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).

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)
• win-sshfs (for Windows)
• Using sshfs

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.