USearch

1 Overview | 2 Using | 2.1 Multicore | 2.1.1 Observation:

Overview

USearch: A unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

We have installed the 32-bit version of USEARCH which is licensed at no charge for individual use. The 64 bit version has to be bought.

Using

Use the module name usearch to discover versions available and to load the application.

Multicore

As according to usearch's multithreading “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" … The -threads option species the requested number of threads, e.g. -threads 4.”

Observation:

We have noticed that if you allocate say 4 cores, and run a multi threaded command without the -threads option, you will see an output of the form:

[]$ salloc -A <account-name> -t 10:00 -c 4
[]$ usearch ...
...
00:00 72Mb   FASTQ base 33 for file Mock_R1.fq
00:00 72Mb   CPU has 16 cores, defaulting to 10 threads
WARNING: Max OMP threads 4

If you trying using the -threads option, when it is not supported, you'll see an output of the form:

[]$ usearch ... -threads 4
...
WARNING: Option -threads not used