THOR: A Versatile Commodity Component of Supercomputer Development
We benchmarked the THOR prototype extensively, when it consisted of 20 450MHz dual Pentium IIs. This benchmarking used a variety of software. The first of two benchmark programs reported here was a three-dimensional Fast Fourier Transform (FFT) program written in FORTRAN using MPI. This software uses the THOR cluster as a parallel machine rather than a serial processor. As can be seen in Figure 3, the speed of a single THOR node using this FFT is comparable to a 450MHz Cray-T3E and the Calgary DEC Alpha cluster (in 1999) and is roughly 50% slower than an SGI Origin 2000 (R10K). As a fully parallel machine, one can see that THOR is competitive with the Calgary DEC Alpha cluster and with the Cray-T3E for this FFT procedure.
The second benchmark was obtained using the code developed to utilize the method of finite differences in the area of seismic modeling, and is written in C using MPI. In this case, the comparison was between the THOR multiprocessor using SCI interconnect, or 100 Mbp/s Ethernet and an SGI Origin 2000. The results are shown in Figure 4. As can be seen, the use of the SCI backplane/network fabric improves the performance of the THOR multiprocessor as compared to an Ethernet network solution. According to this benchmark, the performance of the THOR multiprocessor using SCI becomes comparable to that of the SGI Origin 2000 as the number of processors approaches sixteen.
Over the last year and a half, THOR has grown from just two dual Pentium II machines to over 40 dual Pentium II/IIIs. We found that the maintenance and operation of a two-node array was not much different from running a 40-node array. Another gratifying feature, which has been reported by other groups with Beowulf-type clusters, is the reliability of the THOR cluster. We have been running the PBS batch queuing system since March, 1999, and have logged over 80,000 CPU hours with only one system failure due to a power interruption, which led us to introduce non-interruptible power supplies for the complete cluster. Another important discovery was that the construction and maintenance of THOR did not need a team of highly skilled personnel. We found that only “one quarter” of a person skilled in PC networking and Linux was required to implement the system, with some initial assistance from Dolphin for the SCI network. Also, the use of commodity operating systems allows programs to be developed at researchers' desktop machines for later implementation on THOR, thus easing the task of software development.
Our experience running THOR has been in three main areas: multiple-serial Monte Carlo (or embarrassingly parallel) production jobs, prototyping an Event Filter sub-farm for ATLAS (a time-critical operation using specialized software developed for the ATLAS high-level trigger system) and as a fully parallel processor. Large Linux clusters are probably most effective when running applications that require almost no inter-processor communication where the network does not become a bottleneck. However, many applications that require fully parallel machines for significant message passing still spend most of their time computing.
Because parallel computing is such an important topic, we spent some time assessing how the THOR multiprocessor running Linux can be used to implement applications requiring parallel processing. Since there is currently a high level of support for shared-memory programming under SMP Linux, we have used the THOR Linux cluster with the message-passing construct, Message Passing Interface (MPI). There are several advantages to using this programming model. For example, many parallel applications are limited more by floating-point performance than by inter-processor communication. Thus, SCI and even fast Ethernet are sufficient even when there is a relatively large amount of message passing. Another advantage is that MPI is a standard programming interface that runs on many parallel machines, such as the Cray T3 series, IBM SP series, SGI Origin, Fujitsu and PC/Macintosh clusters. Therefore, code can be moved easily between platforms.
One of the THOR groups involved in Plasma Physics research has developed simulations that follow the motion of about 12 million charged particles. A portion of this code utilizes multi-dimensional Fast Fourier Transforms. We achieved nearly perfect scalability for up to 32 processors (all that was available at the time) on the THOR cluster. The code, following the MPI model, was easily transferred from an SGI Origin 2000 platform to the THOR Linux cluster. The performance of this program on THOR compared with other platforms as shown in Figure 3. Other benchmarks are given in Figure 4. At the time these benchmarks were performed, THOR consisted of only 450MHz machines.
Webinar: 8 Signs You’re Beyond Cron
11am CDT, April 29th
Join Linux Journal and Pat Cameron, Director of Automation Technology at HelpSystems, as they discuss the eight primary advantages of moving beyond cron job scheduling. In this webinar, you’ll learn about integrating cron with an enterprise scheduler.Join us!
- March 2015 Issue of Linux Journal: High-Performance Computing
- Not So Dynamic Updates
- April 2015 Video Preview
- Users, Permissions and Multitenant Sites
- New Products
- Flexible Access Control with Squid Proxy
- Security in Three Ds: Detect, Decide and Deny
- DevOps: Everything You Need to Know
- Non-Linux FOSS: MenuMeters
- Tighten Up SSH