bin/magento setup:upgrade causes metadata locks

[Flowlance]

Preconditions (*)

1. Magento 2.2.6
2. MySQL 5.7.23 (Amazon RDS)
3. Jenkins
4. A huge store with 250000 products, and each product has more than 200 attributes.

Steps to reproduce (*)

1. We're using Jenkins for continuous integration.
2. When running "bin/magento setup:upgrade" from the jenkins build server, it takes a really long time (sometimes 1 hour+).
3. After viewing MySql server processes, I can see that there's a lot queries with "Waiting for table metadata lock".
4. It seems to be stuck on "Magento_Indexer":

Data post-updates:
Module 'Magento_Store':
Module 'Amasty_Base':
Module 'Amasty_Geoip':
Module 'Amasty_Scroll':
Module 'Amasty_ShopbyBase':
Module 'Magento_Directory':
Module 'Amasty_ShopbyBrand':
Module 'Magento_Theme':
Running data recurring...
Module 'Magento_Eav':
Module 'Magento_Customer':
Module 'Magento_Indexer':

Expected result (*)

1. "bin/magento setup:upgrade" shouldn't take so long.
2. No waiting for metadata locks.

Actual result (*)

2.

3. We're getting metadata locks and it can takes over an hour for them to disappear.

[magento-engcom-team]

Hi @Flowlance. Thank you for your report.
To help us process this issue please make sure that you provided the following information:

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• Information on your environment
• Steps to reproduce
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Please make sure that the issue is reproducible on the vanilla Magento instance following Steps to reproduce. To deploy vanilla Magento instance on our environment, please, add a comment to the issue:

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@Flowlance do you confirm that you was able to reproduce the issue on vanilla Magento instance following steps to reproduce?

• yes
• no

[magento-engcom-team]

Hi @TomashKhamlai. Thank you for working on this issue.
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[TomashKhamlai]

@Flowlance do you confirm that you was able to reproduce the issue on vanilla Magento instance following steps to reproduce?

Could you please share your experience? How the products and attributes were moved to vanilla Magento Open Source instance?

[Flowlance]

@TomashKhamlai Hi. I cannot reproduce this on a vanilla installation. setup:upgrade is very quick there.
What's the best way to copy this number of products over to the vanilla instance?
The system->export doesn't seem to handle this amount very well. It crashes.

[orlangur]

@Flowlance you can try using vanilla instance with the copy of this database.

[advcha]

@Flowlance I have an experience on this problem. I don't know exactly why this happened. Probably you have huge product images in pub/media/catalog/product directory. You can temporary move the product directory to somewhere else (outside pub directory). then run again bin/magento setup:upgrade. This should be much faster this time. then move back the product directory to original location. This problem only occur when you run setup:upgrade command. This way may be not you expected but it's working for me.

[magento-engcom-team]

Hi @engcom-backlog-nazar. Thank you for working on this issue.
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