A tour of Fred Hutch scientific computing resources
Welcome!
Scicomp has put together a very nice system
Be kind to sysadmins!
Not going to cover
GUI tools (e.g. motuz, and X login)
Workflow management systems (e.g. nextflow, snakemake, make)
Containerization: Docker/Singularity
Lots of resources for you
https://sciwiki.fredhutch.org/ (please contribute)
http://research.fhcrc.org/coop/en.html
http://www.fredhutch.io/
https://fhbig.slack.com/
Preflight setup
groups set up
cluster access granted
SSH keys uploaded
Interactive compute
the rhinos (for non-intensive use)
`grabnode`
Fun
`finger`
`write`
Your home directory
Shared across every compute resource!
100GB
`.snapshot`
Modules
`ml SAMtools`
`ml fhDev`
https://sciwiki.fredhutch.org/scicomp...
Storage
/fh/fast
Economy storage
`sw2account v2 matsen_e`
`swc ls /`
`swc ls /individual-archive`
`swc upload to-delete /individual-archive`
`swc rm /individual-archive/to-delete`
Scratch storage
`cp to-delete /fh/scratch/delete30/matsen_e/shared/`
`/loc/no-backup` is going to become `/loc/scratch/delete30` etc
gizmo cluster
We use SLURM https://slurm.schedmd.com/documentati...
`sbatch`
`scancel`
`squeue -u $USER`
`tail -f slurm-output-file.out`
`sacct` and variants, e.g. `sacct -u matsen -o JobID,JobName%30,Elapsed,State,MaxRSS,AllocCPUs,MaxVMsize1`
`hitparade`