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MySQL Error Lock wait timeout exceeded

Cross platform database support is really challenging for any dba, specially for them who is working on sql server since long time because who knows what question may raise tomorrow from which database or version or edition. Last week a developer came with her database issue on one of mysql database. Error she was facing “ Lock wait timeout exceeded; try restarting transaction ” during update on  large table having around 15 millions records, she was updating records through joins from another table. She tried 2-3 times on production, after 1-2 minutes this error was throwing.  I said try it on development/local with same data size, result was still same erro. Then started googling found some positive configurations and did some changes on db instance level settings. But result was  just few seconds improvements only & final out put was error. There are below early actions we have taken : SET join_buffer_size = 1024 * 1024 * 42; SET innodb_write_io_threads = 16; SET innodb_l