Forsythia

Description

Forsythia is the Ubuntu server in the McGill lab (currently at Gavin’s desk). It’s a headless server, meaning that there’s no graphical user interface, and it’s typically used by sshing in. There are 64 processors and 251 GB of RAM. A key restriction of this server is that no one in the lab has root access, which means that for adding users and installing programs server-wide need to make a request to the Genome Centre IT. Fortunately they generally reply really quickly and are very helpful.

There is only 1 TB on the make drive mounted at / (which includes /home, where all user directories are). However, there are two larger drives (/data1 and /data2) which have 14 TB each, which people can use when working with large files. Note that none of these directories are backed up though (including /home), so this is not a good place for long-term storage and data loss could easily happen if there are any drive malfunctions.

To allow the user to connect to Forsythia with their ssh key, make sure that their public key is added to /home/$USER/.ssh/authorized_keys

Get access to the gateway server Cousteau and Forsythia

To ssh into Forsythia (even when on the McGill internet network) you need to first ssh into the Genome Centre gateway server called Cousteau. There isn’t anything actually on Cousteau that is relevant to our work: it’s just a stepping stone.

You’ll need to make sure that these steps are taken care of:

• Make sure that Jesse has added you as a student/employee to the Genome Centre spreadsheet called “Job Positions Being Filled Spreadsheet.xlsx”
• Email the Genome Centre IT staff for an account on Cousteau and Forsythia ([email protected]).

SSH commands

One you have an account on Cousteau you will need to first ssh into that server using this command (with your username swapped in). This what the command looks like on my Mac laptop (you’ll need to change the path to the ssh key as well, which the IT staff should explain when you’re setting up your Cousteau account):

ssh -L 5050:forsythia.genome.mcgill.ca:22 -i /Users/Gavin/.ssh/id_rsa [email protected]

(Note that in addition to the username and path to the ssh keyfile, the port 5050 should be replaced with whatever port is specified by the IT staff)

Then open a new Terminal window on your local computer and login to Forsythia using this command:

ssh -p 5050  [email protected]

Transferring files to and from Forsythia

You can only use scp (and not sftp) to transfer files to and from your local computer and Forsythia. Your commands would similar to this (when running on your local computer):

To upload a file from your local computer to Forsythia:

scp -P 5050 -r -i /Users/Gavin/.ssh/id_rsa2 (file.txt)  \
(gdouglas@localhost:/LOCATION/ON/FORSYTHIA/)

To download a file from Forsythia to your local computer:

scp -P 5555 -r -i /Users/Gavin/.ssh/id_rsa2        \
(gdouglas@localhost:/LOCATION/ON/FORSYTHIA/file.txt)    \
(LOCATION/TO/DOWNLOAD/LOCALLY)

You can use sftp or scp to transfer files to and from the Compute Canada server Béluga and Forsythia. This seems to be only possible from the Forsythia side. To connect with sftp to Béluga you would use a command like this (where -i specifies an ssh key that you have configured on the Compute Canada website):

sftp -i /home/gdouglas/.ssh/id_ed25519 [email protected]

Using RStudio Server on Forsythia through your local web browser

The advantage of using RStudio in this way is that you can use all the resources on the server and not have to download files locally to use them with R. RStudio Server is available on port 8787 by default and you can use this command to tunnel to Forsythia at this port (if you’re already logged into Cousteau):

ssh -N -L 8787:127.0.0.1:8787 -p 5050 [email protected]

Once you put in your password nothing will happen on the terminal screen. However you can go to http://localhost:8787/ in your web browser and you should be able to login and use RStudio through your web browser!

Remounting data1 and data2

These drives should mount automatically upon restart, but you can ask Genome IT to run these commands if not:

mount /data1 
mount /data2

Adding a new user to Forsythia as administrator

Note: this needs to be done by the IT staff now, so this likely won't be relevant, but basically we should make sure that users have access the /data1/$USER and /data2/$USER folder in addition to their /home/$USER folder.

For future reference these are the commands that can be used to add a new user (along with folders on /data1 and /data2 (e.g., for the user gdouglas)

sudo adduser gdouglas
sudo mkdir /data1/gdouglas 
sudo mkdir /data2/gdouglas
sudo chown -R gdouglas:gdouglas /data1/gdouglas 
sudo chown -R gdouglas:gdouglas /data2/gdouglas