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

Mahmood Naderan mahmood.nt at gmail.com
Fri Jan 24 17:26:09 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.

Why on terminal I can run, but I can not run via slurm?
I wonder if slurm gets the right value from kernel's cgroup.

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


On Fri, Jan 24, 2020 at 8:45 PM Mark Hahn <hahn at mcmaster.ca> wrote:

> of course not.  "usage_in_bytes" is an output parameter.
> your issue is that Slurm is setting at least some of the input
> controls such as memory.memsw.limit_in_bytes.  if you want to fight
> with Slurm, you could set the memory.memsw.limit_in_bytes value on
> a "live" cgroup.  (note also that above you're referring to the base
> cgroup, not the cgroup for your job.)  of course, manually fighting
> Slurm is a Fairly Bad Idea.
> you should read the documentation on cgroups to understand how these work.
> memsw basically corresponds to VSZ in ps, whereas mem corresponds with RSS.
> regards, mark hahn.
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