id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
7435	Speed up Blast Protein search by using 4 threads	Tom Goddard	Zach Pearson	"Have blastp use 4 threads instead of the default 1 thread when running a Blast Protein search of the large databases, NR and AlphaFold v3.  Probably would be nice (and simpler) to use 4 threads for all of the databases.  The main effect may be parallelizing the database file read speed on the slow beegfs file system.  The plato nodes have 56 cores and I think it is rare to see more than one blast job running on plato at a time.

This sped up the sequence search by a factor of 4 in my tests.  It requires adding the ""--num_threads 4"" option to the blastp command in run_job() in file
cxwebservices/task_runners/blast.py

I tested blastp run on watson with ChimeraX defaults on a length 268 sequence (7u0u chain A) searching the AlphaFold version 3 database.  Took 19 minutes with 1 thread, 5 minutes with 4 threads."	enhancement	closed	moderate		Sequence		fixed						all	ChimeraX