README.md

peregrine

My notes, presentations and testing scripts about the Peregrine cluster.

Presentations

• Running (independent) jobs on the Peregrine computer cluster PDF ODP
• Running jobs with dependencies on the Peregrine computer cluster PDF ODP

Do a git pull

module load git; git pull

Copy from Peregrine to local computer

Must be run on local LWP computer:

scp p230198@peregrine.hpc.rug.nl:/home/p230198/GitHubs/Cer2016/*.RDa ~/Peregrine

Define an alias to log in to Peregrine

On your home/local computer, do:

echo "alias p='ssh p230198@peregrine.hpc.rug.nl'" >> ~/.bashrc

Now just type p to log in to Peregrine

Define an alias to view the queue

On the Peregrine computer cluster, do:

echo "alias q='squeue -u $USER'" >> ~/.bash_profile

Do not use .bashrc, as this will disable using scp.

Now just type q to view your jobs in the queue.

Get a welcome message

echo "cowsay -f stegosaurus 'Welcome master'" >> ~/.bash_profile

echo "module load cowsay; cowsay -f moose 'Welcome to Bianca, NSPHS'" >> ~/.bash_profile

Do not use .bashrc, as this will disable using scp.

Put job first in your queue

scontrol top <jobid>

How much does Peregrine love its users?

Me:

sshare | egrep "p230198" | rev | cut -d " " -f 2

All:

sshare -a

Or, to add the commands love_me and love_all to your profile:

echo "alias love_me='sshare | egrep "p230198" | rev | cut -d " " -f 2'" >> ~/.bash_profile
echo "alias love_all='sshare -a'" >> ~/.bash_profile

View the queue with the long names readable

squeue -u $USER -o "%.8i %.6P %.28j %.8u %.2t %.10M %.6D %R"

View a user's email

finger p123456

View your quotum

pgquota

also

lfs quota -h /home

Remove cached files older than 7 days

cd ~/.cache
find . -type f -mtime +7 -execdir rm -- '{}' \;

Remove empty folders

cd ~/.cache
find . -type d -empty -print0 | xargs -0 -I {} /bin/rmdir "{}"