Closed bioinfo007 closed 5 days ago
The -threads N
option specifies the number of threads, default is min(20, number_of_CPU_cores).
You can verify muscle is using multiple threads using the top
command, e.g. it will show 2000% CPU if it us using 20 cores.
How long are the sequences? time and memory scale like L^2 where L is the sequence length, if they are much longer than around 1,000 letters, then it may be slow.
It seems to be that -super5
ignores the threads option.
It should support the -threads option, I have tested this extensively. please double-check, if you still believe there is a problem please provide test data and script to reproduce the symptom.
You are right. muscle only has a relative long startup phase that is single threaded. After a couple of minutes, it starts to use the defined number of cores.
Is it possible to specify threads and perform parallel processing, i have a large data set that I want to submit via sbatch on HPC, but there is no clear help for specifying threads. Please respond with a suitable solution. As processing a single file with around 600 sequences is taking much time, even with specifying 80 cores. It seems muscle5 is not able to use all the 80 cores. Thank you