[khmer] parition-graph memory requirements

[Jens-Konrad Preem]

Hi,
I am having trouble with completing a partition-graph.py job.
No matter the configurations It seems to terminate with error messages 
hinting at low memory etc. *
Does LOWering the subset size reduce the memory use, what about LOWering 
the amount of parallel threads?
The graafik.ht is 5.2G large, I had the script running as a PBS job with 
240 GB RAM allocated. (That's as much as I can get it, maybe I'll have 
an opportunity in the next week to double it, but I wouldn't count on it).
Is it expected for the script to require so much RAM, or is there some 
bug or some misuse by my part. Would there be any configuration to get 
past this?

Jens-Konrad Preem, MSc., University of Tartu



* the latest configuration after I thought on smaller subset size
./khmer/scripts/partition-graph.py  --threads 24 --subset-size 1e4 graafik
terminated with
cannot allocate memory for thread-local data: ABORT