Clusters and hpc exercises

-See clusters and HPC material here

-For some of the following exercises a Triton account is needed in order to complete the exercises successfully.

-If you do not have cluster access, you can still try them out or leave them undone, it should not affect your overall course performance too much.

What is HPC?

Question 1

Which of the following claims are true when it comes to using Triton (or clusters in general)?

Using the cluster allows me to process my data faster than my laptop

I can use Jupyter to get a terminal to connect to a cluster

I can use an SSH tunnel to copy my Triton files on my home workstation

If I lose my work files, I ask Science-IT to recover my $WRKDIR

After getting my account, I can use the cluster whenever I need

Commands

Write down a command that you would execute to perform asked operation.

Question 1

How do you load software to use on Triton?

Question 2

How would you list available modules in Anaconda?

Question 3

Let’s say you submitted a job with id 7. What command can you use to debug a running job and view its detailed status?

Job script

Take a look at the following scripts named calc_ppmc.py and run_ppmc.sh and answer questions.

calc_ppmc.py below calculates the Pearson product-moment correlation for two 1000x1000 matrices.

rounds = 8
t = time.time()

for i in range(rounds):
    a = np.random.random([1000, 1000])
    b = np.random.random([1000, 1000])
    rslt = np.corrcoef(a,b)

t_taken = time.time() - t

print('Takes {} seconds to calculate pearson product-moment correlation for 1000x1000 matrices'.format(t_taken))

run_ppmc.sh:

#!/bin/bash
#SBATCH --job-name=run_ppmc
#SBATCH --output=ppmc.out
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --time=00:05:00
#SBATCH --mem=2G

module load anaconda

export OMP_PROC_BIND=true
python calc_ppmc.py

Question 1

Running sbatch run_ppmc.sh and then checking sacct history you can see

run_ppmc and the program calc_ppmc ran inside it as separate step.

True

False

Question 2

Total memory reservation for the job is 2G.

True

False

Question 3

The OMP_PROC_BIND variable sets how threads bind to OpenMP places

True

False

Hello world

A+ presents the exercise submission form here.

Pi iters

A+ presents the exercise submission form here.

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