Chapter 3

This chapter is in case the main server is not working so we need to use a local tiny remote resource to go through the materials.

Download the key to get access.

cd
wget https://github.mit.edu/PILM-bioinformatics/support/raw/master/workshops/pim103/pilm103_rsa

Every student will have a user name given during the lecture.

Remote actions

Here, you will learn how to interact with remote computers, transfer files and send jobs to a cluster.

graph LR;
  A[Local computer] -->|connection| B{credentials?}
    B -->|password| C[semi-secure]
    B -->|keys| D[secure]
    C --> E[Server-login node]
    D --> E[Server-login node]
    E -->|job1| F[compute node 1]
    E -->|job2| G[compute node 2]

How you jobs get schedule:

  • According to the requested resources/ available resources
  • According your Fairshare score:
    • number of jobs/resources requested in the past
    • precision of the resources requested vs needed

## Summary

  • transfer
    • sshfs to mount remote folders
    • rsync to transfer files
  • cluster
    • srun for interactive or on the spot Jobs
    • sbatch for automatize Jobs
    • -c to aks for number of cores
    • --mem to ask for memory in Mb (2000 is 2GB)
    • --time=d-hh:mm:00 to define limit duration