Run MobaXterm and click "Start Local Terminal" for Windows base computers.
For Mac just open your "Terminal" app.
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 [UnityID]@login.hpc.ncsu.edu with your personal UnityID.
Input your personal UnityID password.
Input 1 to receive a push notification to connect or 2 to receive a text message to connect.
After everything is inputted properly you will be logged into the HPC
Creating subdirectories
Now that you are in your home directory, you need to begin to organize it with your projects to make working directories.
You will be analyzing an Arabidopsis (Arabidopsis thaliana, "At") project, a Soybean (Glycine max, "Soy") project and you individual Soybean Project for your Final Portfolio ("Portfolio"). Let's make three directories: one for At, one for Soy, and one for your Portfolio:
mkdir At
mkdir Soy
mkdir Portfolio
Next in each directory At, Soy and Portfolio make these sub-directories
mkdir AlignedToTranscriptome
mkdir fastqc
mkdir salmon_align_quant
mkdir starindices
mkdir starOutputfiles
mkdir transcriptome
To edit a file that is uploaded to the HPC you can use the command vi:
vi NameOfFile
To use the functionality of vi to edit:
i = edit mode
Ecs = stop edit mode
:wq = quit with save changes
:q! = quit without saving
:noh = clear yellow highlighting within the script
If you are having issues with hidden characters (like ^M) you can view those by vi -b:
vi -b NameOfFile
In the directory where you want to make the script type
vi jobname.sh
hit the 'i' key to enter insert mode
Paste the script with right click
Hit 'esc' to exit insert mode
Type :wq to save and exit
Make sure to view your script and make sure it copies and pasted correctly. Common issues to check for are:
1) If you forget to hit 'i' before pasting, then the shebang header is almost always cut off. So check the very first line.
2) Depending on where the code is copied from, arguments longer than one line can be broken into two lines instead of one. Make sure arguments are all together in one line.
In the directory where you want to make the script type
cat > jobname.sh
Hit enter. There should appear a blank space.
You can now paste the script from your clipboard with right click.
Once the script is pasted in, hit the 'ctrl' and 'c' keys at the same time to save and exit.
Find present locaton
pwd
This will tell you where you are in the HPC
Change directory
cd path/to/desired/directory
Copy a file
cp path/to/desired/SourceDirectory/FileToCopy path/to/desired/CopyToDirectory/FileToCopy
Move a file
mv path/to/desired/SourceDirectory/FileToMove path/to/desired/MoveToDirectory/FileToMove
List contents of current working directory
ls
list short
ll
list long
Submitting a job to the LSF
bsub < job.sh
(example: bsub < starindex.sh)
bsub without <job.sh will take you into a loop where you will need to "kill" your job
Killing a errant job
bkill JOBID#
(example: bkill 267358)
Check the status of your jobs
bjobs
To read a file
more
To change modifications of a directory for read write execute permissions to your Linux group
chmod g=rwx yourdirectory/
for accessing your computer from globus
This will allow you to transfer files from the HPC to your local computer so you can perform data anaylsis
1) Navigate to File Manager
2) steps
3) Click the download link for your operating system
4) Run the .exe file that downloads to your computer
If Windows/iOS tries to protect your computer, click more info and then Run Anyway.
Run set-up wizard. A webpage asking for permission to access your account should open once done. Click Allow.
A Collection Details window will open. Name your collection. I named mine 'Delorean_Maneki' because this given computer's name is Maneki.
5) Return to the Globus Web App and navigate to your Collections. You should now see your personal computer.