ALICE2 Basics

Here are a few tips for using the ALICE2 high performance computing cluster. This post is not designed to teach you how to use a command line interface, rather to just introduce you to the specifics of ALICE2.

• Logging in: ssh <username>@alice2.le.ac.uk, enter your password and text message verification code if off campus
• Do all of your ‘work’ in /scratch/monoallelic/<username> warning: any file not touched in ~60days is deleted from here automatically
• Any raw data or outputs you want to save should be stored in /data/monoallelic/<username> as they will never be automatically deleted
• ALICE2 uses .PBS scripts to run jobs, see below link for the code needed at the start of every script: https://uniofleicester.sharepoint.com/sites/Research-Computing/SitePages/job-types-hpc.aspx?CT=1650535474108&OR=OWA-NT&CID=6fa1dfea-f123-1e1f-ec8d-7fb3a8b97c23
• It’s important to estimate well the time your job will take (walltime) and the amount of memory used (vmem), poor estimations lead to a lower user score which means your jobs will wait longer in the queue
• Also if you underestimate your time then your job will die and you’ll have to re-start it
• Basic commands to submit your .PBS scripts:
  • qsub <script name>.PBS
  • showq -u <username>
  • qdel <job id from queue>
• To check your job runs and doesn’t have any immediate errors you can run it for 5mins on the development queue before submitting to the main queue, then if it does immediately die because of a typo you can immediately tell without waiting in the queue for hours only for it to immediately die (see above link)
  • to submit to the development queue add: #PBS -q devel to the start of your script
• You can also use an interactive job to test code. Where you work directly on a node with a bunch of memory/threads etc. (see above link)
  • Simple interactive job:

qsub -I -l pvmem=10gb,walltime=01:00:00,nodes=2:ppn=8

• Copying stuff from and to ALICE:
  • On your own computer, from ALICE: scp <username>@alice2.le.ac.uk://scratch/monoallelic/<path_to_file> ./
  • On your own computer, to ALICE: scp ./<file> <username>@alice2.le.ac.uk://scratch/monoallelic/<path_to_directory>