Should I use a multi-threaded (openMP) version of GARLI if I’m using a computer with multiple processors/cores?
The multi-threaded versions will increase the speed of runs by approximately 1.2 to 1.8 times, but will otherwise give results identical to those obtained with the normal version (i.e., the search algorithm is exactly the same). It will perform the best when there are many columns in the alignment, or when using amino acid or codon models. This does not, however, mean that running this version is the best use of computing resources. In particular, if you intend to do multiple search replicates or bootstrap replicates, simply running two independent executions of the program will give a speedup of nearly 2 times, and will therefore get a given number of searches done more quickly than a multithreaded version. One case in which the multithreaded version may be of particular use is when analyzing extremely large datasets for which the amount of memory that would be required for two simultaneous executions of the program is near or greater than the amount of memory installed in the system.
