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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
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Sex chromosome papers RSS


Chromosome-level genome assembly and sex chromosome identification of the pink stem borer, Sesamia inferens (Lepidoptera: Noctuidae)
Link

The genome sequence of a ground beetle, Ophonus ardosiacus (Lutshnik, 1922)
Link

The genome sequence of a hoverfly, Pocota personata (Harris, 1780)
Link