Many search and clustering commands in USEARCH support
multithreading. Multithreading is parallel execution on a single
CPU. All threads belong to the same process and share the same memory space.
You can check if a given
command supports multi-threading by checking the documentation page for a
link to "Multithreading".
Database search commands generally
parellelize very well (e.g. usearch_global, ublast), but commands based on
clustering (e.g. cluster_fast, cluster_smallmem, cluster_otus, unoise2,
uchime2_denovo) typically don't support multithreading or don't achieve much
speedup from running multiple threads.
The -threads option species
the requested number of threads, e.g. -threads 4.
Default is to run
one thread per CPU core, or 10 threads if there are > 10 cores.
Performance may be improved by using more
or fewer threads than the number of cores. If USEARCH is sharing a CPU with
other resource-intensive programs, it may be better to set the number of threads
so that the total number of executing threads in all programs does not exceed
the number of cores. Using fewer threads can be faster if
cache contention is reduced, and more threads can be faster if
output is written via a slow network, in which case many threads
may be stalled waiting for output to complete.