DB Crashed

[Chen, John (IT)]

Hi Genome Members,

Recently our server that is hosting running MariaDB crashed and now we are seeing issues.  Could someone provide feedback on the following error and solution to fix?

2024-10-11 10:04:24 332 [ERROR] mariadbd: Table './hgcentral/namedSessionDb' is marked as crashed and should be repaired

2024-10-11 10:04:24 332 [Warning] Checking table:   './hgcentral/namedSessionDb'

2024-10-11 10:04:24 331 [Warning] Aborted connection 331 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2024-10-11 10:04:24 337 [Warning] Aborted connection 337 to db: 'hg38' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 10:04:24 330 [Warning] Aborted connection 330 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2024-10-11 10:04:24 332 [Warning] Aborted connection 332 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error writing communication packets)

2024-10-11 10:30:56 568 [Warning] Aborted connection 568 to db: 'mm10' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 10:30:56 566 [Warning] Aborted connection 566 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2024-10-11 10:30:56 565 [Warning] Aborted connection 565 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

Rebooted the server to see if that clears up the issue..but still getting the following message.

2024-10-11 11:11:37 13 [Warning] Aborted connection 13 to db: 'hg19' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:11:37 6 [Warning] Aborted connection 6 to db: 'hgFixed' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:11:37 4 [Warning] Aborted connection 4 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:11:37 5 [Warning] Aborted connection 5 to db: 'hg19' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:11:37 12 [Warning] Aborted connection 12 to db: 'hg19' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:11:37 3 [Warning] Aborted connection 3 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:17:08 76 [Warning] Aborted connection 76 to db: 'hg38' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:17:08 65 [Warning] Aborted connection 65 to db: 'hg38' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:17:08 75 [Warning] Aborted connection 75 to db: 'hg38' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:17:08 63 [Warning] Aborted connection 63 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:17:08 66 [Warning] Aborted connection 66 to db: 'hg38' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:17:08 64 [Warning] Aborted connection 64 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:17:08 67 [Warning] Aborted connection 67 to db: 'customTrash' user: 'ctdbuser' host: 'localhost' (Got an error reading communication packets)

2024-10-11 11:17:08 62 [Warning] Aborted connection 62 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

Thanks

~ John Chen

• 
  

[Luis Nassar]

Hi, John.

It looks like you need to run the repair command on the crashed table(s). For example, in your message, you need to repair namedSessionDb. You will want to start a MySQL prompt on your mirror and run:

repair table 'namedSessionDb';

Let us know if that solves the issue or if you have any additional questions we can help with.

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Lou Nassar
UCSC Genomics Institute

[Chen, John (IT)]

Hi Nassar,

I am seeing this issue again, would you know how to fix this?

025-01-09 13:12:12 33 [Warning] Aborted connection 33 to db: 'mm10' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:12 32 [Warning] Aborted connection 32 to db: 'mm10' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:12 31 [Warning] Aborted connection 31 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:12 29 [Warning] Aborted connection 29 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:18 39 [Warning] Aborted connection 39 to db: 'customTrash' user: 'ctdbuser' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:18 37 [Warning] Aborted connection 37 to db: 'mm10' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:18 38 [Warning] Aborted connection 38 to db: 'mm10' user: 'readonly' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:18 35 [Warning] Aborted connection 35 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:18 34 [Warning] Aborted connection 34 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

2025-01-09 13:12:18 36 [Warning] Aborted connection 36 to db: 'hgcentral' user: 'readwrite' host: 'localhost' (Got an error reading communication packets)

Thanks

~ John Chen

• 
  

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From: Luis Nassar <lrna...@ucsc.edu>
Sent: Tuesday, October 15, 2024 1:05 PM
To: Chen, John (IT) <John...@nyulangone.org>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] DB Crashed

 

You don't often get email from lrna...@ucsc.edu. Learn why this is important

[EXTERNAL]

[Gerardo Perez]

Hello, John.

Thank you for contacting the UCSC Genome Browser support team and reporting this issue.

We have created an internal ticket to investigate this issue further. We will follow up with you as soon as we have an update.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/MN0PR18MB61169FF25C3408F0DE3CBA6681132%40MN0PR18MB6116.namprd18.prod.outlook.com.