The invisible microscopic enemy “COVID-19” is now got a fearsome opponent, “Supercomputer”. Computational Biology is about get a shot in the arm in fight against SARS-COV-2 (also known as COVID-19). The titleholder of world’s most powerful supercomputer, IBM Summit” has now joined the fight against COVID-19 in addition to crowdsource distributed supercomputing network from FoldingatHome (FAH). Housed in the US Department of Energy's Oak Ridge National Laboratory (ORNL), IBM Summit supercomputer is primarily assigned with task to solve some of the impractical or impossible tasks in fields of energy, advanced materials, human health, and artificial intelligence.
It’s precious computational time is now allocated to researchers to perform simulation at “unprecedented speed” sifting through thousands of molecules to find potentially druggable compounds that could fight against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the coronavirus responsible for the current COVID-19 pandemic.
Summit against COVID-19
With it’s million times computing power compared to any latest desktop or laptop, Summit allowed researchers to see results of sifting through molecules for druggable compounds in days than what would have otherwise taken months. As of today, researchers have identified 77 small-molecule drug compounds that the ORNL said might warrant further study in the fight against the SARS-CoV-2 coronavirus, which is responsible for the COVID-19 disease outbreak .
The Summit helped in simulation of 8000 compounds to screen for those that will bind to the main protein “Spike” of COVID-19 rendering it unable to infest host cells. The findings are published in a paper that is yet to be “peer reviewed” and available at the preprint server “ChemRxiv”. The SARS-CVO-2 virus surfaces are covered with spikey crown-like proteins which allows the virus to bind it to human cells herein ACE2 receptor . You can view the video herein to learn more.
The below diagram depicts the compound found (identified in gray colored) using Summit supercomputer simulation that binds to SARS-COV-2 spike-protein rendering it unable to infect ACE2 receptor (purple color).
Figure 1. The compound, shown in gray, was calculated to bind to the SARS-CoV-2 spike protein, shown in cyan, to prevent it from docking to the Human Angiotensin-Converting Enzyme 2, or ACE2, receptor, shown in purple. Credit: Micholas Smith/Oak Ridge National Laboratory, US Dept. of Energy. [Courtesy: ORNL]
Computational power of Summit has shortened the time for simulation in finding druggable compounds, now it is time for scientists to start further experiments. “Our results don’t mean that we have found a cure or treatment for the Wuhan coronavirus”, said Jeremy Smith. “We are very hopeful, though, that our computational findings will both inform future studies and provide a framework that experimentalists will use to further investigate these compounds. Only then will we know whether any of them exhibit the characteristics needed to mitigate this virus.”
Summit is considered the title holder of most powerful computer on earth. Housed at Oak Ridge National Laboratory (ORNL), Tennessee, the supercomputer is the size of two tennis courts and is capable of processing over 200 quadrillion calculations per second. It is used by researchers from modeling of supernova to crunching data for cancer and genetic research. Computational biology is not new but use of supercomputer of this kind for computational biology is very promising.
Supercomputing at IBM
The prelude to supercomputer at IBM starts in 1954 when IBM built a vacuum tube computer known as Naval Ordnance Research Calculator (NORC) for United States Navy's Bureau of Ordnance . It calculated upto 3089 digits which was a record at the time. Since then IBM produce a series of computational systems (please refer to figure 2) with most notable first supercomputer that challenged human brain power was deep blue developed in 1997. It defeated Garry Kasparov (a chess grandmaster and world chess champion at the time) at first round of the six games match though Gary won later three games. The next notable supercomputer was Watson developed in 2011 by IBM which challenged human brain power and own first prize in jeopardy competition.
Figure 2. A Brief history of supercomputing at IBM
In 2013, IBM announced that the first commercial application of Watson for the utilization of decisions in lung cancer treatment at Memorial Sloan Kettering Cancer Center, New York City . Following Watson, IBM built Sequoia supercomputer in 2012 and delivered to Lawrence Livermore National Laboratory (LLNL). It performed well against K Computer with 17.17 petaflops compared to 10.51 petaflops by K computer. Soon after Sequoia, IBM developed “Sierra” and it’s sibling “Summit” in 2018. Sierra was delivered to LLNL while Summit to ORNL. Sierra supports upto 4320 nodes for the system delivered to LLNL while Summit supports 4608 nodes. The peak performance of Sierra is 125 petaflops (PF) while performance of Summit is 200 PF. Both systems use NVIDIA GPUs and Mellanox Infiniband EDR.
Peeling the cover of Summit
The Summit supercomputer consists of 4,608 compute nodes each with two 22-core POWER9 (P9) processors and six NVIDIA Tesla V100 (Volta) GPUs. It uses 50Gb/s NVLink2.0 bus to connect each P9 CPU to three V100 GPUs and GPUs to each other as shown in figure 3.
Figure 3. Summit Compute Node Architecture (Larrea, et al., n.d.).
The CPUs are connected to 256 GB DDR4 memory and the system includes 1.6TB NVMe storage. For shared storage centralized Alpine GPFS file system (Larrea, et al., n.d.). Each compute node is stacked in a rack upto 18 x 2 RU compute nodes. The network architecture is build using flat tree topology as depicted in the figure 4.
Figure 4. Summit Supercomputer compute node and deployment architecture (Larrea, et al., n.d; Kahle & Dreps, 2019).
Both infiniband and Ethernet network connectivity provides storage and transport access respectively. The system has total of 256 rack, 10.2 PB memory and 250 Petabytes storage.
If you are interested to learn more, please watch this video.
- ZDNET, 2020. IBM Summit supercomputer joins fight against COVID-19. Available online at https://www.zdnet.com/article/ibm-summit-supercomputer-joins-fight-against-covid-19/
- Chowdhury, D., 2020. LEND POWER OF YOUR COMPUTER TO FIGHT COVID-19. Available online at http://www.dhimanchowdhury.com/2020/03/16/lend-power-of-your-computer-to-fight-covid-19/
- Wikipedia, 2020. IBM Naval Ordnance Research Calculator. Available online at https://en.wikipedia.org/wiki/IBM_Naval_Ordnance_Research_Calculator .
- Wikipedia, 2020. Watson (computer). Available online at https://en.wikipedia.org/wiki/Watson_(computer) .
- Larrea, et al., n.d. Larrea, V.G.V., Joubert, W., Brim, J. M., Budiardja, D. R., Maxwell, D., Ezell, M., Zimmer, C., Boehm, S., Elwasif, W., Oral, S., Fuson, C., Pelfrey, D., Hernandez, O., Leverman, D., Hanley, J., Berrill, M. & Tharrington, A., n.d. Scaling the Summit: Deploying the World's Fastest Supercomputer? Available online at https://www.osti.gov/servlets/purl/1561654 .
- Kahle, A. J., Moreno, J. & Dreps, D., 2019. Summit & Sierra: Designing AI/HPC Supercomputers. IEEE International Solid-State Circuits Conference: ISSCC 2019 / SESSION 2 / PROCESSORS / 2.1.