[slurm-users] blastx fails with "Error memory mapping"

Mark Hahn hahn at mcmaster.ca
Fri Jan 24 17:30:38 UTC 2020

> Excuse me, I have confused with that.
> While the cgroup value is 68GB, I run on terminal and see the VSZ is about
> 80GB and the program runs normally.
> However, with slurm on that node, I can not run.

how much memory are you requesting from Slurm in your job?

> Why on terminal I can run, but I can not run via slurm?

the purpose of slurm is to allocate resources.  logging into a node "bare"
is "evading" everything slurm does.

> I wonder if slurm gets the right value from kernel's cgroup.

you have it backwards.  slurm creates a cgroup for the job (step)
and uses the cgroup control to tell the kernel how much memory to 
permit the job-step to use.

> I would like to locally solve the problem for blast and I am not seeking a
> system wide solution right now.

there's nothing unique about your system or blast (which is extremely common
on many large slurm installs).

regards, mark hahn

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