Nimbix Blog

Super musing about all things supercomputing

How Big Compute Helps Genomics

Big Compute HPC applicationsModern science involves sorting through mountains of data, and nowhere is this truer than in the study of genes. Modern computers have enough power to make sequencing an organism’s genome fairly easy, but that wasn’t always the case. The best way to see the difference computing power can make is to look at the Human Genome Project.

The Human Genome Project

The Human Genome Project had a simple goal. The scientists wanted to sequence every euchromatic gene in the human genome, a process that involved analyzing more than three billion base pairs of nucleotides. The scientists hoped to do it within fifteen years, but technological developments allowed them to pull it off in only thirteen.

Gene sequencing relies on a process that breaks DNA into relatively small sections. It’s possible to use chemical markers to identify the individual base pairs in a small sequence, but large sequences are impossible because it’s impossible to tell where each marker landed. Once the researchers have figured out each small sequence, they can find overlapping sections and use that information to reconstruct the entire chain.

When the project started, researchers had to do that by hand. They quickly developed programs that could automate it, but their core method was still fairly slow. Researchers realized that they were unlikely to finish within fifteen years, which brought the Celera Corporation into the picture. Celera used new programs that could handle huge sections of DNA by matching the ends of long sequences instead of looking for overlap in a variety of small sections.

That method required a lot of computing power. Celera needed a computer with about 700 linked processors to run their program, but it was enough to finish the project in nine months. A weaker computer would have taken much longer, and modern computers can do it much faster. The most powerful modern systems can sequence an individual’s genome in merely 26 hours!

How Nimbix Helps

That sort of feat requires a massive amount of computing power, but modern services such as Nimbix are making it more common. Nimbix is a cloud computing system designed to provide that power and turnkey access to important tools. Our cloud platform makes it easy to work through complex technical problems, which has the potential to make genomics even easier in the future.


bioinformatics applications nimbix

Nimbix offers turnkey bioinformatics workflows that don’t require IT skills to set up.   Our cloud is optimized for bioinformatics processing tasks such as gene sequencing.  Results can be up to 15 times faster than other cloud solutions. One popular example is to use SMRT Portal from Pacific Biosciences, a browser-based application on the Nimbix Cloud to create, submit and monitor secondary analysis jobs as well as view and download the results. With this tool, you can align reads to a reference sequence or assemble reads into a de novo genome.  You can also create interactive visualizations of assembly graphs with Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily).

Getting started on the Nimbix Cloud is easy.  Click here to create your free account then view and choose from our library of applications that will help you visualize and conduct your research.

Trends in the AI Revolution from 2016

Artificial Intelligence TrendsThe AI Revolution is in full swing.  We are lucky to see a lot of activity in the AI Revolution first-hand as the premier cloud provider for accelerated computational resources. 2016 has been an incredible year for machine learning. We have seen powerful frameworks continue to mature. The next generation of GPUs, crafted and designed by NVIDIA for the purpose of accelerating deep learning pipelines, have been released and are available publicly in the cloud. And the quantity of data continues to explode far beyond the capabilities of our incredible computing resources of today.  Machine learning and deep learning were also among some of the hottest topics at Supercomputing 2016.

The three biggest AI trends that we have seen are:

1. Frameworks

The top frameworks are maturing rapidly. Caffe, Torch, and Tensorflow are the three most popular frameworks that we have seen in both academia and industry. Our users have built everything from simple on-demand web services using the JARVICE API to entire businesses based around these powerful machine learning frameworks. Tensorflow’s architecture departs from the traditional deep learning mold and provides really powerful mechanisms for different types of training and inference architectures.  These three frameworks are on the verge of being able to support distributed GPU computations out of the box, and this should drive some powerful innovation in 2017 by being able to leverage technologies such as NVLink and Infiniband RDMA.

2. Accelerators

GPUs and accelerators such as FPGAs are ushering in massively parallel computational capabilities. In 2016, NVIDIA released its new Pascal architecture GPUs, the NVIDIA Tesla P100s. Nimbix has IBM Power8 machines with 4 x P100s available on-demand connected with NVLink for inter-GPU communication, and FDR Infiniband for distributed communication across machines. Our library of on-demand, turn-key applications for Minsky+NVIDIA P100s includes Power AI and NVIDIA DIGITS, and custom applications can be deployed with a simple git push to Github. The NVIDIA P100s are optimized for convolutional neural networks and matrix multiplication with better throughput and memory performance than ever before. 2017 will have a lot of exciting development in hardware acceleration. Much like Google’s Tensorflow Processing Unit (TPU), which is a CPLD, specialized FPGAs in the cloud make it possible to iterate faster than ever by designing specialized logic to accelerate challenging deep learning problems.

3. Massive Data

Data sets are continuing to grow, and almost every industry wants a bite of the AI Revolution apple. As any newcomer to this space will quickly learn, data has mass and moving it around can easily be the bottleneck of your algorithm. New architectures are being envisioned to address this in innovative ways. As the world becomes more connected with IoT sensors of all shapes and sizes, real-time data processing architectures will continue to grow to process and respond to this data more effectively. Machine learning experts will focus on developing algorithms to train more effectively on less data while computational capabilities continue to improve.

We can’t wait to see the innovations in machine learning, deep learning, and artificial intelligence in 2017. What trends have you noticed in AI and machine learning throughout 2016 and what are your predictions for 2017? Tweet us @nimbix!

Nimbix Appoints Stacy Repult as Chief Financial Officer

Stacy Repult, CFORICHARDSON, Texas, Dec. 13, 2016 /PRNewswire/ — Nimbix, a leading HPC cloud platform provider today announced the appointment of Stacy Repult as Chief Financial Officer (CFO).

Repult brings more than 20 years of experience at both public and private companies in financial management, strategic planning, international expansion and corporate development.  Most recently, Repult was Vice President of Finance for Omnitracs where she led the FP&A, tax and treasury departments.  Previously, she held the Managing Director position at SLR Consulting Group where she focused on supporting small to mid-market companies through high growth initiatives.

In her new role as Chief Financial Officer, Repult will be responsible for overseeing all the corporate financial accounting, HR and financial operations for Nimbix. Specifically, she will be tasked with driving business operating mechanisms to monitor and improve key financial metrics and profitability. Repult will also oversee the annual business and strategic planning processes.

“I am very pleased to have Stacy join the Nimbix leadership team,” said Steve Hebert, CEO of Nimbix. “Stacy’s deep experience in finance and operations will serve to further strengthen Nimbix as we continue on a path of rapid growth, particularly as we help enterprises accelerate their adoption of machine learning workflows.”

“I am excited to join the Nimbix team and look forward to helping to manage the financial controls and operational discipline which is paramount to our continued success in scaling the business and growing profitably,” said Stacy Repult, CFO of Nimbix.

Nimbix provides on-demand and scalable compute resources that enable organizations to run large-scale High Performance Computing (HPC) workloads in the cloud. HPC allows scientists, developers, and engineers to solve complex science, engineering, development, big data, and business problems using applications that require high compute capabilities. Nimbix’s growing number of integrated platform services allows organizations to increase the speed and effectiveness of research by running high performance computing in the Nimbix Cloud.

About Nimbix

Nimbix is a leading provider of purpose-built cloud computing for big data and computation. Powered by JARVICE™, the Nimbix cloud provides high performance software as a service, dramatically speeding up data processing for Energy, Life Sciences, Manufacturing, Media and Analytics applications. Nimbix delivers unique accelerated high-performance systems and applications from its world-class datacenters as a pay-per-use service. Additional information about Nimbix is included in the company overview, which is available on the Nimbix website at https://www.nimbix.net.

Nimbix Turned up the Fun at SC16

Over 11,000 attended SC16 in November we are thrilled to have been a part of it!

Nimbix SC booth

This was our 4th year attending SC and our first year exhibiting.  Our booth had a steady flow of guests including current customers, partners including NVIDIA and Xilinx, as well as students excited to learn about supercomputing in the cloud.  Guests were encouraged to watch workflows demos on one of our four devices in our booth.  Once a guest watched a 2-3 minute workflow, they often asked questions and dove further into the Nimbix Cloud with a Nimbix team member lading the way.

Booth guests enjoyed listening to educational presentations by Nimbix CEO and CTO, as well as partners including IBM, Mellanox, NVIDIA, and Xilinx, with great Q&A sessions after each presentation.

Nimbix SC presentation area

Nimbix SC booth presentation

Excited University students participated in what we know as the 1st ever SC Mannequin Challenge, at our booth, and many students were simply thrilled to don a Nimbix hat out and about in Salt Lake City.  Imagine the look on our faces when we saw people at the airport wearing a Nimbix beanie!  We’re glad to keep heads and ears warm.

Nimbix SC presentation area

Nimbix was presented with an HPCWire Editor’s Choice award for Best Use of HPC in the Cloud.  We are proud to be recognized for our use of HPC in the cloud and will continue to be innovative and be a leader in the space.

HPCWire award

One lucky booth guest went home with a 12″ iPad Pro and Apple Smart Keyboard, our grand prize giveaway!

Our 4th annual SC lounge party was a huge success with over 400 registrants and those who attended left with new friends, connections, and smiles on their faces.  Nimbix’s annual SC lounge party is often referred to as “the lounge party to attend” during SC.   We hope to see you at our next SC lounge party.

Nimbix SC lounge party

Read what Nimbix CEO and CTO have to say about SC16:

“We enjoyed having the opportunity to meet with customers and partners at SC16 as well as learn about areas of interest for different organizations.  Machine Learning is clearly the next big thing in the Supercomputing/HPC space, so getting the chance to speak with organizations that are focused in this domain was very useful.” – Steve Hebert, CEO, Nimbix

“The evolution of HPC away from traditional clusters into more dynamic services like what Nimbix offers, no doubt driven by new use cases such as machine learning, was encouraging.” – Leo Reiter, CTO, Nimbix

 

We’ll send you on your way with this… 

We nailed #SC16 first ever mannequin challenge!

A video posted by Nimbix, Inc. (@nimbix) on

Nimbix Teams with Xilinx to Expand FPGA-Based Workload Acceleration in the Cloud

Collaboration will deliver on-demand access to FPGA-based accelerators and development tools for machine learning, data science, and other compute workloads

RICHARDSON, TexasNov. 14, 2016 /PRNewswire/ — Nimbix, a leading HPC cloud platform provider today announced the immediate availability of the Xilinx SDAccel™ development environment for on-demand development, testing, and deployment of FPGA-accelerated workflows in the Nimbix Cloud, powered by JARVICE.  The SDAccel development environment combines the industry’s first architecturally optimizing compiler supporting any combination of OpenCL, C, and C++ kernels, along with libraries, development boards and industry standard development and run‐time experience for FPGAs.

The new offering will dramatically lower the barrier to leveraging the high performance, energy efficient power of FPGAs to accelerate high end computational workflows across all industries.  Developers can now run these tools in the cloud and then test and deploy on the latest Xilinx-accelerated hardware with no upfront investment or equipment purchases.

Together with Xilinx and the broader scientific computing community, Nimbix is also working to onboard FPGA-optimized turnkey workflows for popular machine learning and data science frameworks.  Additionally, developers can take advantage of Nimbix’s newest feature PushToCompute™, which offers a containerized continuous integration and continuous deployment capability. This feature allows developers to build, test, and deploy FPGA-accelerated applications into the JARVICE marketplace.

“Enabling developers is key for large scale adoption of advanced technologies, and we are delighted to help Xilinx expand the FPGA ecosystem in the cloud,” said Nimbix Chief Technology Officer Leo Reiter.  “Combined with PushToCompute™, it’s never been easier to create the next generation of accelerated applications.”

“Xilinx FPGAs are the most compute efficient acceleration devices for cloud data center installations due to their power efficiency and flexibility in handling multiple workloads such as machine learning and video transcoding,” said Ramine Roane, senior director of software and IP product marketing at Xilinx.  “Access to Xilinx accelerator cards and tools on Nimbix is an important enabler to introduce application developers to the benefits of FPGA compute in cloud-scale applications.”

Nimbix provides on-demand and scalable compute resources that enable organizations to run large-scale High Performance Computing (HPC) workloads in the cloud. HPC allows scientists, developers, and engineers to solve complex science, engineering, development, big data, and business problems using applications that require high compute capabilities. Nimbix’s growing number of integrated platform services allows organizations to increase the speed and effectiveness of research by running high performance computing in the Nimbix Cloud.

About Nimbix

Nimbix is a leading provider of purpose-built cloud computing for big data and computation. Powered by JARVICE™, the Nimbix cloud provides high performance software as a service, dramatically speeding up data processing for Energy, Life Sciences, Manufacturing, Media and Analytics applications. Nimbix delivers unique accelerated high-performance systems and applications from its world-class datacenters as a pay-per-use service. Additional information about Nimbix is included in the company overview, which is available on the Nimbix website at https://www.nimbix.net.

Media Contact:
Danielle Scotto
Lumina Communications for Nimbix
nimbix@luminapr.com

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