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?
Regards, Mahmood On Fri, Jan 24, 2020 at 5:22 PM Jeffrey T Frey <f...@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). > > > >
