Unusual memory fail issues on HPC
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caonetto commented
Hi,
Currently trying to run a plant genome with nanopore reads in a node with 1tb of ram and my runs keep on getting killed during the " Starting 'ovS' concurrent execution" of the correction stage with an error from slurm "Some of your processes may have been killed by the cgroup out-of-memory handler"
Is there a way I can troubleshoot this to identify a way to lower the ram requirements as Its unlikely I will have access to additional ram.
The log reports the following allocations before starting canu:
-- Local: meryl 24.000 GB 8 CPUs x 16 jobs 384.000 GB 128 CPUs (k-mer counting)
-- Local: hap 12.000 GB 16 CPUs x 8 jobs 96.000 GB 128 CPUs (read-to-haplotype assignment)
-- Local: cormhap 32.000 GB 16 CPUs x 8 jobs 256.000 GB 128 CPUs (overlap detection with mhap)
-- Local: obtovl 16.000 GB 16 CPUs x 8 jobs 128.000 GB 128 CPUs (overlap detection)
-- Local: utgovl 16.000 GB 16 CPUs x 8 jobs 128.000 GB 128 CPUs (overlap detection)
-- Local: cor -.--- GB 4 CPUs x - jobs -.--- GB - CPUs (read correction)
-- Local: ovb 4.000 GB 1 CPU x 128 jobs 512.000 GB 128 CPUs (overlap store bucketizer)
-- Local: ovs 16.000 GB 1 CPU x 128 jobs 2048.000 GB 128 CPUs (overlap store sorting)
-- Local: red 32.000 GB 8 CPUs x 16 jobs 512.000 GB 128 CPUs (read error detection)
-- Local: oea 8.000 GB 1 CPU x 128 jobs 1024.000 GB 128 CPUs (overlap error adjustment)
-- Local: bat 256.000 GB 16 CPUs x 1 job 256.000 GB 16 CPUs (contig construction with bogart)
-- Local: cns -.--- GB 8 CPUs x - jobs -.--- GB - CPUs (consensus)
Thanks.