Description
Checklist
- There are no similar issues or pull requests for this yet.
- The request is not specific for MICOM Qiime 2 plugin (q2-micom)
Is your feature related to a problem? Please describe it.
I want to analyse the microbial growth rates for a given microbiome profile (single sample) when run on multiple different diets (or media). The idea is to understand how individual growth rates are impacted with changes in the medium. Multiple samples run on the same medium or grow
with the appropriate models has in-built multithreading to take advantage of a multi-core cpu. But growth of a single sample on multiple media doesn't have a multi threading option.
Describe the solution you would like.
Given that a single sample grow
uses only 1 thread, I want to be able to run growth calculations on different media (100-200 types of media) by using multithreading to access all threads simultaneously.
Describe alternatives you considered
I currently use the pool.starmap
function in the standard python multiprocessing library. I am facing an issue of memory pile up (likely due to threads that are not deallocated/ terminated despite the completion of the calculation) that causes the program to crash due to heavy ram usage.