Running eggNOG only uses small percentage of allocated CPU

Question

[Emilie Jensen]

Hi all,

I am running eggNOG to annotate proteins. However, when timing the jobs, the percentage of allocated CPU each job get is very small.

I ran 5 jobs on 1 node with 8 CPU and 38gb for each job. The jobs only uses around 5% of CPU allocated to them. Do you have any idea, why this is the case?

Thanks :)

[jv]

It's not clear what the issue is here. Why do you expect that more resources (i.e. cpus and memory) should be used? Generally speaking, low resource utilization is a good thing and an indication of efficient software programming.

The other thing to note is that most software needs to be told how many cpus to use so unless you are telling eggNOG to use more cpus it is probably by default only using one. Also worth noting not all steps in the software execution will be able to use multiple cpus, for example maybe only ~30% of the computational tasks can actually be parallelized and thus the overall cpu utilization is low compared to what resources were requested to be used.