I am confused with GATK Multi-threading options, -nt / --num_threads controls the number of data threads sent to the processor, -nct / --num_cpu_threads_per_data_thread controls the number of CPU threads allocated to each data thread.

What’s data threads?

Here is an answer from Geraldine Van der Auwera, PhD

In the meantime, what you need to know is that -nct is the number of CPU threads, ie threads that can be run by different cores if you have a multicore CPU, while -nt is the number of data threads, ie number of “clones” of the GATK that are run in parallel on your machine.

So nt is based on how many copies you want to run in the same time.

nct can control the CPU threads. Take CB60-G16 Network Server for example,

Each node has two CPUs (10 cores, 20 threads).

If I use -nct 10, it means I use 10 threads on one node. -nt 10 means I use 10 threads for one data thread(one sample). nt might cause an increasing in memory usage, each data thread would be allowed with the same memory size.