New Linux kernel gets a speed boost

Linux kernel 2.6.38 has been released, bringing performance improvements for databases


The newest update to the Linux operating-system kernel features a number of enhancements that should offer a performance boost, particularly for running databases and other programs that require maximum resources from the server.

The 2.6.38 kernel features some “really deep changes,” noted Linux creator and manager Linus Torvalds in an email announcing the release. This kernel has been released only 10 weeks after the previous version, 2.6.37.

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Linux 2.6.38 comes with a number of significant changes that should speed performance, including the addition of new technologies such as automatic process grouping and transparent huge pages. It also includes significant improvements in the VFS (virtual file system).

With automatic process grouping, the process scheduler groups all processes with the same session ID as a single entity. A single program can spawn multiple processes on a computer, which may then take up more resources than necessary. Advocates say that the process-grouping approach will allow programs to divide the processor time more equitably, resulting in improved performance overall.

Transparent huge pages increases the cache size for storing frequently consulted memory addresses, called pages. Traditionally, page sizes have been limited to 4KB, though modern processors support larger sizes. With larger page sizes, heavier workloads such as database work can use the cache more often, reducing their execution times.

VFS has been made more scalable. Its directory cache and path lookup mechanisms have been revamped, which should make multithreaded workloads more scalable and single-threaded workloads execute faster. Torvalds noted that of all the updates in this release, “my personal favorite remains the VFS name lookup changes.”

Beyond performance enhancements, the updated kernel features a number of other new features as well.

For instance, this is the first version to support BATMAN (Better Approach To Mobile Ad-hoc Networking), an ad-hoc mesh protocol that can start relaying packets before a networking path has been fully established for the operating system. BATMAN “is useful for emergency situations like natural disasters, military conflicts or Internet censorship,” the Kernel Newbies website explains.

The kernel also includes the usual plethora of driver updates, bug-fixes and platform-specific changes.

Maintained by an army of volunteer developers, the Linux kernel is used in a wide variety of desktop and server-based operating systems, such as Red Hat Enterprise Linux, as well as in mobile-device operating systems like Android.

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Exabytes: Documenting the ‘digital age’ and huge growth in computing capacity

Megabytes are dead.

Gigabytes are passe.

So much digital data now moves around the globe that those who endeavor to measure it employ a new – or new to non-nerds – term.

Meet the exabyte.

How much data is an exabyte? It’s a billion gigabytes – and it signifies just how digital and data-intensive the world has become.

In 2007, the global capacity to store digital information – on computer hard disks, smartphones, CDs and other digital media – totaled 276 exabytes, a new report finds.

How much is that? Imagine a stack of CDs – each holding an album’s worth of digital music – shooting from the top of your desk to 50,000 miles beyond the moon.

But not everyone has equal access to those resources. In fact, the digital gap between rich and poor countries appears to be growing, said Martin Hilbert of the University of Southern California, who led the audacious effort to tally all of civilization’s information and computing power.

In 2002, people in developed countries had access to eight times the bandwidth – or information-carrying capacity – of people in poorer nations, Hilbert said, citing data he will publish soon. By 2007, that gap had almost doubled.


“If we want to understand the vast social changes underway in the world, we have to understand how much information people are handling,” Hilbert said.

To address that question, Hilbert and co-author Priscila Lopez spent four years poring over 1,110 sources of information spanning from 1986 to 2007, including sales data from computer and cellphone makers and the music and movie industries.

In 1986, a year after digital CDs widely debuted, vinyl records still accounted for 14 percent of all data on Earth, with audiocassettes holding an additional 12 percent.



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Linux Skills Are Hot on Improving IT Hiring Front

IT professionals enjoyed a dramatically improved hiring landscape in 2010, marked in particular by the fewest job cuts in a year since 2000.

That’s according to global outplacement firm Challenger, Gray & Christmas, which on Monday reported that employers announced plans to cut only 46,825 IT jobs during 2010–a full 73 percent fewer than the 174,629 technology job cuts in 2009.

That 73 percent decline also exceeds by far the 59 percent decrease in overall job cuts across all industries, which fell from 1,288,033 in 2009 to 529,973 in 2010, the firm reported.

Thank You, Smartphone and Tablets

“Many industries are still struggling, even as the economy recovers; the technology sector does not appear to be in this camp, however,” said John A. Challenger, the consultancy’s CEO. “These firms are definitely on the leading edge of the recovery, as companies across the country and around the globe begin to upgrade and reinvest in their technology.”

The popularity of smartphones and tablets, in particular, is helping to drive growth in electronics, telecom and computers, Challenger noted.

Indeed, Forrester Research predicts that 2011 IT spending will increase 7.5 percent in the U.S. and 7.1 percent globally, Challenger, Gray & Christmas noted, while employment research firm Dice expects IT hiring to increase this year.

‘Looking for Linux Talent’

What’s particularly exciting for those with an interest in Linux, however, is that skills in the open source operating system are in particular demand, according to Dice.

Not only are job postings on the IT and engineering site up 40 percent generally compared with last year, but postings seeking Linux knowledge have increased a full 47 percent over last year, the Linux Foundation reports. Windows-related postings, by comparison, have increased by only 40 percent.

“The number of Linux-based projects is rapidly increasing all over this industry,” Intel’s Linux and Open Source Technologist Dirk Hohndel told the Linux Foundation. “More and more devices and systems and services are built based on Linux, and therefore, more and more manufacturers and vendors are looking for Linux talent.”

Linux professionals also tend to get a significant salary premium of as much as 10 percent over other IT workers, Dice reported last year.

An Employee’s Market

We’ve already seen evidence piling up that large enterprises are increasingly turning to Linuxfor mission-critical applications. We’ve also seen that a lack of Linux skills is frequently cited as the key stumbling block preventing businesses from using Linux even more.

Put those two facts together, and it’s not surprising to see a surge in demand for Linux skills.

For SMBs, this could mean that it will be tougher than ever to find the skilled Linux workers you need–and that you’ll have to pay them more when you find them. It may be a good time to bolster your in-house Linux skills instead through educational offerings like the online Master’s Program in Free Software and Free Standards, as I noted last fall.

Advice for IT Professionals

For Linux professionals, on the other hand, the outlook for this year could be very rosy indeed. Among the recommendations from the Linux Foundation’s panel of experts were the following:

  • Participate in the open source community — let your code be seen, and attend relevant events.
  • Demonstrate how you’ve helped a business with Linux or open source software.
  • Don’t generalize too far — pick a niche you love and focus on it.
  • Keep learning. The Linux Foundation offers a variety of courses in embedded and kernel-level Linux development, for example.
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A new computer program is decoding influenza and could unravel other viruses as well. The research could save millions of people around the world from death by not only influenza, but eventually other diseases as well.

Scientists from Stony Brook University in New York have developed a computer program that solves a genetic version of the “traveling salesmen problem.” Using the program, the researchers can create a live but greatly weakened vaccine that should provide greater protection against more strains of the flu.

“Live vaccines are better to provoke an immune response; they act like a real virus,” said Steffen Mueller, a scientist at Stony Brook University in New York and co-author of a recent Nature Biotechnology paper. “But there is always a chance that the virus could revert back to its wild form and infect a person. With our new method, that seems impossible.”

There are essentially two ways to vaccinate against influenza. The first method relies on injecting large doses of a dead virus. The second method involves spraying a live, but crippled, virus through the nose.

The first method is safe but not always effective. The injection occasionally doesn’t immunize and requires large amounts of dead viruses, which means fewer people can be immunized.

Using a live virus provides more protection against the flu and uses far less of the virus, which means more people can be vaccinated. But there is a drawback: Since the virus is still alive, it can mutate back to its wild, virulent form. That doesn’t happen very often, said Mueller, but on very rare occasions a vaccination could create an infection.

Mueller’s new method would make infection-via-vaccination far more unlikely. Today’s live viruses only change two of the eight genetic sequences in the virus (the H and the N of H1N1). Mueller takes a different approach looking at all eight genetic sequences.

Viruses encode genetic information using four nucleotides, commonly abbreviated A, U, C and G. Each group of nucleotides is called a codon. Each codon represents one kind of amino acid, which forms proteins. Those proteins assemble new viruses that infect other cells — and other people.

Over billions of years, viruses have become exceedingly efficient at creating copies of themselves, which is why they can spread so quickly through a population. Mueller aims to constrain that ability by scattering genetic “speed bumps,” as he calls them, through every codon in the genetic code of the virus.

Not all codons are created equal. Some codons are easy to turn into amino acids. Others are more difficult.

Viruses have maximized the number of efficient codons and minimized the number of inefficient codons. Mueller will replace the efficient codons with inefficient ones. Although the final proteins that confer immunity will look exactly the same, they will take much longer to produce. Slowing protein assembly, and in turn virus replication, will save lives.

Here’s how it works. First, Mueller and his colleagues sequence the viral genome they predict will infect people during the upcoming flu season. Then they run that code through a new computer program that finds the efficient codons, and replaces them with inefficient codons.

This is not as easy as simply replacing one codon with another. There are many codons to choose from that code for one amino acid. Changing one codon affects how easily the codons on other side are expressed.

It’s a genetic version of the traveling salesmen problem, said Mueller. In the traditional version of the problem, a traveling salesmen has to visit several clients and needs to find the fastest, most efficient way to visit everyone.

Instead of finding the quickest path to clients, Mueller and his colleagues found the most difficult path to viral replication.

Once the problem has been solved, Mueller pays another company to sequence the new inefficient genetic sequences. He then injects the new sequence into a virus, infects a cell and harvests the resulting viruses for use as a vaccine.

The new technique has two main uses, said Marc Lipsitch, a scientist at Harvard University’s School of Public Health.

The program could be a better way to protect against some viruses, such as polio or influenza. The new software could also be used against other viruses that we can’t currently attenuate, such as the notoriously flexible human immunodeficiency virus (HIV), something that Mueller’s group is currently working on.

The computer program is a good one, said Lipsitch, but whether it works or not “is an open question until someone demonstrates (the vaccine’s) effectiveness in humans.”

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With Cloud Computing, the Mathematics of Evolution May Get Easier to Learn in College…and Easier to Teach in High School

BUFFALO, N.Y. — An innovative, educational computing platform developed by University at Buffalo faculty members and hosted by the cloud (remote, high-capacity, scalable servers) is helping UB students understand parts of evolutionary biology on an entirely new level. Soon, high-school and middle-school students will benefit from the same tool as well.

Pop! World, developed by UB faculty members with a $250,000 National Science Foundation grant, takes advantage of cloud computing, which allows programs to run on remote servers instead of through departmental or institutional servers. That feature allows resource-intensive programs to serve many users regardless of their physical location without sacrificing speed or quality of service.

“The cloud serves as a way to distribute resources for free without limits on how many people can access it and with no regard to what kind of computer you are downloading to,” says Jessica Poulin, PhD, research assistant professor in the Department of Biological Sciences in the College of Arts and Sciences, who developed Pop! World with principal investigator Bina Ramamurthy, PhD, research associate professor in the Department of Computer Science and Engineering in the School of Engineering and Applied Sciences, and Katharina Dittmar, PhD, assistant professor of biological sciences. “Everybody can get there.”

UB faculty members designed Pop! World because they wanted to get college students more excited about population genetics; they also wanted to maintain the university’s unique freshman lab requirements at a time when resources are growing more scarce.

UB is one of the few universities in the U.S. that encourages freshmen interested in biology to begin experiencing labs during their first semester on campus.

“We put our freshmen right into labs because students who might otherwise be lost from the major are captivated when they get to do science,” Poulin says. “When you sit in a lecture hall with 400 people and someone is talking about flatworms, what do you care? Despite the logistical difficulties, and the intense demands on staff time, we think that getting freshmen into labs is one of our department’s great strengths. We didn’t want to discontinue it.”

At the same time, Poulin says that it is difficult to convey the main concepts of population genetics at this level, particularly those that are mathematically demanding.

Hired in 2008 to revamp UB’s evolutionary biology curriculum for Bio 200, Poulin says that the department was seeking ways to maintain and improve the course and the lab for students without requiring additional resources, such as teaching assistants.

“Almost all of evolutionary theory can be mathematically modeled if you know enough information to begin with,” she says. “If you enter the correct parameters into the computer, the computer will tell you what will happen after one generation or a thousand generations. I wanted students to be exposed to something that made them feel they were actually watching evolution happen. I wanted it to be captivating.”

While some computational tools exist to help students with population genetics — the mathematical analysis of evolution — the result is often nothing more dramatic than a line graph.

“Our students grew up in the Internet age surrounded by MP3 players, wireless phones and social networking apps,” says Ramamurthy, “so the visual aspects of Pop! World are certainly very appealing to them.”

The UB team programmed Pop! World in Adobe Flash, which lends a highly visual, nearly tactile look to the program. While the current version illustrates evolution with red and green lizards, it is highly adaptable, so it can be used with any population of organisms. It also is highly scalable, so that it can be made more complex, to serve the needs of population genetics researchers, or less complex, to serve the needs of middle- and high-school students.

A preliminary version of Pop! World is running on the Google App Engine Cloud. It can be accessed by going to

With the help of the NSF grant, the UB team is now creating a sophisticated version of the tool, expected to be available by Fall 2011.

“Our idea was to use general principles of population genetics not only to convey the principle in the context of evolutionary biology but to make sure that students understand visually what’s happening with the mathematics behind it,” explains Dittmar.

When an early version of Pop! World was used to teach evolutionary biology last summer, students and teaching assistants responded enthusiastically.

“The TAs loved it because it facilitated their explanations of a very complicated problem,” Poulin says.

“Pop! World gives students the visual background they need to understand complex mathematical problems,” Dittmar adds. “And it works kind of like a video game, which serves the current population of undergrads well.”

That visual appeal is also expected to go far with middle-school and high-school biology students, groups the UB team hopes to excite about evolution; by spring, they expect to have completed a modified version for them as well.

By making evolutionary biology more visually appealing and, thus, more accessible, Poulin hopes that Pop! World will make evolution itself a more appealing subject for secondary schools to teach.

“There’s a huge disconnect,” she says. “The universities all accept evolution as fact. It’s not a question. But many high schools and middle schools don’t want to touch it. They don’t want to deal with the politics of it.”

Her hope is that the visual and educational appeal of Pop! World and the ease of using it will begin to change that situation.

The UB team’s grant, “A Cloud-enabled Evolutionary Genetics Learning Tool for Engaging the Cyber-savvy Generation” (NSF OCI CI-Team 1041280) from the NSF’s Office of Cyberinfrastructure, will run for two years.

Hongsik Kim, Jungeun Lee and Byunghun Jang, all former UB graduate students in the Department of Computer Science and Engineering, also were involved in the project.

The University at Buffalo is a premier research-intensive public university, a flagship institution in the State University of New York system and its largest and most comprehensive campus. UB’s more than 28,000 students pursue their academic interests through more than 300 undergraduate, graduate and professional degree programs. Founded in 1846, the University at Buffalo is a member of the Association of American Universities.


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Unhackable data in a box of bacteria: Future of InfoSec?

Students at Hong Kong’s Chinese University may be onto a type of memory media that could be a truly secure way to store data — text, images, music, and video. It takes up almost no space, can be encrypted, and is so gross that it’s unlikely many people would attempt to steal it. That is, if the thief would even consider searching  a refrigerator for massive data storage inside E. Coli— the bacteria responsible for 90% of urinary tract infections, which can cause food poisoning and is the reason for many food recalls. The bacteria can successfully and securely be used for biostorage, the storage of data in living things.

According to an AFP report, the U.S. national archives take up more than 500 miles of shelves, but one gram of bacteria used for storing data could hold the same amount of information as 450 hard drives with 2,000 gigabytes (2 TB) each of storage capacity.

“This means you will be able to keep large datasets for the long term in a box of bacteria in the refrigerator,” said student instructor Aldrin Yim about the biostorage project. Also according to Discovery News, another student instructor, Allen Yu said, “Bacteria can’t be hacked. All kinds of computers are vulnerable to electrical failures or data theft. But bacteria are immune from cyber attacks. You can safeguard the information.”

Student researchers spent 10 months developing the project from scratch,reported their professor Chan King-ming. The team of 11 students from the Biochemistry program at the Chinese University of Hong Kong were the 2010 gold medalist in MIT’s International Genetically Engineered Machine (iGEM) competition. The students describe their bioencryption project as turning fantasy into reality and even coined a new term of biocryptography. These students report having high expectations for the future of a biocomputer; “we believe this could be an industrial standard in handling large scale data storage in living cells.”

Hardy strains of bacteria can be found everywhere. One type of bacteria can even survive nuclear radiation. The Hong Kong team checks against a master database to make sure their manipulations have no toxic effects. The biological cryptography could protect from information leakage and, as Hong Kong University stated, herald in a new era of information security.

The student researchers developed a method to overcome storage capacity limitations by compressing the data, splitting it into chunks and distributing it between different bacteria cells. The Declaration of Independence can be stored in 18 bacteria cells. You can try out the team’s modeling demonstrationthat simulates the required minimum number of bacteria it would take to store your inputted text message.

In a post-WikiLeaks world, could security professionals latch onto securely storing data in bacteria cells and mapping the DNA to easily locate specific information? Although a Petri dish PC may not be anywhere close to market-ready, there may come a day when we want bacteria in our computers.


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