lecture05

Lecture 05: Introduction to remote computing

Erick Matsen (@ematsen, matsen.group)

Learning objectives

After this course, you should:

• Understand the computational resources available at the center
• Be able to use the interactive and cluster nodes

Class materials

I'll give a tour of the FH computational environment during class.

Here is an outline of the tour:

• Welcome!
  • Scicomp has put together a very nice system
  • Be kind to sysadmins!
• Not going to cover
  • motuz file transfer
  • getting a graphical user interface session on the remote machines
  • Economy cloud storage
  • Cloud computing
• Lots of resources for you
  • https://sciwiki.fredhutch.org/ (please contribute)
  • http://www.fredhutch.io/
  • https://fhbig.slack.com/
• Interactive compute
  • the rhinos (for non-intensive use)
  • grabnode
  • top, htop
  • You need to use some strategy to avoid your jobs being killed when you close your laptop. Options here. My notes on tmux.
• Modules
  • ml SAMtools
  • ml fhDev
  • Available modules
• Your home directory
  • Shared across every compute resource!
  • 100GB
  • .snapshot
• Storage
  • /fh/fast
  • Scratch storage: cp to-delete /fh/scratch/delete30/matsen_e/ (replace matsen_e with your PI's name once you have one)
  • Economy cloud storage
• gizmo cluster
  • We use the SLURM job scheduler
  • sbatch
  • scancel
  • squeue -u $USER
  • tail -f slurm-output-file.out
  • sacct and variants, e.g. sacct -u $USER -o JobID,JobName%30,Elapsed,State,MaxRSS,AllocCPUs,MaxVMsize
  • hitparade

Here is a recorded video with some of the same content.

Interactive work

Shell variables

Shell variables are variables that are associated with your shell session. If you want to use their value, you write them with a $ at the beginning. They are typically written in all caps.

For example, the $PWD variable will always have your current working directory, just as if you had executed pwd. We can learn the value of variables using echo. For example, try the following commands:

• echo $PWD
• echo $HOST
• echo $USER

If you want to know more (e.g. how to set a variable), here are two excellent resources describing variables in shell (in fact, in Bash, but most people use Bash).

• An excellent and short introduction
• A more detailed introduction

Playing with the FH computational environment

• Grab a node with grabnode
• Run htop
• Log out from it
• See who is hammering the cluster using hitparade

Cluster use

The slow.sh script in this lecture05 directory is the same one that I demoed in the video.

• change it so that it emails you, not me
• change the job output file names
• try running it with sbatch
• watch the output accumulate using tail -f
• see your job with squeue -u $USER
• copy the job ID from that command and cancel your job with scancel
• see your recent cluster history with sacct