Supercomputer for biomedicine
I-SCALARE Laboratory at MIPT
achieved new research successes
The project is being implemented with the participation of employees of MIPT and Intel Corporation, and the RSK group of companies has developed and installed an innovative computing cluster used to conduct the entire spectrum of research within the framework of the laboratory.
Bioinformatics and drug modeling are among the fastest growing areas where there is an urgent need to use high-performance computing on supercomputers.
The relevance of the research conducted on the basis of the I-SCALARE laboratory is that breakthroughs in the field of new methods of medical diagnostics, treatment, creation of new drugs, etc. are possible only with the development of new computational models and platforms that take into account the specifics of bio-medical-pharmaceutical tasks.
The joint implementation of this project by employees of MTFI, specialists of Intel Corporation and the RSK group of companies undoubtedly allows us to bring research in this area to a new level.
"The I-SCALARE laboratory, under the handiwork of Vladimir Pentkovsky, has been tasked with solving important problems in the field of modern bioinformatics," said Nikolai Nikolaevich Kudryavtsev, Rector of the Moscow Institute of Physics and Technology. – The professionalism, dedication and enthusiasm of the team contribute to the successful solution of the tasks set."
The new scientific results achieved by the laboratory staff after the start of using the upgraded supercomputer and further development prospects were presented at a press conference held at MIPT with the participation of Intel Corporation and the RSK Group of companies. Sergey Nikolayevich Garichev, Dean of the Faculty of Radio Engineering and Cybernetics (FRTC), at which the I-SCALARE laboratory was established, delivered a welcoming speech and a story about the tasks and prospects for the development of scientific activities.
Kamil Isaev, General Director for Research and Development of Intel Corporation in Russia, presented the main activities of the I-SCALARE laboratory, created at MIPT with the participation of Intel. The main one is the development of problem-oriented architectures of computing systems for biomedicine, pharmacology and small-sized structures. Several applied computational tasks related to the modeling of viruses, cell membranes, as well as the interaction of proteins and external fields with cell membranes were selected as "targets". All of them, on the one hand, have great practical value, and on the other hand, they cannot be solved on the available computing resources and require new approaches to cluster architecture.
For example, a research group led by Professor Roman Efremov at the Institute of Bioorganic Chemistry of the Russian Academy of Sciences uses the upgraded computing cluster of the I-SCALARE laboratory at MIPT for research in the field of designing a new class of antimicrobial compounds based on natural lantibiotics. During the development of this project, calculations and modeling, microsecond trajectories of the molecular dynamics (MD) of the target of the action of antibiotics (lipid-II molecules) in the bacterial membrane were obtained.
The use of the updated supercomputer of the I-SCALARE laboratory makes it possible to obtain trajectories of such duration for systems containing more than 50 thousand atoms in about a week. For comparison, on a computing cluster based on Intel® Xeon® E5450 processors of the previous generation, which is currently actively used at IBH RAS, such a calculation would take about 100 days, that is, now, thanks to the high performance of the new computing cluster, the speed of obtaining scientific results has increased by more than 14 times. Analysis of the obtained MD trajectories allowed us to establish the characteristic features of the structure of the bacterial membrane. This year, a more detailed simulation of the interaction of lantibiotics with lipid-II in the membrane will be carried out on the upgraded supercomputer of the I-SCALARE laboratory. In the future, such studies may lead to the creation of a new class of antibiotics that are not susceptible to the appearance of resistance in bacteria.
About the problem of modeling the structure of the protein envelope and molecular dynamics of viruses of the Flavivirus type dangerous to humans (for example, Dengue fever virus) and the processes of their interaction with body cells, solved on a new powerful supercomputer of the I-SCALARE laboratory by scientists of the research group of the Faculty of Chemistry of Lomonosov Moscow State University under the leadership of academician N.S. Zefirov, told leading researcher V.A. Palyulin.
In the course of the conducted research, molecular models of the virion membrane and a fragment of the protein envelope, including millions of atoms, were constructed. This made it possible to obtain information about the spatial structure of the viral protein that is not available by experimental methods, and then analyze its dynamic behavior and the binding of molecules to it that prevent the fusion of flaviviruses with human cells. Based on such models, a computer search for potential inhibitors of tick-borne encephalitis virus fusion was carried out and promising compounds that showed the necessary activity in in vitro tests were identified.
As part of the work on the design of new neuroprotective substances, models of the complete structure of the NMDA receptor are constructed, its molecular dynamics in a phospholipid membrane with an aqueous environment is simulated using a supercomputer, as well as interactions with known neuroprotectors (the system includes hundreds of thousands of atoms). The regularities of the relationship of their structure with activity have been studied, a possible mechanism of action of receptor modulators has been proposed, and on this basis, a search is being conducted for new promising structures with neuroprotective activity. Such structures can serve as a basis for the future development of drugs for the treatment of severe neurodegenerative diseases, in particular Alzheimer's disease.
Grigory Rechistov, a post-graduate student at MIPT, told about the principles of architecture modeling and the results achieved. The main result of the modeling group's research is the development of a methodology for studying the operation of applications on next-generation supercomputer computing systems in advance, even before their physical availability. The experimental results obtained so far allow us to fully characterize the possibility of applications running on computing complexes that include 16 times more processor cores than are physically present in the cluster used. Thus, the technique allows you to study computer systems with a capacity of up to 665 TFLOPS.
Computer system modeling technologies developed on the basis of the Wind River Simics software product will allow architects and users of supercomputer systems to have the means to measure full performance, find bottlenecks limiting it, and evaluate the effects of using optimizations. As a result of this analysis, it becomes possible to make decisions about the compliance of the selected hardware configuration for solving practical scientific problems.
Creation of an innovative computing cluster at MIPTThe RSK Group of Companies, a leading developer and integrator of a "full cycle" of new-generation supercomputer solutions based on Intel Corporation architectures and advanced liquid cooling, developed and installed a pilot system based on advanced technology in 2011 in the laboratory of supercomputer technologies for biomedicine, pharmacology and small-sized structures in the framework of a contract with MIPT. the architecture of "RSK Tornado" and processors of the previous generation of the Intel® Xeon® 5600 family.
This year it was upgraded to the level of a powerful computing cluster, which is a complete solution of the RSK Minicode class with a peak performance of 41.57 TFLOPS. This system ranks 20th in the current edition of the Top50 list of the most high-performance supercomputers in Russia and CIS countries (March 2012).
The upgraded cluster of the I-SCALARE laboratory consists of 112 computing nodes based on two new–generation Intel® Xeon® E5-2690 processors (a total of 224 processors, 1792 cores). The use of these most high–performance processor models of the new Intel® Xeon® E5-2600 server family became possible precisely thanks to the use of advanced liquid cooling, which is the basis of the RSC Tornado architecture. At the same time, a large amount of RAM per node is provided – 64 GB (in the pilot system there were 36 GB per node), which totals 7.1 TB of RAM.
According to Alexander Moskovsky, CEO of RSK Technologies, a member of the RSK group of companies, this MIPT supercomputer is based on the innovative architecture of RSK Tornado. This is the world's first energy-efficient supercomputer solution with advanced liquid cooling for mass-available standard server boards based on Intel® Xeon® processors, originally created for traditional systems with air-blown electronic components. The architecture of RSK Tornado provides flexibility in the configuration of computing nodes with standard interfaces and ease of building a solution, high maintainability (ease of replacing RAM modules and increasing its volume, updating to new processor models), the ability to integrate with any external products with standard interfaces (PCI Express).
At the moment, the updated cluster system at MIPT is equipped with a data storage system with a capacity of 10 TB (previously it was 3 TB), and the communication network is based on the high-speed Infiniband QDR interface. The architecture of RSC Tornado provides this computing cluster with the following unique characteristics:
- Simplicity and high reliability;
- Economic efficiency;
- High energy efficiency is a record indicator of energy efficiency (PUE) of less than 1.2, that is, no more than 20% of energy consumption will be spent on cooling;
- Compact and high density;
- A large coefficient of computational efficiency – more than 90% on the LINPACK test;
- High scalability;
- The possibility of using accelerators (Intel® MIC architecture).
About the history of the creation of the I-SCALARE laboratory at MIPTIn 2010, Intel Corporation employee Vladimir Pentkovsky, together with MIPT scientists, submitted to the competition announced by the Ministry of Education and Science of the Russian Federation as part of the implementation of Russian Government Decree No. 220, a program for the research and development of software and hardware architectures that would be most effective in solving complex bioinformatics and pharmacology problems that require large computing resources.
Vladimir Pentkovsky, a well-known developer of software and hardware architectures, an honored Intel researcher, has extensive experience in creating research teams in Russia, the USA and India. He owns 40 international patents, which confirms his high authority. The project of Dr. Pentkovsky, who acted as the head of the project team, was among the 40 winners and received a grant of 150 million rubles. to create a laboratory at MIPT and conduct research on the project proposed by him. In total, more than 500 applications were submitted for the competition.
Intel Corporation has been actively cooperating with Russian universities for a long time in the field of scientific research, the introduction of new curricula, the formation of an ecosystem of innovations through the cooperation of higher education institutions and industry. Intel is the base organization for the Faculty of Radio Engineering and Cybernetics of MIPT, therefore, a joint project with allocated state funding has become a logical development of this cooperation.
It is worth noting that the I-SCALARE laboratory carries out not only scientific, but also educational activities. Its employees have developed a training course on the use of simulators for modeling various computing systems. In addition, scientific seminars are regularly held in the laboratory, and Vladimir Pentkovsky became the supervisor of several graduate students and students of MIPT.
Portal "Eternal youth" http://vechnayamolodost.ru31.05.2012