NEWS HIGH-PERFORMANCE COMPUTING NERSC finalises supercomputer contract
The National Energy Research Scientific Computing Center (NERSC), the mission high-performance computing facility for the US Department of Energy’s Office of Science, has moved another step closer to making its next-generation GPU-accelerated supercomputer, Perlmutter, available to the science community in 2020. In mid-April, NERSC finalised its contract
with Cray – which was acquired by Hewlett Packard Enterprise (HPE) in September 2019 – for the new system, a Cray Shasta supercomputer that will feature 24 cabinets and provide 3-4 times the capability of NERSC’s current supercomputer, Cori. Perlmutter will be deployed at NERSC
in two phases: the first set of 12 cabinets, featuring GPU-accelerated nodes, will arrive in late 2020; the second set, featuring CPU-only nodes, will arrive in mid-2021. A 35-petabyte all-flash Lustre-based file system using HPE’s ClusterStor E1000 hardware will also be deployed in late 2020. ‘We are excited about the progress our
applications teams are making optimising their codes for current and upcoming GPUs,’ Deslippe said. Across all of our science areas we are
seeing applications where a V100 GPU on Cori is outperforming a CPU Cori node by five times or greater. These performance gains are the result of work being done by tightly coupled teams of engineers from the applications, NERSC, Cray, and NVIDIA. The enthusiasm for GPUs we are seeing from these teams is encouraging and contagious.’ Since announcing Perlmutter in October
LABORATORY INFORMATICS Transforming a clinical lab into a Covid-19 ready lab
L7 Informatics and Contamination Source Identification (CSI) have partnered to accelerate the implementation of testing for Covid-19. L7 Informatics, a
provider of in data and workflow management, and Contamination Source Identification (CSI) are deploying ‘ready to go’ Covid-19 workflows based on the CDC testing protocol for testing laboratories supporting coronavirus patient screening. Vasu Rangadass, CEO of L7, said: ‘We are pleased to have CSI as our partner in developing Covid-19 testing
workflows using the ESP platform. As testing reagent shortages are addressed, laboratory capacity will become the limitation in diagnosing Covid-19. We decided to make these workflows available to ensure broad access to these critically important tests.’ Through a partnership
with CSI, L7 has developed and qualified an integrated workflow for performing Covid-19 diagnostic testing based on the CDC recommended protocols. L7’s Enterprise Science Platform (ESP) is used to digitise Covid-19 testing procedures, connect testing processes
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with laboratory instruments and software systems, and integrate data management and reporting. ESP’s process engine supports standardising laboratory processes while providing flexibility to local laboratories to rapidly adapt protocols without the need of software programming. Justin Wright, Co-Founder
of CSI said: ‘This rapid response would not have been possible without the dedicated efforts from our partners at L7, who have worked with us in real-time to develop a comprehensive LIMS platform that permits efficient and accurate processing of our critical samples.’
2018, NERSC has been working to fine-tune science applications for GPU technologies and prepare users for the more than 6,000 next-generation NVIDIA GPU processors that will power Perlmutter alongside the heterogeneous system’s AMD CPUs. Nearly half of the workload currently running at NERSC is poised to take advantage of GPU acceleration, and NERSC has played a key role in helping the broader scientific community leverage GPU capabilities for their simulation, data processing, and machine learning workloads. At the core of these efforts is the NERSC
Exascale Science Applications Program (NESAP). NESAP partnerships allow projects to collaborate with NERSC and HPC vendors by providing access to early hardware, prototype software tools for performance analysis and optimisation, and special training. Over the last 18 months, NESAP teams have been working with NERSC staff and NVIDIA and Cray engineers to accelerate as many codes as possible and ensure that the scientific community can hit the ground running when Perlmutter comes online. As part of NESAP, in February 2019
NERSC and Cray also began hosting a series of GPU hackathons to help these teams gain knowledge and expertise about GPU programming and apply that knowledge as they port their scientific applications to GPUs. The fifth of 12 scheduled GPU hackathons was held in March at Berkeley Lab. Located at Lawrence Berkeley National
Laboratory, NERSC is a DOE Office of Science user facility.
LABORATORY INFORMATICS
Optibrium adopts cheminformatics toolkits from OpenEye Scientific
Optibrium and OpenEye Scientific (OpenEye), have announced efforts to integrate their software platforms to provide scientists with added functionality for small molecule drug discovery. StarDrop, Optibrium’s software for small molecule design, optimisation and data analysis, is now powered by OpenEye Scientific’s cheminformatics toolkits. These cheminformatics libraries will assist StarDrop users to more effectively harness computational software suite to meet the demands posed by future drug discovery projects. Dr Anthony Nicholls, OpenEye
Scientific’s CEO, said: ‘It’s always exciting when we get the opportunity to empower great people with the same foundational software platform that has allowed us to grow and develop for the last 20 years. Optibrium has always had a fantastic product in StarDrop, and it’s an honour to be a part of what they offer to the pharmaceutical industry.’ StarDrop, is an integrated software package deployed by pharmaceutical and biotech companies to support their drug discovery programs. StarDrop’s integration of the libraries and toolkits developed by OpenEye Scientific, including OEChem, OEDepict and OMEGA, enables accelerated development of Optibrium’s in silico drug discovery technologies and artificial intelligence services. OpenEye Scientific is an industry leader in the field of cheminformatics software for drug discovery, providing high-performance and robust libraries with a developer-friendly Application Programming Interface, supporting the development of highly customisable software solutions and workflows. The company directly supports pharmaceutical and biotechnology companies as well as making its cheminformatics platform available to software companies, such as Optibrium, enabling high- performance cheminformatics software solutions. The companies will work together
to leverage future opportunities to advance their respective platforms.
Summer 2020 Scientific Computing World 33
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