Out of memory-job ended

IFB Core Cluster
1

Dear,
I tried to use metaspades for the individual assembly of metagenomes, but it failed with the error "slurmstepd: error: Detected 1 oom-kill event(s) in StepId=36313702.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler."

The parameter settings are as follows:
#SBATCH --mem 200G
#SBATCH --cpus-per-task 24

I don't know how to solve it, could you help me?
Thanks.

Best,
Rui Zhang

2

Dear @rzhang

"out-of-memory" clearly indicates that you need more memory.

So, you have to rise the memory requested. You can maybe double the value.

#SBATCH --mem 400G

You can use the new standards nodes (2TB RAM) or bigmem (3TB RAM).

Once your job is terminated, you can check the memory/cpu used with seff <jobid>

Best regards

3

Thank you, it works now.