.2 ca-mongo | 2023-02-19T11:49:50.264+0000 I STORAGE [initandlisten] Flow Control is enabled on this deployment. ca-mongo | 2023-02-19T11:49:50.264+0000 I STORAGE [initandlisten] createCollection: local.startup_log with generated UUID: 48415917-8462-4661-8518-fa1699db7289 and options: { capped: true, size: 10485760 } ca-mongo | 2023-02-19T11:49:50.333+0000 I INDEX [initandlisten] index build: done building index id on ns local.startup_log ca-mongo | 2023-02-19T11:49:50.334+0000 I FTDC [initandlisten] Initializing full-time diagnostic data capture with directory '/data/db/diagnostic.data' ca-mongo | 2023-02-19T11:49:50.337+0000 I CONTROL [LogicalSessionCacheReap] Sessions collection is not set up; waiting until next sessions reap interval: config.system.sessions does not exist ca-mongo | 2023-02-19T11:49:50.337+0000 I NETWORK [listener] Listening on /tmp/mongodb-27017.sock ca-mongo | 2023-02-19T11:49:50.337+0000 I NETWORK [listener] Listening on 0.0.0.0 ca-mongo | 2023-02-19T11:49:50.337+0000 I NETWORK [listener] waiting for connections on port 27017 ca-mongo | 2023-02-19T11:49:50.337+0000 I STORAGE [LogicalSessionCacheRefresh] createCollection: config.system.sessions with provided UUID: 26709a37-d3d4-4eb4-9418-7175e9465f0a and options: { uuid: UUID("26709a37-d3d4-4eb4-9418-7175e9465f0a") } ca-mongo | 2023-02-19T11:49:50.510+0000 I INDEX [LogicalSessionCacheRefresh] index build: done building index id on ns config.system.sessions ca-mongo | 2023-02-19T11:49:50.608+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 ca-mongo | 2023-02-19T11:49:50.608+0000 I INDEX [LogicalSessionCacheRefresh] build may temporarily use up to 200 megabytes of RAM ca-mongo | 2023-02-19T11:49:50.608+0000 I INDEX [LogicalSessionCacheRefresh] index build: collection scan done. scanned 0 total records in 0 seconds ca-mongo | 2023-02-19T11:49:50.609+0000 I INDEX [LogicalSessionCacheRefresh] index build: inserted 0 keys from external sorter into index in 0 seconds ca-mongo | 2023-02-19T11:49:50.625+0000 I INDEX [LogicalSessionCacheRefresh] index build: done building index lsidTTLIndex on ns config.system.sessions ca-mongo | 2023-02-19T11:49:50.631+0000 I COMMAND [LogicalSessionCacheRefresh] command config.system.sessions command: createIndexes { createIndexes: "system.sessions", indexes: [ { key: { lastUse: 1 }, name: "lsidTTLIndex", expireAfterSeconds: 1800 } ], $db: "config" } numYields:0 reslen:114 locks:{ ParallelBatchWriterMode: { acquireCount: { r: 2 } }, ReplicationStateTransition: { acquireCount: { w: 3 } }, Global: { acquireCount: { r: 1, w: 2 } }, Database: { acquireCount: { r: 1, w: 2, W: 1 } }, Collection: { acquireCount: { r: 4, w: 1, R: 1, W: 2 } }, Mutex: { acquireCount: { r: 3 } } } flowControl:{ acquireCount: 1, timeAcquiringMicros: 1 } storage:{} protocol:op_msg 293ms ca-back | prikey does not exist ca-back | pubkey does not exist ca-idx exited with code 127 ca-back | 2023-02-19 11:49:51.333783: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA ca-back | 2023-02-19 11:49:51.355351: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2399995000 Hz ca-back | 2023-02-19 11:49:51.355829: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x5b9fe80 initialized for platform Host (this does not guarantee that XLA will be used). Devices: ca-back | 2023-02-19 11:49:51.355891: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version ca-back | handler named "updateMarksLabel" not found (rule 23 handler 0) ca-back exited with code 1

[catweis]

Meanwhile, I found the error. The Linux system I used was not "strong" enough for mongo. By testing a single mongo docker installation I found this.

[birm]

Can please you tell me what the commit hash and file are for the compose file you're using?

[catweis]

I am using the latest from 2 months ago. Its hash is 4f107ac.

[birm]

Have you resolved/explained this issue?

I'm not sure why ca-back has complained about the "updateMarksLabel" as 3.10.0 should have it -- https://github.com/camicroscope/Caracal/blob/v3.10.0/handlers/dataHandlers.js#L258

[birm]

Closing since we've had a release since, so I think this issue is stale. Please reopen if the problem persists.