NTU win Silver Award at the 2014 Asia Student Supercomputer Challenge (ASC14)

 Taken from  SPMS Website

Congratulations to Team NTU for winning the Silver Award at the 2014 Asia Student Supercomputer Challenge (ASC14) held in Sun Yat-sen University, Guangzhou (China).

In the finals, the finalists had to build their own supercomputer system architecture within a 3000W power budget and execute a series of applications including HPL (Linpack), Quantum Espresso, LICOM, SU2, and mpiBLAST (secret application). In the code optimisation category, the 3D-EW code was executed on the world’s fastest supercomputer, Tianhe-2.

During the finals, a new Linpack record was established at 9.272TFlops by Sun Yat-sen University. It was Team NTU's maiden attempt and they were competing amongst veteran teams from China (National University of Defense Technology, Huazhong University of Science and Technology).
Team NTU was described as the 'dark horse' of this challenge during the preliminary and the final rounds, and they overcame all odds to emerge runners-up in this multinational challenge.

Understanding the Parameter for ulimit in a glance on CentOS

If you need to look and understand the parameters of the ulimit. Just use the command

# ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 311296
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 10240
cpu time               (seconds, -t) unlimited
max user processes              (-u) 311296
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

Look at the output and you will see that the parameter are within the ()

For example, if you wish to tweak the max locked memory to be unlimited, you can use -l

# ulimit -l unlimited 

Or

For example if you wish to  tweak the core file size to be unlimited, you can use -c

# ulimit -c unlimited

Fire-Eye unqiue approach to combat malware

I thought we should take a look at Fire-Eye approach to combating malware. NetworkWorld Review: FireEye fights off multi-stage malware has written a interesting article on FireEye. Here are some excerpts.....

FireEye takes a new approach to malware detection with its NX appliances. As this Clear Choice test shows, the FireEye device allows advanced malware to proceed – but only onto virtual machines running inside the appliance.

Conventional approaches to fighting malware have limitations in combating multi-stage malware threats. A signature-based system might detect the existence of a malware binary file, but only once it’s been reassembled on the target – and by then the target is already compromised. Newer sandbox systems stop traffic before it reaches target machines, but they may not be able to assemble and analyze all the constituent parts of a multi-stage attack. Indeed, a key step in some exploit kits is to “fingerprint” versions of the hypervisor, OS, browser, and plug-ins before deciding whether to proceed.
......
......
Virtualization is FireEye’s key differentiator. Its appliances run multiple versions of Windows OSs, browsers, and plug-ins, each in its own virtual machine. Malware actually compromises a target (virtual) machine – and then and only then does the FireEye software record a successful attack. Network managers can configure the FireEye appliance to block such attacks, preventing their spread into the enterprise.
.......
......
FireEye’s technology complements rather than replaces an intrusion detection system (IDS). Unlike an IDS or IPS, it doesn’t have a library of thousands of attack signatures. Instead, it looks for actual compromises on its virtual machines......
......
.....
The appliance’s virtual machines represent various service pack levels of Windows 7 and Windows XP, along with many combinations of browser and Adobe Flash and Microsoft Silverlight versions. FireEye wrote its own hypervisor that makes virtual machines appear to run on bare metal. That’s useful to thwart exploit kits that skip execution on machines if they detect VMware hypervisors.......

E297: Write error in swap file

If you open up a file using an editor and you see a quick error "E297: Write error in swap file", it is likely your partition is full or your quota has been reached. Do the necessary check and clean-up

mothur Software

The Mothur Project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. mothur is the most cited bioinformatics tool for analyzing 16S rRNA gene sequences and can be easily used to analyze data generated by Sanger, PacBio, IonTorrent, 454 and Illumina (HiSeq/MiSeq).

Installation is total breeze. First thing take a look at Download Mothur Page . There is a CentOS executable there including the GUI

Make a new directory and unzip Mothur.cen_64.zip

# mkdir mothur-1.33.3
# cd mothur-1.33.3
# unzip Mothur.cen_64.zip

Make a new directory and unzip MothurGEN.cen_64.zip

# mkdir MothurGUI.cen_64.zip
# cd  mothur-1.33.3
# unzip MothurGUI.cen_64.zip