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5.5 versus 10.0/5.6 performance issues


Because of performance issues with our DBMS we recently decided to migrate our software to MySQL or one of its forks. We would prefer MariaDB.
We created a performance test suite so that we are sure to make the right decision.
Beside other values our test measured the average workflow processing time including multiple database transactions. The unexpected outcome was, that we had a big difference in the processing times between 5.5 and 5.6 based databases.

                  average-time [ms]
                  (lower = better)
MySQL 5.6              233
Percona 5.6pre         208
MariaDB 10alpha        194
MariaDB 5.5           1248
MySQL 5.5              993
(Firebird 2.5         9694)

We are bound to very special hardware, the biggest bottleneck there is USB-stick based storage (cannot be changed for now).

Our  interpretation of the results and the research we were doing so far is, that the changes within InnoDB/XtraDB storage engine in connection with our "very special" storage solution causes this differences.
Can anybody confirm that the changes had a high impact on storage mediums with slow access rates?
Or does anybody have an idea if it possible to optimize MariaDB 5.5 (we would like to go with MariaDB) to get the same performance with MySQL 5.6?

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