Brings a smile to my face … #BioIT #HPC accelerator

Way way back in the early aughts (2000’s), we had built a set of designs for an accelerator system to speed up things like BLAST, HMMer, and other codes. We were told that no one would buy such things, as the software layer was good enough and people didn’t want black boxes. This was part … Read moreBrings a smile to my face … #BioIT #HPC accelerator

Fully RAMdisk booted CentOS 7.2 based SIOS image for #HPC , #bigdata , #storage etc.

This is something we’ve been working on for a while … a completely clean, as baseline a distro as possible, version of our SIOS RAMdisk image using CentOS (and by extension, Red Hat … just need to point to those repositories). And its available to pull down and use as you wish from our download … Read moreFully RAMdisk booted CentOS 7.2 based SIOS image for #HPC , #bigdata , #storage etc.

Been there, done that, even have a patent on it

I just saw this about doing a divide and conquer approach to massive scale genomics calculation. While not specific to the code in question, it looked familiar. Yeah, I think I’ve seen something like this before … and wrote the code to do it. It was called SGI GenomeCluster. It was original and innovative at … Read moreBeen there, done that, even have a patent on it

When the revolution hits in force …

Our machines will be there, helping power the genomics pipelines to tremendous performance. Performance is an enabling feature. Without it you cannot even begin to hope to perform massive scale analytics. With it, you can dream impossible dreams. This article came out talking about a massive performance analytics pipeline at Nationwide Children’s Hospital in Ohio. … Read moreWhen the revolution hits in force …

stateless booting

A problem I’ve been working on dealing with for a while has been the sad … well … no … terrible state of programmatically configured Linux systems, where the state is determined from a central (set of) source(s) via configuration databases, and NOT by local stateful configuration files. Madness lies in wait for those choosing the latter strategy, especially if you need to make changes.
All sorts of variations on the themes have been used over the last decade or so, with this. Often programmatic things like Chef or puppet, are there to do a push of configuration to a system. This of course breaks terribly with new systems, and the corner cases they bring up.
Other approaches have been to mandate one particular OS and OS version, combined with a standard hardware configuration. Given how hardware is built by large vendors, that word “standard” is … interesting … to say the least.

Read morestateless booting