HPC and the life sciences

Connected network cablesThis week, a team from our company visited a large laboratory located in the Chicago area. IT representatives there told us how a major focus for them has been migrating their computing resources from a model of individual workgroups using separate clusters to a shared private cloud that all research teams in the facility can access for running their jobs. This shift to private clouds for getting the most out of dedicated clusters is a hot topic of conversation in the HPC world.

HPC in the Cloud recently published an article responding to a case study written by Platform Computing about the implementation of a private cloud at the Harvard Medical School. Both are worth a read if you are interested in the challenges encountered by small- and medium-sized life sciences organizations when they try to adopt HPC clusters.

HPC holds much promise for organizations such as the Harvard Medical School. With middleware such as Platform Computing (we are biased, I must admit, since this is what HPC clusters by ICC deploy as well) it is getting easier to operate an HPC cluster with hosts running different operating systems and applications. It used to be that this multiplicity of software on the same cluster would cause extensive compatibility and usability problems, but not so much anymore. End-users in the life sciences (such as medical researchers) are benefiting from computing applications that are productive and easy to use.

So Harvard Medical School, as the HPC in the Cloud article describes, has migrated from an inefficient computing model of unshared individual computers scattered across various laboratories to a centralized private cloud that can be accessed by any of those users and managed as one unit. Simplifying maintenance while maximizing accessibility to HPC resources by medical school staff is most likely going to save money and increase the pace of innovation in the long run.

While this is a hopeful case study that sheds light on how other organizations can pool their computing resources to great effect, challenges remain for spreading this model to other small- and medium-size laboratories and businesses. For one, private medical companies are heavily regulated by the government and their IT infrastructure has to incorporate many time-consuming applications to store detailed records.

HPC is becoming more affordable and easier to use, but software has to continue evolving to accommodate the particular context of each industry. Only then will the life sciences (not to mention other markets) have a truly turn-key HPC solution that can benefit labs and private companies of every size.

GPUs in the news: medical imaging

Next time you feel like bemoaning the state of today’s big thumbed, small minded, video-game generation, think about the social benefit all those gaming man-hours are contributing to medical research.

A team from UC San Diego created an algorithm for CT scan image reconstruction using an NVIDIA GPU, discovering, in the process, the superior effectiveness in creating  targeted images of tumor cells. This improvement over traditional medical scans reduces the total radiation cancer patients need to endure. Current technology requires repeated scans in order to produce a detailed enough image for doctors to identify potential tumors. Using GPU’s and gaming hardware, scientists were able to reduce the amount of radiation by a factor of as much as ten.

“In my mind, the most interesting and compelling possibilities of this technique are beyond cancer radiotherapy,” Steve Jiang, senior author of the study and a UCSD associate professor of radiation oncology, said in a statement. “CT dose has become a major concern of the medical community. For each year’s use of today’s scanning technology, the resulting cancers could cause about 14,500 deaths. Our work, when extended from cancer radiotherapy to general diagnostic imaging, may provide a unique solution to solve this problem by reducing the CT dose per scan by a factor of 10 or more.”

CT scanning is widely used and extremely useful in the field of computerized imaging.  A scanner snaps a series of X-ray pictures whilst rotating around the subject body.  The pictures are assembled to create a cross section of the body. These cross sections are then combined to generate a 3D image.  Throw in a large number of Fourier transforms, where data about neighboring points is used to improve information on each individual point, mix in a few b-spline interpolations (I am not making this stuff up)- a mathematical technique that accurately fits smooth curves to data points-and you wind up with the sort of computational dynamic that benefits tremendously from parallel processing.

Where CPU’s perform interpolations one data point at a time, GPU’s can take multiple points and interpolate them in parallel. The high resolution (8000×8000 pixels) of the images and large file sizes make this the sort of computational problem ideally suited to parallel processing.  This translates to a 3.6X speedup of segmentation time, compared with CPU-only processing on an Intel quad core Nehalem-class processor. More recent tests point to a speedup of up to 15X. Klaus Mueller at the State University of New York-Stony Brook found that using GPU processing could reduce the time needed for a CT scan reconstruction from 135 seconds to less than seven seconds.

Software has also allowed GPU’s to perform their tasks much more quickly. Solving non-graphics problems on the GPU involved treating non graphic data like vertices or pixel data points and using complicated graphics API’s to process the information. Now, someone with a background in ‘C’ can write a program to get around this issue.

Escaping in to the virtual reality of video games, appeals to a growing segment of the population. Providing them with the best user experience drives sales.

Now it also drives medical innovation.

HPC helps combat malaria

Scientific American reports (accessed via HPCwire) that a project partly funded by the Bill and Melinda Gates Foundation will use supercomputing to help stop the spread of malaria, which kills about a million people a year.

The team tasked with working on the malaria project is sharing a 1,104-core HPC (high-performance computing) supercomputer with a nuclear reactor research company. With the help of mathematical modeling, researchers are trying to find patterns in nature that would allow them to predict and control malaria outbreaks. From the Scientific American article:

The software pulls biological data on the behavior and reproductive rates of the Plasmodium parasites and the mosquitoes that carry them, as well as information on infection patterns and immune responses among humans. Other data include where people live and how they travel, environmental factors (temperature, rainfall and elevation) that are important to malaria transmission, and the locations of different species of mosquitoes.

The article also features an interesting discussion about cloud computing compared to local servers. The malaria research team is using local servers and not cloud computing for their simulations, even though the Microsoft software they are using is geared towards the cloud (see our post about the new Microsoft Technical Computing Group).

The team uses local servers for national security reasons – servers in the cloud frequently operate outside of the United States and many government-sponsored research projects can not put their data at risk in such a way. This illustrates that, despite the unifying effects of science and globalization, politics is still a formidable factor in even the noblest of global projects.

The article also notes that cloud computing is still far behind in performance compared to running local servers. As a systems engineer working on the malaria project observes, using local servers is about ten times faster than using the cloud.

While cloud computing technology still has a long way to go to catch up to the performance capabilities of locally-run servers, HPC in all of its forms is nevertheless helping people to battle some of the earth’s deadliest diseases.

Healthcare industry slow to adopt “green IT”

Greenbiz.com reports that a new survey published by BridgeHead Software suggests that the healthcare industry is relatively slow in adopting green IT practices. According to the global survey, only about 25% of respondents said that their organizations have targets for reducing their carbon footprint.

It is understandable that the healthcare industry gets less heat for not reducing their carbon footprint than other industries – they are, after all, busy with saving human lives. But, especially now that the recession may finally be cooling off, the healthcare industry should once again look to increase their energy efficiency.

Luckily, the healthcare industry is poised to be one of the biggest growth industries in energy efficiency spending, according to a recent study. IT and sales professionals should take note.