Connect to the cluster using SSH to:

• captainsisko.statgen.ncsu.edu
• brccluster.statgen.ncsu.edu
• brccluster.cos.ncsu.edu
• captainkirk.statgen.ncsu.edu
• brccluster2021.statgen.ncsu.edu

These are just different names for the same machine. This machine is known as sisko within the cluster.

From October 18th 2021 OIT blocked the default SSH port (port 22) at the campus gateway. You should connect to the campus VPN and then use SSH to get to the cluster. SFTP, SCP, and SSHFS are also affected by this change.

Alternatively, you can connect to port 222 on the cluster. This requires you setting your SSH client to use port 222 (the “-p” option on command-line ssh). For command-line scp and sftp the option is “-P” (uppercase).

Under Windows you can use putty or some other ssh client. e.g. ssh comes with the MinGW shell, openssh for windows, MobaXterm, or Windows Subsystem for Linux.

On a Mac you can just use the Terminal app to run ssh from the command line. There are more fancy ssh clients e.g. iTerm2.

Once at a command line you can connect to the cluster using a command like one of these:

ssh username@brccluster.statgen.ncsu.edu
ssh -p 222 username@brccluster.statgen.ncsu.edu

You will be prompted for your password. When you type your password, no characters will be displayed as you type (not even asterisks or dots).

If you have started a long-running job on the head node from your command line, or are running a job using srun, then a network glitch, or forgetting and closing your laptop lid, will drop your connection and kill your job.

It is best to run jobs using sbatch which detaches the job from the shell, but you can also use a terminal multiplexer. The cluster has 3 such programs installed: screen, byobu, and tmux. These programs start up shells that are immune to your network connection to the cluster being dropped (as well as letting you run multiple shells from the one connection). If your network connection drops, you can log in again and re-attach to the shells running under the terminal multiplexer.

• Screen: https://www.gnu.org/software/screen/
• Byobu: https://www.byobu.org/
• Tmux: man tmux

Finally, you can use the bash built-in disown command to detach a job from your terminal.

./mycoolprogram > coolprog.out 2>&1 &
disown

These commands start your program with output redirected to a file, put it in the background, and then tell bash to detach the program from your terminal.

All of the copying methods in this section are SSH-based and use port 22 by default. So to copy a file to the cluster from off-campus, without being connected to the NCSU VPN, you will need to configure your client program to use port 222 instead. For command-line scp this is the “-P” (uppercase) option. Your command will look something like this:

scp -P 222 my_important_file myusername@brccluster.cos.ncsu.edu

For other client programs you should look at the respective documentation.

pscp

• For Windows
• Single binary file (easy to install).
• from the putty website

scp

• Available on Linux and Mac systems.
• Available for Windows as part of MinGW.
• Cygwin
• Windows Subsystem for Linux

WinSCP

• Windows GUI Application

SFTP Net Drive

• https://www.nsoftware.com/sftp/netdrive/download.aspx
• for Windows
• mount your cluster home directory on your local machine.
• Can use the usual drag and drop copy between folders.

sshfs

• Allows you to mount a cluster directory as a subdirectory on your local machine.
• https://osxfuse.github.io/ (for Mac, see note below about permissions)
• win-sshfs (for Windows)
• sshfs-win (for Windows)
• Using sshfs

If you are using sshfs on a Mac and find that you cannot access directories (folders) through sshfs that you can access on the cluster because of supplementary groups that you user belongs to, then you may want to try this option:

sshfs -o defer_permissions username@brccluster.cos.ncsu.edu:/directory mountpoint

Globus

You can use Globus Connect Personal to create a Globus endpoint allowing you to copy files to or from the cluster using the Globus interface. The instructions for doing so are here: https://docs.globus.org/how-to/globus-connect-personal-linux. You should use the “Running with no GUI” instructions, or see below.

Globus Connect Personal is available as a module on the cluster (with name “globuspersonal”).

The first time you run globusconnectpersonal you will be given a URL (to auth.globus.org) and a prompt for an auth code. Visit the URL on your local machine and log in to Globus to get the authorization code. Copy and paste the auth code into the cluster terminal window.

You can then start globus with:

globusconnectpersonal -start &

You should then be able to find your cluster endpoint within your Globus account.

Check status of your Globus connection with:

globusconnectpersonal -status

End your Globus session with:

globusconnectpersonal -stop

If you want to add directories outside your home directory to your Globus endpoint, take a look at the bottom of the page pointed to by the URL above where the format of the config-paths file is described.

You can download files directly to the cluster if you are logged on and have a URL for the file. To do this you can use wget. For example:

wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/est_human.gz

wget will do FTP, HTTP, HTTPS protocols.

(curl will do the same thing. Both can do simple authentication, but in general, if your data is behind a login you may not be able to get it with wget or curl.)

You can also use sftp or ftp directly.

ftp ftp.ncbi.nlm.nih.gov
ftp>binary
ftp>cd genomes
...
ftp>get est_human.gz
ftp>quit

(binary is not always necessary, but it doesn't hurt to include it.)

Use prompt and mget to fetch multiple files.