overleaf / overleaf/toolkit

dependency failed to start: container mongo is unhealthy

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Description

I got this error with setup on Ubuntu 22.04, please help me fix:
mongo | {"t":{"$date":"2024-02-05T17:23:54.197+00:00"},"s":"I", "c":"STORAGE", "id":22315, "ctx":"initandlisten","msg":"Opening WiredTiger","attr":{"config":"create,cache_size=47708M,session_max=33000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),builtin_extension_config=(zstd=(compression_level=6)),file_manager=(close_idle_time=600,close_scan_interval=10,close_handle_minimum=250),statistics_log=(wait=0),verbose=[recovery_progress,checkpoint_progress,compact_progress],"}}
mongo | {"t":{"$date":"2024-02-05T17:23:55.004+00:00"},"s":"E", "c":"STORAGE", "id":22435, "ctx":"initandlisten","msg":"WiredTiger error","attr":{"error":1,"message":"[1707153835:4279][1:0x7f7a31cd7c80], file:WiredTiger.wt, connection: __posix_open_file, 815: /data/db/WiredTiger.wt: handle-open: open: Operation not permitted"}}
mongo | {"t":{"$date":"2024-02-05T17:23:55.011+00:00"},"s":"E", "c":"STORAGE", "id":22435, "ctx":"initandlisten","msg":"WiredTiger error","attr":{"error":1,"message":"[1707153835:11365][1:0x7f7a31cd7c80], file:WiredTiger.wt, connection: __posix_open_file, 815: /data/db/WiredTiger.wt: handle-open: open: Operation not permitted"}}
mongo | {"t":{"$date":"2024-02-05T17:23:55.017+00:00"},"s":"E", "c":"STORAGE", "id":22435, "ctx":"initandlisten","msg":"WiredTiger error","attr":{"error":1,"message":"[1707153835:17592][1:0x7f7a31cd7c80], file:WiredTiger.wt, connection: __posix_open_file, 815: /data/db/WiredTiger.wt: handle-open: open: Operation not permitted"}}
mongo | {"t":{"$date":"2024-02-05T17:23:55.018+00:00"},"s":"W", "c":"STORAGE", "id":22347, "ctx":"initandlisten","msg":"Failed to start up WiredTiger under any compatibility version. This may be due to an unsupported upgrade or downgrade."}
mongo | {"t":{"$date":"2024-02-05T17:23:55.018+00:00"},"s":"F", "c":"STORAGE", "id":28595, "ctx":"initandlisten","msg":"Terminating.","attr":{"reason":"1: Operation not permitted"}}
mongo | {"t":{"$date":"2024-02-05T17:23:55.018+00:00"},"s":"F", "c":"-", "id":23091, "ctx":"initandlisten","msg":"Fatal assertion","attr":{"msgid":28595,"file":"src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp","line":689}}
mongo | {"t":{"$date":"2024-02-05T17:23:55.018+00:00"},"s":"F", "c":"-", "id":23092, "ctx":"initandlisten","msg":"\n\n***aborting after fassert() failure\n\n"}

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing toolkit setup on Ubuntu 22.04 and inspect the Mongo container configuration and its /data/db volume permissions. Compare the container's expected data-directory access with the mounted path and check the reported WiredTiger error. Done when the Mongo dependency becomes healthy during setup without the Operation not permitted failure.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, mongodb, shell, ubuntu
Domain
databases, devops, infrastructure
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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