NUS HPC Tutorial¶
SSH connection¶
Try to connect to the server by (replace NUSNETID to your own)
Don’t execute random command before login because it may destroy your computer. After login to the server, you can feel free to make directory, create files.
Enable SSH for Windows
If you're using a Windows PC, you need to enable the SSH function first.
While waiting for NUS HPC to activate your account, windows user should install the essential SSH software for accessing server: (macOS user skip this step)
Follow the steps (the text you should enter in step 6 is openssh):
SSH for macOS and Linux (including WSL)
The SSH for accessing the remote server (orion, NUS HPC, fornax, etc.) should be ready after the above-mentioned steps. It is strongly recommended that you install the “windows terminal” in the Microsoft App Store.
Optionally you may want to have WSL installed.
Using third-party softwares for SSH¶
You can use PuTTY or VS Code if you wish but using terminal at the very beginning will help you get more familiar. See SSH for more details for VS Code.
Copy tutorial files to remote machine¶
You will be provided a file start.tar.gz to study the process. Try to get it here
After get the start.tar.gz in your local computer, change to the directory in your local machine and run the following command on your local machine: (replace NUSNETID to your own)
Further connect to the NUS HPC by ssh NUSNETID@atlas9.nus.edu.sg , You will find the start.tar.gz appears in your home directory. Unarchive it by
There will be several files released. If you ls the directory again you will see:
Data storage on NUS HPC¶
Note that NUS HPC only has 50GB permanant storage in the home directory. However, there are scratch storage for up to 1TB available. To make use of them, ssh to atlas9 first and (replace NUSNETID to your own ID):
mkdir /hpctmp/NUSNETID
mkdir /scratch2/NUSNETID
cd ~
ln -s /hpctmp/NUSNETID hpctmp
ln -s /scratch2/NUSNETID scratch2
You will notice that there are two new folders appear in your home directory, hpctmp and scratch2. Each of them has a capacity of at least 500GB available and can be increased upon request. However, do notice that the data in these two will be removed periodically (60 days) so it is extremely important to back up the hpctmp and scratch2 folder into your own/cloud storage.
Try to submit a VASP job¶
Submission of VASP jobs on the NUS HPC happens through a queuing system, based on PBS. What we want to do is using the qsub to submit our job to the computing node. Try to run this in order to submit the job following the submit_calculation.pbs script that prepared for you.
Some PBS commands are available here
Check job status¶
You can run qstat -x on NUS HPC to see the status of your job. In The “S” column (status), Q means that your job is queueing because NUS HPC is a shared server, R means that your job is running and F means that your job is finished (either success or fail).
Try to use the cat command to check the output of your files by running cat FILENAME, for example, the output of VASP is vasp.out so we need to run cat vasp.out. You will gradually understand it.
VASP tutorial¶
Try to do these tutorials