Frequently Asked Questions

Why is the job only allocated ~7 GB?

The default memory allocation for a job is ~7 GB. Depending on the node type being requested more memory can be allocated for the job.

Partition Duration Cores Memory [GB] Example Slurm Flags
development (1 standard-mem, 1 MIC, 1 P100) 2 hours Various Various -p development
htc 1 day. 1 6 -p htc --mem=6G
standard-mem-s 1 day 36 256 -p standard-mem-s --mem=250G
standard-mem-m 1 week 36 256 -p standard-mem-m --mem=250G
standard-mem-l 1 month 36 256 -p standard-mem-l --mem=250G
medium-mem-1-s 1 day 36 768 -p medium-mem-1-s --mem=750G
medium-mem-1-m 1 week 36 768 -p medium-mem-1-m --mem=750G
medium-mem-1-l 1 month 36 768 -p medium-mem-1-l --mem=750G
medium-mem-2 2 weeks 24 768 -p medium-mem-2 --mem=750G
high-mem-1 2 weeks 36 1538 -p high-mem-1 --mem=1500G
high-mem-2 2 weeks 40 1538 -p high-mem-2 --mem=1500G
mic 1 week 64 384 -p mic --mem=374G
gpgpu-1 1 week 36 256 -p gpgpu-1 --gres=gpu:1 --mem=250G
fp-gpgpu-2 Various 24 128 -p fp-gpgpu-2 --gres=gpu:8 --mem=120G
fp-gpgpu-3 Various 40 384 -p fp-gpgpu-3 --gres=gpu:2 --mem=370G

How do I change the format of the output of the squeue command?

You can change the output of squeue using the “-o” flag, which can be used to set different fields and their widths (see “man squeue” for all the fields). To use the same configuration repeatedly you can setup an alias such as following in your ~/.bashrc file.

alias cq="squeue -u ${USER} -o \"%.20i %.15P %.8T %.12M %.6D %.15j %R\""

How can load all dependency packages of a package built via Spack?

Many packages on M2 have been built using the Spack package manager. This system allows for the complete dependency chain of packages to be built as needed for the specific package being installed. When using an application that was built via Spack only the package module needs to loaded as it will automatically find its own dependencies as needed. However, when building an application outside of Spack, but using Spack-built packages, it is useful to be able to have all dependency packages loaded into the build environment. This can be accomplished via:

module load spack <compiler>
source <(spack module loads --dependencies <package_name>)

Here <compiler> and <package_name> are the module names for your chosen compiler and the package needed, respectively.