Closed aforsythe closed 2 years ago
Hi,
thanks for your interest in nextNEOpi.
I'm sorry that you ran into troubles, but according to your error log it seems that your machine is running out of memory:
slurmstepd: error: *** JOB 16525322 ON hpc3-20-22 CANCELLED AT 2022-10-21T18:55:47 *** slurmstepd: error: Detected 2 oom-kill event(s) in StepId=16525322.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.
You might need or tell SLURM to reserve more memory.
Or you can also try to request more memory by setting a global 'memory' option in nextNEOpi conf/process.config
(right after the cpus line).
memory = '64 GB'
or you can do this as per process option in conf/process.config:
withName:make_uBAM {
beforeScript = "ulimit -n 4096"
memory = "64 GB"
}
I'm trying to track down the source of an error in the
nextNEOpi
pipeline. It's not immediately obvious what the issue is (memory, a singularity issue, something else?)Any help would be greatly appreciated.
I'm encountering an error at :
My slurm error log says :
Looking into
.command.err
in the work directory I see:My configurations and inputs are