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A DB compare operation takes an hour on my machine. I see that CPU and IO are under-utilized. I am running SQL server and Data Compare locally, connecting via shared memory. I am running with i7 4 core and SSD for the database.

Would the application benefit from some multi-threading?

The tool works in multi-threading as it is.

We recommend you to check the server's performance and the tables' content. We suppose the weak place may lie in data transmission.

Thanks for getting back to me.

In what way is it multi-threaded?

Retrieving, comparing and caching data are multi-threaded.

That's not what Microsoft Process Explorer shows:

We will reconsider the current behavior in future product versions.