Hello everyone I'm actually using a soft called RepeatMasker, in this pipeline I can run parallelized job via slurm with the command -pa
here is a doc about this command :
RepeatMasker -h
-pa(rallel) [number]
The number of sequence batch jobs [50kb minimum] to run in parallel.
RepeatMasker will fork off this number of parallel jobs, each
running the search engine specified. For each search engine
invocation ( where applicable ) a fixed the number of cores/threads
is used:
RMBlast 4 cores
To estimate the number of cores a RepeatMasker run will use simply
multiply the -pa value by the number of cores the particular search
engine will use.
so in a slurm batch script I should add :
#SBATCH --cpus-per-task=8
RepeatMakser -pa 2, right?
since 8/4 =2
But I wondered if I should also add others #SBATCH parameters or if --cpus-per-task is sufficient ?
Thanks al ot