I am using the -num_threads option for magicBLAST and running from a linux shell. However only one thread is used (tried on 2 machines). The file.fa is only 20MB.

    magicblast -query file.fa -db nt -num_threads 16 -out out.sam -no_unaligned

Any ideas?
After 20 min was using multiple threads. I presume there is a stage when magicBLAST only uses a single thread when starting. NB I also reduced num_theads to 4 but havent tested if that has anything to do with it (24 thread machine)