Stepping towards noiseless Linux environment

Abstract

Scientific applications are interrupted by the operating system far too often. Historically operating systems have been written efficiently to time-share a single resource, the CPU. We now have an abundance of cores but we are still swapping out the application to run other tasks and therefore increasing the application's time to solution. Current task scheduling in Linux is not tuned for a high performance computing environment, where a single job is running on all available cores. For example, checking for context switches hundreds of times per second is counter-productive in this setting. One solution to this problem is to partition the cores between operating system and application; with the advent of many-core processors this approach is more attractive. This work describes our investigation of isolation of application processes from the operating system using a soft-partitioning scheme. We use increasingly invasive approaches; from configuration changes with available Linux features such as control groups and pinning interrupts using the CPU affinity settings, to invasive source level code changes to try to reduce, or in some cases completely eliminate, application interruptions such as OS clock ticks and timers. Explained here are the measures that can be taken to reduce application interruption solely with compile and run time configurations in a recent unmodified Linux kernel. Although these measures have been available for a some time, to our knowledge, they have never been addressed in an HPC context. We then introduce our invasive method, where we remove the involuntary preemption induced by task scheduling. Our experiments show that parallel applications benefit from these modifications even at relatively small scales. At the modest scale of our testbed, we see a 1.72% improvement that should project into higher benefits at extreme scales.