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

Mark Hahn hahn at mcmaster.ca
Fri Jan 24 17:13:07 UTC 2020

> I see this
> # cat /sys/fs/cgroup/memory/memory.memsw.usage_in_bytes
> 71496372224
> which is about 68GB.
> As I said, running from terminal has no problem.
> Is is just fine to set a larger value (130GB) as below?
> echo 139586437120 > /sys/fs/cgroup/memory/memory.memsw.usage_in_bytes

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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