HPC NEWSLETTER
Rikky Purbojati, Research Computing, NUS Information Technology, on 17 April 2023
Artificial intelligence (AI) has been a popular topic of discussion for many decades, but with the advent of advanced algorithms and powerful computing systems, it has now become a reality. One of the most significant advancements in AI technology is the development of chatbots and language models like OpenAI’s ChatGPT. These systems have elevated people’s imagination beyond expectation and have the potential to revolutionise the way we interact with technology.
Ku We, Research Computing, NUS Information Technology, on 17 April 2023
AlphaFold2 has enabled structural modelling of proteins with accuracy comparable to experimental structures. A variety of modifications of AlphaFold2 have been developed to facilitate specific applications such as ColabFold (Mirdita et al., 2022), which accelerates the program and exposes useful parameters. AlphaFold-Multimer can also be applied to screen large datasets of proteins for new protein-protein interactions (PPIs) (Humphreys et al., 2021; Bryant, Pozzati, and Elofsson, 2022) and to model combinations and their fragments when modelling complexes (Mosalaganti et al., 2022).
Alphapulldown was developed as a Python package that streamlines PPIs screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.
Hu Zhengyu and Prof Pearl Li Yuzhu, Civil and Environmental Engineering, NUS, on 17 April 2023
Sea-level rise, extreme marine events, together with increasing flood risk due to climate change put coastal communities at a growing danger. Seawalls, which serve as a major coastal defense approach can effectively contribute to dissipating local hydrodynamic energy and protecting the shoreline from erosion. The existing seawalls are often designed to be hard structures. However, traditional seawalls have to suffer costly maintenance and repair, especially after extreme storms.
Therefore, investigating and optimising the characteristics of seawalls to improve their resistance against wave action is important.
Miguel Dias Costa, Research Computing, NUS Information Technology, on 17 April 2023
A common first reaction of new users to shared computing resources such as HPC clusters is to ask, “why can’t I just use yum/apt/etc. to install the software I need?”
Package managers like yum and apt require administrative access and naturally users of a shared resource cannot be given administrative access as they have in their own laptops and desktops, but that’s not the only reason not to use such package managers.
Rikky Purbojati, Research Computing, NUS Information Technology, on 24 May 2022
Quantum computing is undeniably one of the most hyped technologies in recent years. With seemingly frequent advancements and milestone announcements, this field has attracted billions of investments into both established and nascent quantum computing vendors. The penultimate promise of quantum computers is that they will enable the computation of intractable problems that classic computers cannot easily solve.
Ku Wee Kiat, Research Computing, NUS Information Technology, on 11 May 2022
In this article, we will cover how to train a segmentation model using Detectron2 on your COCO-annotated dataset on NUS HPC GPU Cluster.
Wang Junhong, Research Computing, NUS Information Technology, on 6 June 2022
Artificial Intelligence (AI) adoption and Machine Learning (ML) have become hot topics and trends in many domains. In NUS, many researchers and students are carrying out AI training for various research projects. In this article, three interesting AI training projects carried out in the central AI/GPU platform will be shared by the statistics nature of the performance of the AI training and the researchers’ valuable feedback. The three researchers are selected from the list of top AI/GPU users in Q1 of 2022.
Xie Weihang, Canepa Research Group, Department of Materials Science and Engineering, College of Design and Engineering, on 29 April 2022
The Vienna Ab initio Simulation Package (VASP) is a well-known and largely used software package for performing DFT calculations. VASP requires a significant amount of computing resources and was ranked top 5 used applications on NSCC (National Supercomputing Centre) in terms of CPU hours. Starting from version 6.2.0, VASP is officially capable of acceleration by GPU through the OpenACC port.
Pranab Kumar Das, Senior Research Fellow, Singapore Synchrotron Light Source, on 9 May 2022
I am a researcher at the Singapore Synchrotron Light Source of NUS, primarily working on experimental projects where we study the electronic band structure of various novel and functional materials by employing Spin- and Angle-Resolved Photoemission Spectroscopy (Spin-ARPES).
Kuang Hao, Research Computing, NUS Information Technology, on 17 May 2022
Anomaly detection is widely used in behavioural analysis to determine the types of anomalies occurring in a given data set. In domains such as fraud detection, intrusion detection, fault detection and system health monitoring, anomaly detection helps to avoid system damages and potential financial breaches.
Following up on our last article posted in 2020, we will introduce an additional complex machine learning algorithm in anomaly detection and demonstrate how we can do that on our HPC cluster in this article.
