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Cluster building
With all of Bioteam’s talk about cloud computing, I was a bit surprised to find myself building an honest-to-goodness non-cloud, non-virtual compute cluster a couple of weeks ago. There were wires, blinking lights, whirring fans, circuit breakers, and all sorts of messy real-world details to contend with. The servers were heavy and unwieldy, and I [...]
Tuesday, in Haiti
This will be a quick update, because I suspect that I would be asleep long before I could even summarize our entire trip. We’re in the ‘Blanchard’ or ‘Terre Noir’ neighborhood, perhaps a mile north of Cite Soleil – in Port au Prince. The clinic building where we are working survived the earthquake in remarkably [...]
Epigenomics & massively parallel sequencing
Masako Suzuki, DVM PhD from the Center for Epigenomics, Department of Genetics at Albert Einstein College of Medicine in New York recently gave a presentation at the 2009 “Next Generation Sequencing Data Analysis” meeting held in Providence, RI. The talk was called “Epigenomic analysis using massively-parallel sequencing”, the presentation slides can be downloaded here: Epigenomic [...]
Big Storage
82 terabyte desktop folder, originally uploaded by ChrisDag. This screencap is from my Apple laptop; it’s a NFS mount to a *really big* folder hosted on the network. ~90 terabytes of storage in a single namespace/folder costs a million dollars or more if you go with the Tier 1 vendors and have to pay for [...]
US Roadshow: “Storage for Life Sciences”
Isilon Systems is doing a series of roadshows and talks beginning in early October with locations all over the east and west coasts of the USA. BioTeam is participating in the event series by giving a talk on “Storage for Life Sciences” – our part of the presentation is not meant to be vendor-specific so [...]
Talk slides from 2008 OSGC event
Chris Dagdigian has posted his talk slides from the 2008 OSGC meeting including “LSF & SGE”, “Fun with SGE XML” and “SGE and Amazon EC2″.
The Cloud, on NPR
Yes, the Cloud is hot. We just listened to a brief, non-technical piece on Cloud Computing on National Public Radio: http://www.npr.org/templates/story/story.php?storyId=90180142&ft=1&f=1019 The issues they touch on include security, using the Cloud to compute your genealogy, and how the consumer has access to super-computation for the first time.
Instead of spending 20 minutes to format an ext3 volume every time you need one, you could just snapshot a ...
Let me add a few remarks about Ext3 as well.
The reason we usually recommend Ext3 instead of XFS is because ...
I'm using these slides to tune SGE 6.2 @ European Space Agency, thanks a lot! 
Great post.
Can you also try our native scale out NFS protocol? Next 3.1 release of Gluster will include it ...
So far my mental architecture is shaping up to be something like this:
Use the ephemeral disks for scratch space and ...
This shows that on-demand HPC still has a ways to go, it is very unfortunate that only ext3 is supported ...
We have had sge62u3 working fine in a 10.5 cluster using cron to startup the sge_execd process on clients. Trying ...
Instead of increasing your disk image size, you could have decreased the memory by writing a very short C program ...