Choose the Software for High-performance computing

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we detailed the hardware choices and benchmarked the various GPUs and CPUs used in the HPU4Science scientific long life battery computation cluster. The cluster is built in a master-worker configuration in which the master dispatches jobs to the workers, compiles and processes the results, and handles data storage. The master is equipped with a dual Intel XEON processor, a four-SSD RAID array for short-term storage, and an array of five 2TB hard drives for archival Powerful http://www.goodlaptopbattery.com.au/laptop-ac-adapter/liteon/travelmate-4200.htm storage. The networking is a simple Gigabit Ethernet.

Currently, there are three workers in the cluster running Intel i7 or Core 2 Quad processors and using GPUs for highly parallelized computation. In the last paper, the third and newest worker had four GTX 580s that give four TFlops of measured, peak computational performance (this equates to six TFLOPs of theoretical performance, which is the measure used for the 1 year waranty Top500 http://www.goodlaptopbattery.com.au/apple/a1185.htm supercomputers list). The hardware for a fourth worker with the same configuration as the third has just arrived, so the cluster will soon comprise a total of four workers with eight GTX 580s, three GTX 480s, three GTX 285s, a C1060 Tesla GPU, and a GTX 295 dual GPU. The estimated computational power of the whole system is 20 TFLOPS in theory, and 12.5 TFLOPS in practice. Some brand new GTX 590s are currently being ordered for a fifth worker, so the total computational power is still increasing.

Obviously, a cluster of this scale requires careful software selection to maximize the performance of the hardware. In this article, we detail the software choices for the HPU4Science cluster and discuss the areas where software and performance collide.
Operating system: Linux

Linux is the current standard bearer for high performance computing operating systems, with almost 92 percent of the top 500 supercomputers. Every major scientific Fast shipping http://www.goodlaptopbattery.com.au/acer/aspire-5500.htm computation project in the world, including the Large Hadron Collider, runs on Linux. The key features of Linux are stability, the ability to pick from a wide variety of file systems (more on this in a moment), the large existing code base for high performance computing, and the ease of tailoring the OS to the specific hardware requirements. Availability of open-source projects with code that can be configured for highly parallelized processing was also an important consideration.

The master and all workers run Ubuntu server edition, installed with the minimal OpenSSH server profile. The current kernel on the system is 2.6.35. All of the system software—including Python, SAGE, CUDA (a GPU programming library from NVIDIA)—and standard development Discount http://www.goodlaptopbattery.com.au/dell/inspiron-1520.htm software like gcc is installed using Python/Bash scripts and apt-get . All machines are headless to minimize the OS memory footprint, so all interaction with the cluster is done at the command prompt through ssh. The cluster is monitored using a home-made display based on gnu screen, byobu, htop and nvidia-smi. The entire operating system has a memory footprint of around 100MB (this includes a few additional administrative scripts beyond the bare-bones operating system).

There is a central code repository server using GIT for backup, but the cluster mostly uses local git repos that are synced locally. Git Brand new laptop ac adapter branches are used to explore new software configurations on a testing machine before applying them to the cluster.

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