Interacting with files on Great Lakes

Prerequisites

Need a Great Lakes account
UM VPN (for off campus connections)
Atom
You can do ssh glc from the command line to connect to Great Lakes by editing your ~/.ssh/config file to contain…

Host glc
  HostName greatlakes.arc-ts.umich.edu
  RemoteForward 52698 localhost:52698
  User pschloss

Host glx
  Hostname greatlakes-xfer.arc-ts.umich.edu
  User pschloss
    
Host *
  AddKeysToAgent yes
  UseKeychain yes
  IdentityFile ~/.ssh/id_rsa

The glx is useful for logging into Great Lakes if you are transferring files in and out of Great Lakes. It doesn’t require Two Factor Authentication so that’s a convenience.

Two terminal windows…

nano/vim/emacs in one
R in one
Copy and paste back and forth to test
Notes:
- Pretty tedious
- There are R packages for vim/emacs, but then you’ll have to learn them

Connect to server through GUI

Connect to UM with VPN

Go -> Connect to server

  smb://schloss-lab.turbo.storage.umich.edu/schloss-lab/pschloss

Navigate to desired directory
Three options…
- Use the two terminal windows approach and use this to see images
- Open in RStudio by double clicking on RProj file
- In Atom
  - File->Open… and navigate to project and open project
  - copy/paste or send code to R running on GL
  - R-exec atom package allows you to put cursor on line and run in terminal
Notes:
- Lags and gets painful; Seems to work much better from on campus (VPN?)
- RStudio doesn’t seem happy with this

Reverse tunnel w/ Atom (other text editors have this ability too)

The second line in the .ssh/config file we created allows for the reverse tunneling
https://atom.io/packages/remote-atom
remote server is Great Lakes
Install remote-atom package on your laptop

On Great Lakes, run…

curl -o rmate https://raw.githubusercontent.com/aurora/rmate/master/rmate
chmod +x rmate
mv rmate ~/bin/ratom

Log out of Great Lakes
Turn Remote Atom package on in Atom (before you log into Great Lakes)
Log into Great Lakes
On Great Lakes, navigate to your directory. Open file using…
```
ratom README.md
```
Should open in Atom.
Notes:
- No obvious lagging
- Can open files in separate panes of Atom, but can’t open project directory
- This is a pretty good, all around solution

Open OnDemand

Good for interactive jobs and using RStudio
There is also a Remote Desktop app that is analogous to the Connect to Server approach above
Browser based interface to use Great Lakes
Navigate to http://greatlakes.arc-ts.umich.edu/
Interactive apps -> RStudio

Fill in the specs for your job…

account: pschloss99
Number of Hours: (however long you want it for)
Number of Cores: 1
Partition: standard
Memory per node (GB): 4

Press “Launch”
You will then need to wait a moment or two as it starts your instance. Then click “Launch RStudio” when presented with the button
RStudio will open. You can fiddle with the window layout
In the Files panel (lower right corner) you can click on the button with “…” to navigate to /nfs/turbo/schloss-lab/ and from there to your project. Select the directory with your project and then do "More"->"Set As Working Directory" and you're good to go
When you’re done, close the window and