Thesql multi threading for a single query

I am not very familiar with your needs, but perhaps storing each data point in the database is a bit of overkill. It sound almost like taking the approach of storing an image library by storing each pixel as a separate record in a relational database.

As a general rule, storing binary data in databases is wrong most of the time. There is usually a better way of solving the problem. While it is not inherently wrong to store binary data in relational database, often times the disadvantages outweigh the gains. Relational databases, as the name alludes to, are best suited for storing relational data. Binary data is not relational. It adds size (often significantly) to databases, can hurt performance, and may lead to questions about maintaining billion-record MySQL instances. The good news is that there are databases especially well suited for storing binary data. One of them, while not always readily apparent, is your file system! Simply come up with a directory and file naming structure for your binary files, store those in your MySQL DB together with any other data which may yield value through querying.

Another approach would be using a document-based storage system for your datapoints (and perhaps spectra) data, and using MySQL for the runs (or perhaps putting the runs into the same DB as the others).

The innodb threads have their place; but they do not help you out in your SELECT query. With MySQL, unfortunately, your SELECT can only use one single core.

This immediately means that if you want to use more cores, you must parallelize your queries. Very often this is possible. Do you have this huge script you're running? Are there independent parts to it? Parallelize them.

But if you cannot parallelize for some reason, you're more limited. Take a look at Shard Query. Either use it or get some ideas from it.