Can large data deletion affect Innodb buffer pool performance? At the beginning of this year we lunched a lot of massive data deletions (millions of rows per week) in our production database. Also, there is an automatic integration of new data (insert/updates) of 10 to 25 .CSV files per day with a global/average size of 400MB.
We noticed that reading performance on data even with full using of index became too slow. We have about 122GB of daya with 60GB of RAM and I configured 48GB for the Innodb buffer pool (please check details in images).
Is the deletion affect buffer pool performance ? What is the best/fast way to resolve that issue ?
Thank you for your help.


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(UPDATED)

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It's not really a fragmentation issue, I added a 3rd image for more information.
(updated)
It is not indexes (the use is about 90% - 100%) but the bad way the app is using the db model made is too bad.
I restarted yesterday the server with making some changes in the configuration file :
innodb_buffer_pool_size = 48
innodb_buffer_pool_instances = 32
innodb_read_io_threads  = 16
innodb_write_io_threads 8

The buffer pool is used, no more slowness noticed until now (after some refresh).
However, still not understand the reason of the impact of deletion on the buffer pool. Thus I believe that the bad way the app is using queries via ORM is the source of this issue.