gstacks issue

[Carly Graham]

Hello,

I am running into some issues with gstacks in the 2.1 version. I seem to be running out of memory on the cluster after gstacks runs for about 15 mins. Its a rather large dataset with >500 samples but I have access to a whole node with 250GB of memory so Im not quite sure whats going on. The error message I am getting in the log file is:

/var/spool/slurmd/job6427593/slurm_script: line 13: 22314 Killed /home/graham9c/scratch/Software/stacks-2.1/bin/gstacks -P ./LocalAdaptationStacks -M popmap-LocalAdaptation.txt -t 48 --ignore-pe-reads slurmstepd: error: Detected 1 oom-kill event(s) in step 6427593.batch cgroup.

Thanks!

Carly

[Nicolas Rochette]

Hi Carly,

How much memory did gstacks consume? Is there a default memory cap in your job scheduler?

Otherwise, reducing the number of threads will reduce memory consumption (with 48 threads you have 5Gb/thread which is not particularly high). Reducing the number of threads to 8-16 may actually also improve runtime altogether, because the bottleneck fairly quickly becomes the writing of output files anyway. Using too many threads is likely to create jamming and we haven't really had time to dedicate to this issue.

Best,

Nicolas

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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