Interesting NUMA issues in current SuSE kernel

One of our development systems is a dual socket system with 2 dual core Opteron 275 chips. 4 GB ram, nice disk config, and a quadro fx/1400. This is a good machine t work on.
I had set it up with SuSE 9.x, and had left it at 9.3 for quite a while. Recently we upgraded it to SuSE 10.0 Pro. More modern kernel, somewhat updated apps. I thought it would be nice to stay somewhat current.
We use this for building and testing our accelerated HMMer code. This code is 1.6-2.5x faster than the binaries from the WUSTL site. Source code changes, and we are finalizing a new release of it.

Read moreInteresting NUMA issues in current SuSE kernel

SCSI vs FC vs SATA

I have heard this argument come up again several times recently. Lots of folks out there from the enterprise storage realm still love their FC drives. The SCSI crowd like their units. Both handily disparage SATA as being inferior, poorly performing, or with higher failure rates.
This is an interesting point.
As far as I am aware, all the drives come physically off the same manufacturing production line. The only significant difference between the units that I am aware of (modulo newer motors on newer units) are the electronics that connect to the bus.

Read moreSCSI vs FC vs SATA

In the limit, as N(cores) -> infinity …

So way back in the good old days, programming a single core CPU in a high performance manner was a challenge. Compilers promised much and delivered small fractions of maximum theoretical performance. To get nearly optimal performance, you had to hand code assembly language routines. You would never be able to achieve 100% utilization of the processor capabilities, but you might be able to sufficiently balance memory operations with floating point and integer operations so that you were utilizing a sizeable fraction of the chips subsystem capabilities.

Read moreIn the limit, as N(cores) -> infinity …

MEDC update

According to the MEDC site, 505 applications were turned in for mostly commercial efforts. 505… The mind boggles. Of those 505, 139 are commercialization. Another smattering are also commercial, though hidden. Call that 150 commercial ones. In all the previous competitions; the MLSC (Michigan Life Science Corridor), the MTTC (Michigan Tri Technology Corridor), the commercial … Read moreMEDC update

HPC in the critical path

Is high performance computing a critical path technology? Is it a technology that you cannot do without? This is a question some potential partners were discussing this evening. Very interesting question. If HPC is not critical, then demand for it should be quite moderate. If it is not critical, then the market would have basically … Read moreHPC in the critical path

The coming of the "grid" (the hopefully hype-free or hype-reduced model that is)

Someone gets it. I can’t say much more now, or even point to who gets it. Then again, with all companies and decisions comes baggage. While they get the idea, there is this little manner of the baggage they attached to their grid to fix another problem. Customers bringing application code over to their grid, … Read moreThe coming of the "grid" (the hopefully hype-free or hype-reduced model that is)