Cluster tips
Cluster usage tips for Mac.
Remove need for password
This is particularly useful for the speedy click-to-download iTerm2 integration.
Full instructions here.
Briefly, generate key
ssh-keygen -t rsa
(leave passphrase empty)
Upload to host
ssh-copy-id -i ~/.ssh/id_rsa.pub [email protected]
iTerm2
Setup profile for each cluster
Allows to quickly start a new connection
Preferences > Profiles > plus button
General tab
- name (cluster name)
- shortcut key (Ctrl-Cmd-2)
- Command (Login Shell
ssh [email protected]) - Working directory (Home directory)
Colors tab - choose a colour scheme to uniquely identify it from a local terminal
Keys tab > presets > Natural text editing - Allows to navigate with alt-arrow, cmd-arrow and insert # in vim
Advanced tab
Code your own commands accessible by clicking terminal selections. For example to allow to sftp to a file through BBEdit (this is not needed anymore. Simply right click on any file and it opens in default app on your Mac):
Smart selection > Word bounded by whitespace > edit actions
make a new one
- Title - Open in BBEdit
- Action - Run Command...
- parameter -
/usr/bin/open -a BBEdit sftp://\u@\h/\d//\0
Install iTerm integration
log in to cluster
iTerm2 > install Shell integration
Allows to click to download files shown on screen and Alt-drag files from the mac to the iTerm2 window to upload them to current folder.
If right click to download results in wrong hostname (check by hostname -f)
Add one line on top of bash_profile
export iterm2_hostname=HOSTNAME # (eg login.hpc.vub.be )
.bashrc
Useful commands for slurm
start interactive job
alias int="srun --time=4:00:00 --ntasks=1 --nodes=1 --partition=sixhour --pty /bin/bash -l"
Queue of your jobs only (edit "user")
alias sq="squeue -u user"
queue of (inaccurately) estimated start time of your jobs only (edit "user")
alias sqs="squeue -u user --start"
Available processors in queue of choice
sp="sinfo -o%C --partition QUEUE"
Available memory in queue of choice
sm="sinfo -o%e --partition QUEUE"
Completed job information to make efficient usage of future jobs
seff -jobID
Set vim as default (used in broot)
export VISUAL=vim;
export EDITOR=vim;
Other slurm commands
Information on available resources
crctool
sinfo
Usage by user
sreport user top start=0101 end=0201 TopCount=50 -t hourper --tres=cpu,gpu
report user top start=0101 end=0201 TopCount=50 -t hourper --tres=mem