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

Mahmood Naderan mahmood.nt at gmail.com
Fri Jan 24 16:05:09 UTC 2020

Yes, it uses a large value for virtual size.
Since I can run it via terminal (outside of slurm), I think kernel
parameters are OK.
In other words, I have to configure slurm for that purpose.
Which slurm configuration parameter is in charge of that?


On Fri, Jan 24, 2020 at 5:22 PM Jeffrey T Frey <frey at udel.edu> wrote:

> Does your Slurm cgroup or node OS cgroup configuration limit the virtual
> address space of processes?  The "Error memory mapping" is thrown by blast
> when trying to create a virtual address space that exposes the contents of
> a file on disk (see "man mmap") so the file can be accessed via pointers
> (with the OS handling paging data in and out of the file on disk) rather
> than by means of standard file i/o calls (e.g. fread(), fscanf(), read()).
> It sounds like you don't have enough system RAM, period, or the cgroup
> "memory.memsw.limit_in_bytes" is set too low for the amount of file content
> you're attempting to mmap() into the virtual address space (e.g. BIG files).
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