My Other Computer Is a Supercomputer
In November 2002, I was called by Mitch Davis (Executive Director of Academic Technology, ITSS, Stanford University) and Carnet Williams (Director of Academic Technology, ITSS, Stanford University) regarding an aggressive, high-profile project. While I was Director of Network Operations at the Stanford Law School, I had the pleasure of working with both Mitch and Carnet during their respective terms as Associate Dean/CIO of Stanford Law School. They told me Dr Vijay Pande, the principal investigator behind the Folding@home Project, wanted to purchase a large commodity cluster, and they sent my name to Vijay as someone who could manage projects effectively to completion. Instinctively, I agreed. We discussed more details of the project, and right before I hung up, I asked, “How big will it be?” They responded, “300 dual-processor nodes.” I thought, “600 CPUs...that should do some damage.”
While Mitch, Carnet and Vijay worked with Dell and Intel to negotiate the purchase of the cluster, I sent an e-mail to Vijay Pande, stating that I could assist him with the network and hardware side of the project and that I hoped to learn more about the software side during the process. The last line in my message said, “I want to be part of something great.” Vijay responded promptly and welcomed my assistance. We set up our first meeting to discuss the scope of the project.
At that initial meeting, it seemed most things were up in the air. Everyone knew equipment was coming, but no real plans were in place. Vijay said he knew that authentication and filesystem choices had to be made, and of course the opportunity to use existing Stanford services was considered.
Vijay also mentioned running PBS, MPI and MOSIX. I knew very little about any of these, but took notes and, back at my desk, did a Google search for those names along with the words “beowulf” and “cluster”. I came across a presentation about building a cluster using an open-source distribution named Rocks from an organization called NPACI (www.rocksclusters.org). The presentation was excellent. It answered so many of my questions, such as, how would we put together such a cluster, how would we manage software on nodes, how would we configure the master node and how would we monitor nodes. Basically, the presentation was a framework for how we would build our cluster. I printed copies of the presentation and brought them to our next meeting. The idea of using a packaged solution was well received.
During the time these two meetings were taking place, the cluster was being racked and stacked by Dell in Stanford's Forsythe Data Center, which took seven days. I was able to download a copy of Rocks version 2.3 and run through the installation process on what is defined as the front-end node in Rocks nomenclature. This task was simple, and I was quite impressed at this point. At our third meeting, my role in the project had expanded from being involved only with hardware and the network, to handling software also, as I already had brought up the front end with Rocks successfully. I felt confident that I could handle the rest of it as well, but at this point I didn't realize the true scope of the project. I was embarking on building the largest-known Rocks cluster.
The first issue I ran into was trying to install compute nodes. A Rocks utility called insert-ethers is used to discover compute nodes' Ethernet MAC addresses, assign them an IP address and hostname and then insert this information into a database, during a negotiated process using PXE and DHCP. Following the node insertion, the node is built and configured as defined in a Red Hat Kickstart file, completing the PXE boot process. Unfortunately, I had problems with the network interface cards in the Dell PowerEdge 2650, as the Broadcom Ethernet controllers did not appear to be supported in Rocks. I sent my issue to the Rocks discussion list, and I also called Dell for support and opened a ticket for service under our Gold support contract. The Rocks developers quickly provided an experimental version of their cluster distribution that contained updated drivers, which solved the problem, and soon I saw my suggestions and observations incorporated into the maintenance release of Rocks version 2.3.1.
The final issue, which was discovered at scale, was the inability to have more than 511 active jobs. My users were screaming about the 100 idle processors, because many of the jobs run on Iceberg are short-lived, one- to two-processor jobs. While working with the Rocks Development team, we looked for a defined constant in the Maui scheduler code. I eventually found it, and under the guidance of the Rocks team, recompiled and restarted Maui. The front end now can schedule as many active jobs as there are processors.
|PostgreSQL, the NoSQL Database||Jan 29, 2015|
|HPC Cluster Grant Accepting Applications!||Jan 28, 2015|
|Sharing Admin Privileges for Many Hosts Securely||Jan 28, 2015|
|Red Hat Enterprise Linux 7.1 beta available on IBM Power Platform||Jan 23, 2015|
|Designing with Linux||Jan 22, 2015|
|Wondershaper—QOS in a Pinch||Jan 21, 2015|
- PostgreSQL, the NoSQL Database
- Sharing Admin Privileges for Many Hosts Securely
- HPC Cluster Grant Accepting Applications!
- Internet of Things Blows Away CES, and it May Be Hunting for YOU Next
- Ideal Backups with zbackup
- Wondershaper—QOS in a Pinch
- Designing with Linux
- Red Hat Enterprise Linux 7.1 beta available on IBM Power Platform
- Slow System? iotop Is Your Friend
- January 2015 Issue of Linux Journal: Security
Editorial Advisory Panel
Thank you to our 2014 Editorial Advisors!
- Jeff Parent
- Brad Baillio
- Nick Baronian
- Steve Case
- Chadalavada Kalyana
- Caleb Cullen
- Keir Davis
- Michael Eager
- Nick Faltys
- Dennis Frey
- Philip Jacob
- Jay Kruizenga
- Steve Marquez
- Dave McAllister
- Craig Oda
- Mike Roberts
- Chris Stark
- Patrick Swartz
- David Lynch
- Alicia Gibb
- Thomas Quinlan
- Carson McDonald
- Kristen Shoemaker
- Charnell Luchich
- James Walker
- Victor Gregorio
- Hari Boukis
- Brian Conner
- David Lane