CommunityData:Hyak Ikt (Deprecreated)

Setting up SSH

When you connect to SSH, it will ask you for a key from your token. Typing this in every time you start a connection be a pain. One approach is to create an .ssh config file that will create a "tunnel" the first time you connect and send all subsequent connections to Hyak over that tunnel. Some details in the Hyak documentation.

I've added the following config to my .ssh/config (you will want to change the username):

Host hyak hyak.washington.edu
   User makohill
   HostName login3.hyak.washington.edu
   ControlPath ~/.ssh/master-%r@%h:%p
   ControlMaster auto
   ControlPersist yes
   ForwardX11 yes
   ForwardX11Trusted yes
   Compression yes

ONE WARNING: If your SSH connection becomes stale or disconnected (e.g., if you change networks) it may take some time for the connection to time out. Until that happens, any connections you make to hyak will silently hang. If your connections to ssh hyak are silently hanging but your Internet connection seems good, look for ssh processes running on your local machine with:

ps ax|grep hyak

If you find any, kill them with kill <PROCESSID>. Once that is done, you should have no problem connecting to Hyak.

Setting Up Hyak

When setting up Hyak, you must first add this to your BASHRC file. Generally, you can simply edit the following file on Hyak: ~/.bashrc

##  hyak specific options
alias rgrep='grep -r'
alias big_machine='qsub -W group_list=hyak-mako -l walltime=500:00:00,mem=200gb -I'
alias any_machine='qsub -W group_list=hyak-mako -l walltime=500:00:00,mem=100gb -I'
PYTHON_PATH="/com/local/lib/python3.4:$PYTHON_PATH"
LD_LIBRARY_PATH="/com/local/lib:${LD_LIBRARY_PATH}"
PKG_CONFIG_PATH=/com/local/lib/pkgconfig:/usr/share/pkgconfig
MC_CORES=16
PATH="/com/local/bin:$PATH"
module load revolutionr_7.2
module load parallel_sql
umask 007

The final line is particularly important. If you do not do this, the files you create on Hyak will be able to be read or written by others in the group!

Once you do this, you will need to restart bash. This can be done simply by logging out and then logging back in or by restarting bash with the command exec bash.

I also add these two lines to my Hyak .ssh/config:

ForwardX11 yes
ForwardX11Trusted yes

These lines will mean that if I have "checked out" an interactive machine, I can ssh from my computer to Hyak and then directly through an addition hop to the machine (like ssh n0652). Those FowardX11 lines means if I graph things on this window, they will open on my local display.