exercises2_hpc.md

Exercise 1: "Quality trimming on 6 Fastq files, in serial with multithreading"

• Log into O2 using Terminal (on Macs) or Git BASH (on Windows)
• Start an interactive session with a single core
• Change directories into the ~/unix-intro/, and copy over files using the following command:

$ cp /n/groups/hbctraining/unix-intro/other/*-slurm* . 

• Open the trimmomatic-serial-slurm.sbatch script with nano
• Modify the SLURM (SBATCH) options to use only 4 cores
• Add the SBATCH options to make sure that you get an email when the job completes/ends
• Submit the script to the SLURM queue using sbatch
• Once submitted, immediately check the status of your job. How many jobs do you see running? Is there a difference in the "partition" on which they are running?
• When the job is completed it will create a new directory with new files: What is the name of the new directory? How many new files and directories were created within it?
• List only those files that end in .zip,

Exercise 2: "Quality trimming on 6 Fastq files, in parallel with multithreading"

• Check and make sure you have an interactive session going and also that you are in the ~/unix-intro/ directory.
• Use nano to open the trimmomatic-multithreaded-slurm.sh file and make note of the sbatch submission command in it. Name some of the SLURM/SBATCH options that we are requesting for each job in the loop.
• Run trimmomatic-multithreaded-slurm.sh using sh instead of sbatch.
• How many job submission notifications did you get?
• Once submitted, immediately check the status of your jobs. How many are running and how many are pending?
• Once again, when the job is complete a new directory with new files will be created. Use ls -l to determine if the same output was generated for both.
• What do you think the advantage is of running the job(s) this way as compared to Exercise 1?