So … I’ve had this blog since 2005. I installed it from original sources. And WP made upgrades in the 2.x time frame, quite painless. Or so it seemed. Slowly, over time, some configuration/settings/whatever got out of whack. And with the last update, from a system originally installed in final form in 2013 or so, something broke. I am not sure what. But the symptoms were simple … new posts would replace the most recent posts.

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 of an overall accelerator strategy that we had put together at the time, and were seeking to raise capital to build.

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 site. Ok, so what does it do? Simple. It boots an entire OS, into RAM. No disks to manage and worry over.

Ok. Here’s the problem. Small environment for customers, whom are not really sure what they want and need for authentication. Yes, they asked us to use local users for the machines. No, the number of users was not small. AD may or may not be in the picture. Ok, I am combining two sets of users with common problems here. In one case, they wanted manual installation of many users onto machines without permanent config files.

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 the time, hiding the massively parallel nature of the computation behind a comfortable interface that end users already knew.

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. This pipeline runs on a cluster attached to Scalable Informatics FastPath Unison storage. This is a very dense, very fast system, interconnected with Mellanox FDR Infiniband, Chelsio 40GbE, and leveraging BeeGFS from thinkparq.

Its that time of year, when the inventory fairies come out and begin their counting. Math isn’t hard, but the day job would like a faster and easier count this year. So, the day job is working on selling off existing inventory. We have 4 units ready to go out the door to anyone in need of 70-144TB usable storage at 5-6 GB/s per unit. Specs are as follows: 16-24 processor cores 128 GB RAM 48x {2,3,4} TB top mount drives 4x rear mount SSDs (OS/metadata cache) Scalable OS (Debian Wheezy based Linux OS) 3 year warranty As this is inventory reduction, the more inventory you take, the happier we are (and the less work that the inventory fairies have to do).

This will be fun to watch run … Scalable Informatics FastPath Unison for the win!

For Scalable Informatics Unison product. The whole system: [ ](/images/dash-2.png) Watching writes go by: [ ](/images/dash-3.png) Note the sustained 40+ GB/s. This is a single rack sinking this data, and no SSDs in the bulk data storage path. This dashboard is part of the day job’s FastPath product.

This has been an itch we’ve been working on scratching a few different ways, and its very much related to forgoing distro based installers. Ok, first the back story. One of the things that has always annoyed me about installing systems has been the fundamental fragility of the OS drive. It doesn’t matter if its RAIDed in hardware/software. Its a pathway that can fail. And when it fails, all hell breaks loose.

Config now comes from some nice and simple json, and it handles multiple machines with aplomb. See the git repository for the latest. The config file example is in there, and you can replicate the n01-ipmi section with more nodes trivially. Coming next is getting config from a trusted web server, along with registering the client to the trusted web server. This prevents things like passwords from showing up in the clear, though you can always create a lower privileged user to access the console for monitoring.

See the Systems Engineering position here, and the System Build Technician position here. I’ll get these up on the InsideHPC.com site and a few others soon (tomorrow). But they are open now. For the Systems Engineering position, we really need someone in NYC area with a strong financial services background … Doug made me take out the “able to leap tall buildings in a single bound” line, as well as the “must be able to talk customers through complex vi sessions on system configuration files while driving 70 mph on a highway.

Oh yes we did. Oh yes. We did. This is the fastest storage box we are aware of, in market. This is so far outside of ram, and outside of OS and RAID level cache … [root@siFlash ~]# fio srt.fio ... Run status group 0 (all jobs): READ: io=786432MB, aggrb=23971MB/s, minb=23971MB/s, maxb=23971MB/s, mint=32808msec, maxt=32808msec This is 1TB read in 40 seconds or so. 1PB read in 40k seconds (1/2 a day).

[warning: longer post] I mentioned this on twitter (@sijoe). The day job has been in business for 10 years. We’ve not taken outside investment to date, and we’ve not sold the company yet. We’ve been profitable and growing continuously during our lifetime. The preceding 3 years have seen growth, accelerating hard. The company was built starting with a conviction that practitioners and users of HPC systems needed better designs, better systems than were being pushed out by traditional vendors in the early 2000’s.

Will be up on the day job site tomorrow. We are very excited by these developments, and look forward to a productive relationship JRTI and Scalable Informatics Form Strategic Partnership to Provide High Performance Storage and CPU & GPU Clusters to Organizations Seeking Exceptional Results Richmond, Virginia (January 18, 2011)-James River Technical, Inc (JRTI), specialists in accelerated and HPC solutions for the higher education, research, government, and commercial market segments, has entered into a reseller agreement with Scalable Informatics (Scalable) to provide Storage and HPC solutions throughout North America.

Univa grabs GridEngine. Specifically: Hat tip to Chris D for pointing it out. This directly addresses one of my major concerns on the longevity of GE. It also makes me feel a bit safer about using/deploying GE for users/customers. Specifically, if a committed and large/stable enough OSS project and/or committed company were to drive this, engage and work with the community to grow it, yeah … I am comfortable with this.

Here in Detroit, we have the big 3 … Ford, GM, and Chrysler. Well, maybe no longer. This morning the government passed judgment on this industry, which had been requesting capital to survive, as the credit markets, despite protestations to the contrary from various sources, is still frozen … and they (and all other businesses) need capital (and credit) to survive. The government has said (basically) … its Chapter 11 (or 7) for you.

Grab the tarball from the open fabrics alliance (or from here) Grab the build_new.sh from here, place it in the OFED-1.2 directory as root on your machine mv /usr/src/linux-2.6.18.2-34/include/linux/miscdevice.h /usr/src/linux-2.6.18.2-34/include/linux/miscdevice.h.original ln -s /usr/include/linux/miscdevice.h /usr/src/linux-2.6.18.2-34/include/linux/miscdevice.h Then run the build_new.sh. Voila. Works. Binary RPMs are here.

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 replacement level growth rates. If end users did not see a value in HPC, they wouldn’t use it, as their time would be spent elsewhere.

At the excellent Cluster Monkey Doug Eadline mused on a number of topics of interest, specifically on why Cluster HPC is hard. There were some excellent points made. The OSC is working on an initiative to increase access to high performance computing resources for end users. Their effort is in part by making access to HPC hardware easier, and in part by helping people (users and commercial entities) make better use of computational gear.

So there should be lots of folks at SC05 to answer questions about technology, products, performance, TCO, and most anything else connected with supercomputing you could want to ask. Some questions I want to ask are from the good folks at Microsoft (Bill Gates is giving the opening keynote), what specifically their HPC initiative is supposed to give us that we don’t already have? This is not an OS war, or OSS zealotry, just a simple question as to what their offering will bring to the table.