High Performance Computing (HPC) Malaysia

Consultant of VYROX HPC and Quantum Molecular Dynamics

Dr. Tang Wai Kit, City University of Hong Kong
Quantum Chemistry
Molecular Dynamics
Computer Aided Molecular Simulations
Supercomputers Clustering
High-performance Computing (HPC)
Data Intensive Computing (DIC)
https://scholar.google.com/citations?user=E11TLncAAAAJ&hl=en&oi=sra

High-Performance Computing (HPC) is defined as an ability of a computer system to process large-scale data, and to perform complex calculations at super high speeds. HPC parallelizes sequential codes into multi-threaded codes and run them simultaneously on multiple processors and shared memory via Message Passing Interface (MPI) in order to result the super high speed computing power in combined.

VYROX consults and deploys HPC solutions for universities and institutions in Malaysia. we engineer, supply, and install for laboratories of research, development, and test. Overall, VYROX has three types of HPC solutions at different level of costs that designed to fit to your budget and requirements. Beside the HPC machines, VYROX designs also the key HPC engineering requirements like power, cooling, ventilation, ELV, network, IoT-based security, and safety for an efficient, scalable, and flexible HPC/supercomputer/server rooms.

How to build a HPC that fits?

Building an inappropriate HPC setup is a common problem of universities and research institutes in Malaysia. A wrong HPC build would lead to unnecessary computational capacity and energy waste. Hence, it is important to know the desired HPC characteristics beforehand.

If your tasks are interruptible, or you want to do many things at once, go for concurrency. “Concurrency of HPC is defined as the ability of a computer system to process multiple calculations at the same instance.” Practical Implication: Build with more computers as one.

If your tasks are Independent, or you want to get single task done faster, go with parallelization. “Parallelization of HPC is defined as the breakdown of a calculation into smaller parts and compute them with multiple computers.” Practical Implication: Build with more processor cores as one.

Rating of Builds:

Serial (Worst)
Parallel (Fair)
Concurrent (Good)
Concurrent + Parallel (Better)

If you still do not know what to do? Just focus on concurrency as it will solves most of your unknowns (Rob Pike, 2013).

VYROX HPC Engineering Services:

Supply and install high-performance computers.
Setup and configure HPC clusters.
Design and build HPC infrastructure (structured wiring, structured cabling, HVAC, etc.)
Supply and install IoT-based security and safety systems of HPC rooms.
Supply and install HPC facility booking and management software.
HPC technical support and machine maintenance services.

VYROX HPC-based Computational Quantum Chemistry Services:

Quantum molecular dynamic simulation (Dresselhaus, Bungey, Knowles, & Manby, 2020; Kühne et al., 2020; Ramesh et al., 2020).
Classical molecular dynamic simulations.
Biological simulation (eg. enzymes, drugs, vaccines, etc.).
Materials simulation and design (eg. battery cells, solar cells, water splitting cells, etc.).
Bioinformatics (eg. patternizing mechanism and actions of gene, protein, etc. ).
Workshops, seminars, webinars, training courses, and consultation services.

Source: https://www.youtube.com/watch?v=dqKWfXsEcWs

Source: https://www.youtube.com/watch?v=17QpHFoQKMM

VYROX HPC-based Artificial Intelligence Services:

Deep neural network machine learning.
Computer vision (eg. object detection, tracking, recognition, etc.).
AI-based biometric machine learning.
AI-Based speech/voice recognition.

References

Dresselhaus, T., Bungey, C. B., Knowles, P. J., & Manby, F. R. (2020). Coupling electrons and vibrations in molecular quantum chemistry. The Journal of Chemical Physics, 153(21), 214114.

Kühne, T. D., Iannuzzi, M., Del Ben, M., Rybkin, V. V., Seewald, P., Stein, F., . . . Schiffmann, F. (2020). CP2K: An electronic structure and molecular dynamics software package-Quickstep: Efficient and accurate electronic structure calculations. The Journal of Chemical Physics, 152(19), 194103.

Ramesh, P., Lydia Caroline, M., Muthu, S., Narayana, B., Raja, M., & Aayisha, S. (2020). Spectroscopic and DFT studies, structural determination, chemical properties and molecular docking of 1-(3-bromo-2-thienyl)-3-[4-(dimethylamino)-phenyl]prop-2-en-1-one. Journal of Molecular Structure, 1200, 127123. doi:https://doi.org/10.1016/j.molstruc.2019.127123

Akhgarnusch, A., Tang, W. K., Zhang, H., Siu, C. K., & Beyer, M. K. (2016). Charge transfer reactions between gas-phase hydrated electrons, molecular oxygen and carbon dioxide at temperatures of 80–300 K. Physical Chemistry Chemical Physics, 18(34), 23528-23537.

Chu, I. K., Siu, C. K., Lau, J. K. C., Tang, W. K., Mu, X., Lai, C. K., ... & Siu, K. M. (2015). Proposed nomenclature for peptide ion fragmentation. International Journal of Mass Spectrometry, 390, 24-27.

Demissie, E. G., Tang, W. K., & Siu, C. K. (2019, July). Enhancing GaSe Catalysis for Hydrogen Evolution Reaction via Ni Doping and External Electric Field. In 5th International Conference on Advanced Materials Modelling, ICAMM 2019.

Demissie, E. G., Tang, W. K., & Siu, C. K. (2019, May). Reactivity of Hydrated Monovalent Cobalt (I) Toward Nitrous Oxide in the Gas Phase. In 26th Symposium on Chemistry Postgraduate Research in Hong Kong.

Dresselhaus, T., Bungey, C. B., Knowles, P. J., & Manby, F. R. (2020). Coupling electrons and vibrations in molecular quantum chemistry. The Journal of Chemical Physics, 153(21), 214114.

Herber, I., Tang, W. K., Wong, H. Y., Lam, T. W., Siu, C. K., & Beyer, M. K. (2015). Reactivity of hydrated monovalent first row transition metal ions [M (H2O) n]+, M= Cr, Mn, Fe, Co, Ni, Cu, and Zn, n< 50, toward acetonitrile. The Journal of Physical Chemistry A, 119(22), 5566-5578.

Lai, C. K., Tang, W. K., Siu, C. K., & Chu, I. K. (2020). Evidence for the Prerequisite Formation of Phenoxyl Radicals in Radical‐Mediated Peptide Tyrosine Nitration In Vacuo. Chemistry–A European Journal, 26(1), 331-335.

Mu, X., Tang, W. K., Dong, N., Li, M., Siu, C. K., & Chu, I. K. (2019). Cα–Cβ bond cleavage occurs at the side chain of the N-terminal phenylalanine residue during CID of tyrosine-containing peptide radical cations. International Journal of Mass Spectrometry, 435, 333-341.

Tang, W. K., Chau, M. C., & Siu, C. K. (2019). Role of water in molecular oxygen activation in hydrated chromium (I) cluster ions: A theoretical insight. International Journal of Mass Spectrometry, 436, 118-126.

Tang, W. K., Leong, C. P., Hao, Q., & Siu, C. K. (2015). Theoretical examination of competitive β-radical-induced cleavages of N–Cα and Cα–C bonds of peptides. Canadian Journal of Chemistry, 93(12), 1355-1362.

Tang, W. K., Mu, X. Y., Chu, I. K., & Siu, C. K. (2019, May). Dissociation of N-terminal Cα-Cβ bond induced by electron transfer between N-terminus and tyrosine side chain in molecular peptide radical cation. In 26th Symposium on Chemistry Postgraduate Research in Hong Kong.

Tang, W. K., Mu, X., Li, M., Martens, J., Berden, G., Oomens, J., ... & Siu, C. K. (2020). Formation of n→ π+ interaction facilitating dissociative electron transfer in isolated tyrosine-containing molecular peptide radical cations. Physical Chemistry Chemical Physics, 22(37), 21393-21402.

TANG, W. K., SIU, C. K. A., Van Der Linde, C., & Beyer, M. K. (2018, June). Electrons Mediate The Gas-Phase Oxidation of Formic Acid with Ozone. In HKSMS Symposium 2018.

Tang, W. K., van der Linde, C., Siu, C. K., & Beyer, M. K. (2017). Hydration Leads to Efficient Reactions of the Carbonate Radical Anion with Hydrogen Chloride in the Gas Phase. The Journal of Physical Chemistry A, 121(1), 192-197.

Tang, W. K., Van Der Linde, C., SIU, C. K. A., & Beyer, M. K. (2018, June). Kinetics of the reaction of CO3•–(H2O) n, n= 0, 1, 2, with nitric acid, a key reaction in tropospheric negative ion chemistry. In HKSMS Symposium 2018.

Thompson, H., Tang, W. K., & Siu, C. K. (2018, April). Theoretical Examination on Reaction Mechanisms of Hydrated Cobalt (I) with Nitrous Oxide in the Gas Phase. In 25th Symposium on Chemistry Postgraduate Research.

van der Linde, C., Tang, W. K., Münst, M. G., Ončák, M., Siu, C. K., & Beyer, M. K. Chemistry and Spectroscopy of Hydrated CO3-Radical Anions Investigated with FT-ICR Mass Spectrometry.

Xu, M., Tang, W. K., Mu, X., Ling, Y., Siu, C. K., & Chu, I. K. (2015). α-Radical-induced CO2 loss from the aspartic acid side chain of the collisionally induced tripeptide aspartylglycylarginine radical cation. International Journal of Mass Spectrometry, 390, 56-62.

Yu, X., Chau, M. C., Tang, W. K., Siu, C. K., & Yao, Z. P. (2018). Self-Assembled Binuclear Cu (II)–Histidine Complex for Absolute Configuration and Enantiomeric Excess Determination of Naproxen by Tandem Mass Spectrometry. Analytical chemistry, 90(6), 4089-4097.