THOR: A Versatile Commodity Component of Supercomputer Development
The world's highest energy particle accelerator, the Large Hadron Collider (LHC), is presently being constructed at the European Center for Particle Physics Research (CERN) near Geneva, Switzerland. The planned date for first collisions is 2005. Since the demise of the US Superconducting Super Collider (SSC) in 1993, CERN has essentially become a world laboratory where American, African, European, Asian and Australian physicists work side by side. The LHC will penetrate deeper than ever into the microcosm to recreate the conditions prevailing in the universe just a millionth of a millionth of a second after the big bang when the temperature was ten-thousand-million-million degrees.
Our group is a small part of the team of approximately 1500 physicists, from over 100 institutions around the world, engaged in the construction of the ATLAS (A Toroidal LHC ApparatuS) experiment, one of two general-purpose detectors preparing to take data at the LHC. The experimental environment of ATLAS is punishing. For example, ATLAS has hundreds of thousands of detector channels and must keep up with a collision rate that can give rise to approximately 30 new events every 25 nanoseconds. Also, detectors and their accompanying electronics often must operate in high-radiation environments. It is obvious that the computing requirements in such an arena are, to say the least, demanding. CERN is no stranger to software developments required to solve the unique problems presented by international particle physics. For example, the World Wide Web was initially designed at CERN to help communication among the several hundred members scattered in numerous research institutes and universities.
The particle physicists in our group are involved in two areas which pose large computing problems. The first is in the area of time-critical computing, where the raw rate must be reduced from an event rate of around one gigahertz to about 100Hz by a three-stage, real-time data selection process called triggering. We are involved, along with groups from CERN, France, Italy and Switzerland, in the final stage of triggering, called the Event Filter, that reduces the data rate from 1GB/s to 100MB/s, fully reconstructs the data for the first time and writes the data to a storage medium. It is estimated that this last stage of processing would currently require on the order of a thousand “Pentiums”, if current trends in the development of processor speed continue.
We are also actively involved in simulating the response of the ATLAS detector to the physics processes that will be, or might be, present. This second task is not time-critical, but requires large simulation programs and often many hundreds of thousands of fully simulated events. Neither of these applications requires nodes to communicate during processing.
In order to pursue our research aims in these two areas, we had to develop a versatile system that could function as a real-time prototype of the ATLAS Event Filter and also be able to generate large amounts of Monte Carlo data for modeling and simulation. We needed a cost-effective solution that was scalable and modular, as well as compatible with existing technology and software. Also, because of the time scale of the project, we required a solution with a well-defined and economical upgrade path. These constraints led us inevitably toward a “Beowulf-type” commodity-component multiprocessor with a Linux operating system. The machine we finally developed was called THOR, in keeping with the Nordic nature of the names of similar-type systems such as NASA's Beowulf machine and LOKI at Los Alamos National Laboratory.
During our design discussions on THOR, it soon became clear to us that the benefits of scalability, modularity, cost-effectiveness, flexibility and access to a commercial upgrade path make the commodity-component multiprocessor an effective approach for providing high-performance computing for a myriad of scientific and commercial tasks—capable of being utilized for both time-critical and off-line data acquisition and analysis tasks. The combination of commodity Intel processors with conventional fast Ethernet and a high-speed network/back-plane fabric (Scalable Coherent Interface (SCI) from Dolphin Interconnect Solutions Inc.) enables the THOR machine to run as a cluster of serial processors, or as a fully parallel multiprocessor using MPI. It is also possible to rapidly reconfigure the THOR machine from a fully parallel mode to an all-serial mode, or for mixed parallel-serial use.
In order to demonstrate the basic ideas of the THOR project, a prototype has been constructed. A photograph of a slightly earlier incarnation of THOR is shown in Figure 1. This prototype at present consists of 42 dual Pentium II/III MHz machines (40 450MHz and 44 600MHz processors), each with 256MB of RAM. Each node is connected via a 100Mb/s Ethernet 48-way switch. A 450MHz dual Pentium II computer provides the gateway into the THOR prototype. The prototype has access to 150 gigabytes of disk space via a fast/wide SCSI interface and a 42-slot DDS2 tape robot capable of storing approximately half a terabyte of data. The THOR prototype currently runs under Red Hat Linux 6.1.
Sixteen of the 40 nodes have been connected into a two-dimensional 4x4 torus, using SCI, which allows a maximum bi-directional link speed of 800MB/s. We have measured the throughput of the SCI to be 91MB/s, which is close to the PCI bus maximum of 133MB/s. This maximum will rise when the 64-bit version of the SCI hardware, in conjunction with 64-bit PCI bus widths, are available. The use of SCI on THOR permits the classification of these THOR nodes as a Cache Coherent Non-Uniform Memory Access (CC-NUMA) architecture machine. This 16-node (32-processor) subdivision of the THOR prototype was implemented and tested as a fully parallel machine by a joint team from Dolphin Interconnect Solutions Inc. and THOR in the summer of 1999. A schematic diagram of the THOR Linux cluster is shown in Figure 2.
The THOR prototype described above is now being benchmarked as a parallel and serial machine, as well as being used for active physics research. Researchers have access to full C, C++ and FORTRAN compilers, CERN and NAG numerical libraries and MPI parallel libraries for their research use. We also plan to acquire the recent Linux release of IRIS Explorer for THOR research use in the near future. PBS (a Portable Batch System developed at NASA) has been running on THOR since March, 1999.
|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!
- Designing with Linux
- Wondershaper—QOS in a Pinch
- January 2015 Issue of Linux Journal: Security
- Internet of Things Blows Away CES, and it May Be Hunting for YOU Next
- Ideal Backups with zbackup
- Red Hat Enterprise Linux 7.1 beta available on IBM Power Platform
- Slow System? iotop Is Your Friend
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