Begin Using the HPC at NCSU

Code to login to the HPC using the secure shell

• Reminder, if working off campus you MUST be connected to NCSU SSL VPN.

• To login to HPC using a terminal you will need to use your unique NC State Unity ID to adapt the following command:

ssh YourUnityID@login.hpc.ncsu.edu

• Once you have submitted this command, you will be prompted to enter your NCSU password. Do not be alarmed when you do not see any characters typed

• This will set you in you home space (where you cannot do work because it has basically no storage space). You can confirm your location by using the command 'pwd' to print your working directory

  • • You should get a response of /home/YourUnityID

• YourUnityID must be customized to your actual UnityID. Ex: Dr. Sjogren's UnityID is casjogre.

• Do not do any work in your home directory or on the head node. Only use our class directory and submit work as a job to the scheduler. 

CHANGE DIRECTORY

1. Before you change your directory, check your current location. This command is print working directory (pwd).

pwd

• You should get a return line telling you that you are in the login node with a path: /home/UnityID

2. Change your directory

cd /share/bitcpt/S23

• Now that you are in our course project space you can set up your working directory where you will perform RNA sequence analysis!

• Whenever you change locations, get into the habit of checking by printing your working directory AKA your current location

pwd

3. List out what is in your current working directory

ll

• If you use the command to list ll or ls (all lower case letter L) you will see all our learning community working directories.

  • ll is for list long

  • ls is for list short

• You should see UnityID directory has been made automatically.

• If you do not see your UnityID as a subdirectory within the S23 make this new directory now:

mkdir UnityID

• Please change permissions on this directory so that your instructors can gain access

chmod g=rwx UnityID

4. Accessing your project working directory

• From now on, after you login on terminal, you can change your directory here

cd /share/bitcpt/S23/UnityID

SELF-CHECK FOR UNDERSTANDING PATHS

Write the paths for each of the following directories and files (there should be 12). 

I used ‘pwd’ to tell me what directory I was in. 

pwd

Return line: /gpfs_common/share03/bitcpt/S23/casjogre/

Then I used 'tree' to tell me all the directories and files nested with my current working directory.

tree

.

├── data

│   ├── sequences

│   └── trimmed_sequences

├── delete

│   └── delete2

├── output

└── scripts

• Current working directory (.) path:

• data path:

• sequences path:

• trimmed_sequences path:

• delete path:

• delete2 path:

• output path:

• scripts path: