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[GH-ISSUE #1412] Backup Core Database failing #16555
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Reference: github-starred/komodo#16555
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Originally created by @version-au on GitHub (May 9, 2026).
Original GitHub issue: https://github.com/moghtech/komodo/issues/1412
Recently having issues with the Core Database Procedure failing. Was working fine prior to this. Tried doing some googling etc to see if it was a known issue but couldn't find anything that relates. Could it be something i have changed that is causing this?
The stdout is:
🦎 Komodo Database Backup Utility 🦎
Backup all database contents to gzip compressed files.
Source Address: mongo:27017
Source Username: admin
Source Db Name: komodo
Backups Folder: "/backups"
Max Backups: 14
2026-05-09T03:40:08.877267Z INFO Backing up to "/backups/2026-05-09_13-40-08"...
2026-05-09T03:40:08.885126Z INFO [ApiKey]: Backed up 1 items
2026-05-09T03:40:08.885215Z INFO [Builder]: Backed up 1 items
2026-05-09T03:40:08.886388Z INFO [Tag]: Backed up 7 items
2026-05-09T03:40:08.886448Z INFO [OnboardingKey]: Backed up 1 items
2026-05-09T03:40:08.891522Z INFO [Server]: Backed up 7 items
2026-05-09T03:40:08.893472Z INFO [GitProviderAccount]: Backed up 1 items
2026-05-09T03:40:08.893555Z INFO [Procedure]: Backed up 4 items
2026-05-09T03:40:08.895429Z INFO [Alerter]: Backed up 1 items
2026-05-09T03:40:08.898290Z INFO [User]: Backed up 1 items
2026-05-09T03:40:08.901818Z INFO [Stack]: Backed up 11 items
2026-05-09T03:40:08.909447Z INFO [Alert]: Backed up 107 items
2026-05-09T03:40:09.024632Z INFO [Update]: Backed up 777 items
2026-05-09T03:40:15.185313Z ERROR [Stats]: Failed to get next document: Kind: Command failed: Error code 43 (CursorNotFound): cursor id 1370667525201814467 not found, labels: {}, source: None, server response: Some(RawDocumentBuf { data: "6c000000016f6b000000000000000000026572726d73670028000000637572736f722069642031333730363637353235323031383134343637206e6f7420666f756e640010636f6465002b00000002636f64654e616d65000f000000437572736f724e6f74466f756e640000" })
@appleimperio commented on GitHub (May 12, 2026):
I'm having the same issue did you manage to solved this?
`🦎 Komodo Database Backup Utility 🦎
Backup all database contents to gzip compressed files.
Source Address: mongo:27017
Source Username: komodo_admin
Source Db Name: komodo
Backups Folder: "/backups"
Max Backups: 14
2026-05-12T00:23:41.890029Z INFO Backing up to "/backups/2026-05-12_00-23-41"...
2026-05-12T00:23:41.897838Z INFO [Tag]: Backed up 1 items
2026-05-12T00:23:41.898746Z INFO [ApiKey]: Backed up 1 items
2026-05-12T00:23:41.902407Z INFO [User]: Backed up 2 items
2026-05-12T00:23:41.902806Z INFO [Builder]: Backed up 1 items
2026-05-12T00:23:41.905817Z INFO [GitProviderAccount]: Backed up 1 items
2026-05-12T00:23:41.906753Z INFO [OnboardingKey]: Backed up 1 items
2026-05-12T00:23:41.906955Z INFO [Procedure]: Backed up 2 items
2026-05-12T00:23:41.908062Z INFO [Stack]: Backed up 9 items
2026-05-12T00:23:41.908438Z INFO [Alerter]: Backed up 1 items
2026-05-12T00:23:41.908955Z INFO [Server]: Backed up 5 items
2026-05-12T00:23:41.912030Z INFO [Alert]: Backed up 59 items
2026-05-12T00:23:42.075272Z INFO [Update]: Backed up 1127 items
2026-05-12T00:24:03.968545Z ERROR [Stats]: Failed to get next document: Kind: Command failed: Error code 43 (CursorNotFound): cursor id 9075404807240354672 not found, labels: {}, source: None, server response: Some(RawDocumentBuf { data: "6c000000016f6b000000000000000000026572726d73670028000000637572736f722069642039303735343034383037323430333534363732206e6f7420666f756e640010636f6465002b00000002636f64654e616d65000f000000437572736f724e6f74466f756e640000" })`
@version-au commented on GitHub (May 12, 2026):
One thing that fixed it for a little bit was clearing the database in the mongo container. It helped for awhile but eventually the same thing happened.
Suprisingly it has just started backing up again without issue. It failed for 7 days then for no reason completed the backup today without erroring.
@sammyke007 commented on GitHub (May 18, 2026):
This fixed it for me after updating to kernel v7!
https://github.com/moghtech/komodo/issues/1320
@version-au commented on GitHub (May 19, 2026):
Cheers. Can confirm that adding
GLIBC_TUNABLES: glibc.cpu.hwcaps=-SHSTK
to the environment settings for mongo container has fixed the issue. If it happens again i will update with more info.
Thanks