Closed dllahr closed 1 year ago
Hi Dave,
Apologies that the program has been slow on your 9 samples. The python CLI tool is memory inefficient, and does not make proper use of multiprocessing during the NMF routine, leading to long processing times. I am no longer actively maintaining this repo and highly recommend that you switch to using the more optimized R library.
I will leave an archive notice on the python package's README file this week with plans to archive in March 2023.
Thanks, Frank
Thank you for the response - much appreciated. I'll try that out.
Hi
First, thank you for providing the degNorm tool (and writing the paper describing it) - it seems like a great resource - very much appreciated.
I'm writing to ask for some help / guidance in running the tool (details of setup / command below.). I'd like to get a sense of if I'm heading in the right direction or not, a rough sense of the compute required to run, any guidance would be very helpful and much appreciated:
-p 8
option, it appears to have used ~3 CPUs briefly, then ~1.6 CPU for 5 hours, has been using 1 CPU for the last 5 hoursHere's the command I used to run:
I'm using an AWS EC2 instance t3a.2xlarge (8 CPUs, 32 G RAM) running AWS linux (CentOS variant). Installation of degnorm was normal, tests passed.
Any ideas / suggestions would be much appreciated - thank you in advance, Dave