» High-throughput computational screening of MOFs for gas adsorption and separation
By Tang Hongjian, Department of Chemical & Biomolecular Engineering, Faculty of Engineering, on 24 September 2020
Metal–organic frameworks (MOFs) have emerged as a versatile material due to their structural diversity and facile tunability. For practical application, it is highly desired to identify the best candidates with targeted properties among ~100,000 MOFs that have been experimentally reported. High-throughput computational screening paves a way to such demand, which has been successfully implemented in a broader research domain. Such method has been validated as time-efficient and technically practical. It shortlists candidate structures from the whole MOF database to boost experimental synthesis and performance evaluation. Our group supervised by Prof. Jiang Jianwen is specialized in this field.
» Text Analytics Starting with NLTK
By Kuang Hao, Research Computing, NUS Information Technology, on 24 September 2020
NLP (Natural Language Processing) is not easy. When you are getting interested in it, immediately you realize that raw texts cannot be fed to our machine who only understands 0s and 1s. To make things harder, meaning of words can be ambiguous; sentences’ interpretation varies depending on the context; and there are hundreds of languages with different syntax & grammar rules. Fortunately, thanks to recent pioneers in NLP, there are standardized pipelines to follow and easy-to-use tools at hand.
This article introduces the most popular tools in NLTK, how to set up and use them, as well as its availability on our HPC clusters.
» Securing Your Data in The Cloud with Open-Source Software
By Yeo Eng Hee, Research Computing, NUS Information Technology, on 24 September 2020
The use of the Cloud to store data and to run HPC analysis jobs has become more pervasive, and one important question users of Cloud storage should ask is: “How secure is my data in the Cloud?”. While some cloud storage providers give users the assurance that their storage in the Cloud is encrypted, and some even provide encryption services and, key management services. It is always good to have an additional layer of assurance. We explore one such open-source tool for encrypting files and folders in the Cloud: Cryptomator, an open-source encryption tool that allows us to safely store the key to our data in our own computer, instead of in the Cloud.
» Command Line Tips 2
By Ku Wee Kiat, Research Computing, NUS Information Technology, on 24 September 2020
As HPC users, we often work in the Linux terminal. We need to be productive in a pure text environment where the only interface you can use to control it is the keyboard. What you enter is what you get, if you do not execute the command to list a directory’s contents, you will not know what is inside the directory. So how can we do the things in the most productive way? Yes, by using shortcuts!
» GANs and their applications
By Kumar Sambhav, Research Computing, NUS Information Technology, on 24 September 2020
Generative Adversarial Networks (GANs) are an approach to do generative modelling using deep learning methods. GANs comprise of competing neural networks that try to outperform each other at a given task. Given a dataset, GANs try to generate synthetic datasets which have similar statistical properties as the given dataset.
» Running Abaqus in HPC Cloud: A Personal Experience
By Tang Haibin, Research Fellow, Mechanical Engineering, on 24 September 2020
A personal account on how computational efficiency of research work is improved when running in HPC Cloud
» Hadoop on AWS: Benefits of EMR
By Kumar Sambhav, Research Computing, NUS Information Technology, on 15 May 2020
Managing Big Data on Hadoop clusters has seen a lot of paradigm shift in the recent times. From Sysadmin managed clusters at the command line level to on-prem centrally managed platforms like Cloudera, Hortonworks and MapR. All of these platforms have a primary problem of being dependent on physical hardware resources. Read on to discover how EMR addresses this shortcoming in the cloud.
» Tackling HPC issue for parallel computing in MATLAB
By Vamshidhar Gangu, Research Computing, NUS Information Technology, on 15 May 2020
Tips on how to run MATLAB Parallel Computing Toolbox jobs properly in our HPC cluster. Potential conflict between multiple concurrent jobs is addressed in this article.
» New Computational Cluster in the Cloud
By Yeo Eng Hee, Research Computing, NUS Information Technology, on 15 May 2020
Over the past few articles in the HPC Newsletter, I have been writing on Cloud resources and how computational jobs can be run in the Cloud. The Research Computing team here has been working hard to make the Cloud resources available to registered HPC users in a secure and simple way, so that our HPC workloads can be run in the Cloud as well.
» Friendly Email Alert for HPC Batch Jobs
By Wang Junhong, Research Computing, NUS Information Technology, on 15 May 2020
A customised email alerting function is developed and enabled in the HPC system to send an email alert reporting the summary of jobs completed in the last hour to an individual user. So the individual user can get almost instant updates of his/her jobs via email App on a mobile devices anytime anywhere. This overcomes the inconvenience where users need to log into the HPC system from a computer terminal to check. Other useful information of the jobs can also be added into the alert report. Read on for more details.