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Fortran, Python, and Hadoop for Safer Nuclear Waste Disposal - Part I
PremiseThis is the first in a series of posts that I intend to make detailing a real use of Hadoop to do some actual publishable science in a field that is still dominated by traditional,...
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What "university-owned" supercomputers mean to me
The opinions and analysis expressed here are solely my own and do not reflect those of my employer or its funders.insideHPC ran an article yesterday called "Purdue Supercomputing Empowers Researchers"...
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Intel's Xeon Phi Uptake Measured from Real Users
IntroductionLSU announced yesterday that they received a $4m grant from the NSF to deploy a cluster rich in Intel's Xeon Phi (MIC) coprocessor cards, and that 40% of this machine will become available...
View ArticleTrack 2 and Comet/Wrangler
Just before our federal government shut down, the National Science Foundation announced that SDSC would be awarded a $12 million piece of its most recent ACI Track 2 solicitation, Track 2F. The Track...
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A supercomputer IS a computer
HPCwire recently ran a featured article in which the author states that, when selling the idea of high-performance computing (HPC) to scientists or technical people, the following distinction should be...
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On the road to SC'13
It's been about a year since I decided to quit the life of a research scientist and move across the country to get into the supercomputing business, and coincidentally, it's also time for this year's...
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A Photographic Tour of Gordon and Trestles
I took a bunch of photos of Gordon and Trestles, the supercomputers at the San Diego Supercomputer Center, in case I needed some material for background graphics or flash for any of the presentations...
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Booth Activities for SC'13
As much as I try to shy away from shilling for SDSC on my personal blog here, the SDSC official booth (#3313) schedule has been finalized and I wanted to post it online for the world to see. I've...
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High-Performance Virtualization: SR-IOV and Amazon's C3 Instances
Amazon recently announced their next-generation cluster compute instances dubbed C3" which feature newer Ivy Bridge Xeons with higher clock rates, about the same amount of RAM, and 16 physical cores...
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High-Performance Virtualization: SR-IOV and InfiniBand
About a week ago I posted a brief introduction to SR-IOV and a few early results from comparing the MPI performance of Amazon's new SR-IOV-enabled C3 instances to C3 instances using their older...
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Netra T1 105
I accidentally became the owner of a new old Sun Netra T1 model 105 yesterday. I had asked our super-helpful systems administrator if he had any old 1U servers to loan me as a prop for a tabletop demo...
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The $1000 Genome - A Computational Perspective
I haven't written a lot of domain-specific posts, but some recent news in genomics got me thinking about how high-performance and data-intensive computing is having to become an integral part of...
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Revisiting Perl and Python's Speed
I was really surprised to see the discussion that was generated as the result of my previous post comparing the speed of Python and Perl. Many people much wiser than me posted a lot of valuable...
View ArticleDeploying Hadoop on Traditional Supercomputers
Some time ago I posted a guide on my website that outlined some of the details involved in allowing users of SDSC's Gordon supercomputer and FutureGrid's cloud clusters to deploy semi-persistent Hadoop...
View ArticleLinux perf, libquadmath, and GFortran's Insane Behavior
Executive Summary: libquadmath was introduced in GFortran 4.6 which fundamentally changed what the -fdefault-real-8 switch does. Rather than promoting all floating point arithmetic to double...
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NSF's 2014 Science & Engineering Indicators
Sometimes the Sun Goes 'Round the MoonChapter 7 of the NSF's recently released Science & Engineering Indicators report for 2014 has been making its rounds because of some figures that, when taken...
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Quantum ESPRESSO: Compiling and Choice of Libraries
We recently upgraded our two big machines at work, and as a result of that upgrade, a number of our users had to rebuild their installation of Quantum ESPRESSO. As it turns out, little quirks in our...
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Quantum ESPRESSO: Performance Benefits of Vendor-Optimized Libraries
In my previous post, I presented a lot of different options you can use to build Quantum ESPRESSO which are (admittedly) very confusing. At the end of the day, the set of options that produce the...
View ArticleParallelizing R on Supercomputers
Executive summary: I've posted a tutorial on how to parallelize R codes on my website. This post is a more personal reflection on how I got there."Parallel Options for R" was the title of the first...
View ArticleBeing a Successful Researcher
The bioinformatics community is an interesting one in that, as a result of its relative infancy, is highly connected to the social internet in a way that "older" sciences have yet to catch up (Google...
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