Better than Native: Using Virtualization to Improve Compute Node Performance Brian Kocoloski Jack Lange Department of Computer Science University of Pittsburgh 1/12/2019

Linux is becoming the dominant supercomputing OS … Source: http://en.wikipedia.org/wiki/File:Operating_systems_used_on_top_500_supercomputers.svg

… but some applications need less overhead Lightweight Kernels (LWKs) provide low overhead access to hardware Q: How do we provide LWKs to applications that need them, but not to those that don’t? A: Virtualization Applications running in a virtual environment can outperform the same applications running natively Virtualization - We can launch LWKs inside of virtual machines (VMs) to provide isolated, low overehad environments to applications. In doing so, we improve the performance of the host OS

Drawbacks of Linux Memory Management OS Noise Non-technical Biggest problem Widely recognized as a source of overhead OS Noise HPC apps are tightly synchronized Timing is a big deal Non-technical Noise: any events that interrupt a running program Ex: kernel timer, task schedulers, and even general management processes such as mail clients Overheads experienced by 1 node of a bulk synchronous parallel application are often inflicted on other nodes, as all nodes execute in lockstep Non-technical: Linux is not inherently an HPC OS, so it requires modification to avoid the overhead inherent in it’s design Huge burden on OS developers that have to keep up with the ever-changing Linux code base

Disadvantages of Current Schemes ZeptoOS “Big Memory” Memory is statically sized, allocated at boot time Compatibility Cray’s CNL HugeTLBfs Maximum of 2MB-sized memory regions available ZeptoOS compute node Linux consists of modifications to improve the usability of the Linux kernel for HPC ZeptoOS - “Big Memory” – preallocation of large contiguous regions of memory at boot time Preallocated memory is static and at boot time Compatibility – latest version based on kernel version 2.6.19 (released in 2006) Cray’s CNL is a runtime environment based on the Linux kernel CNL – appears to mimic the use of hugetlbfs architecture Limits the size of contiguous regions that can be given to applications

Application Completes Our Approach Linux Compute Node OS Hardware No Linux Compute Node OS HPC Application Yes Lightweight Kernel Application Completes Needs LWK? Hardware LWKs are able to manage memory more efficiently and eliminate OS noise After: 1. VMs allow us to launch LWKs when they are “needed” – memory available to host if not 2. Requires no modification to host OS 3. Requires no system reconfiguration 4. We are able to deliver large allocations in a way that requires no modification to the Linux kernel, in contrast to previous schemes VMM layer Linux Compute Node OS Hardware

Palacios OS-independent embeddable virtual machine monitor Strip resources away from host OS Low noise, low overhead memory management Developed at Northwestern University, University of New Mexico, and University of Pittsburgh Open source and freely available Raw resources allow low overhead access for guest OS http://www.v3vee.org/palacios

Kitten Lightweight Kernel from Sandia National Labs Moves resource management as close to application as possible Mostly Linux-compatible user environment Modern code-base with Linux-like organization Open source and freely available Like many LWKS, emphasizes efficiency over functionality – provide only what is necessary for applications – this limits noise and makes memory management easier Familiar user-environment and code-base makes it easier for application developers http://software.sandia.gov/trac/kitten

System Architecture

System Architecture (1) Insertable as a kernel module at runtime – thus, requires no modification or reconfiguration of any kind to the Linux kernel

System Architecture (1) Resource Managers – strip control of raw hardware from host OS Raw access allows us to bypass host OS, and control two main areas (1) Memory Management, and (2) When and where Linux scheduler runs (2) LWK/HPC on top of Palacios (3) Finally, again, the Linux based kernel only needs to expose the module API for this approach to be feasible

Palacios’ Approach Memory Management OS Noise Bypass the Linux memory management strategies completely, at run time OS Noise Control when the Linux scheduler is able to run Take advantage of tickless host kernel Linux Management Linux Management Palacios Management Offlined Linux Management 1. Initially, we have the Linux kernel managing all of the memory in the system. 2. Hotpluggable memory interface provided by Linux allows us to “offline” – this has the effect of making the memory seem unavailable to Linux. Our approach is to offline only contiguous regions. Thus, when we take control of these offlined blocks, the resulting simplicity of guest to host memory address translations allows us to manage it with very little overhead 3. Finally, when guest OS is finished, we can return the memory to the Linux host 4. OS noise – control when by determining which VM exits will yield control to the Linux scheduler 5. Tickless host kernel – avoid frequent host timer interrupts – more on this later

Evaluation Two part evaluation: Evaluation is preliminary Microbenchmarks – Stream, Selfish Miniapplications – HPCCG, pHPCCG Evaluation is preliminary Currently limited to a single node running a commodity Fedora 15 kernel Environments are not fully optimized Microbenchmarks – used to measure memory performance and ability to control noise Miniapplications – used to measure performance with a “real” HPC app

Environment Two 6-core processors and 16 GB memory NUMA design Kitten VM was configured with 1 GB of memory Stream, HPCCG used OpenMP for shared memory and ran 10 times 1 GB – due to initial limitations

Stream Palacios provides ~400 MB/s better memory performance on average than Linux (4.74%) 0.34 GB/s lower standard deviation on average Stream is a microbenchmark that measures memory bandwidth

Selfish Detour Linux Kitten Selfish Detour - microbenchmark that measures and detects interruptions of its execution Fair amount of low level noise in both environments, but… Quick: Kitten significantly less noisy – consistent, predictable

Selfish Detour Linux Virtualized Kitten There is overhead – low level noise goes from roughly 7 ms to around 10, but … …Notice host 100 HZ timer gone – thanks to tickless With few exceptions, Palacios is indeed able to isolate the noise of the Linux host – and it doesn’t insert too much noise itself

HPCCG Performs the conjugate gradient method to solve a system of linear equations represented by a sparse matrix Workload similar to that of many HPC applications Separate experiments to represent both CPU and memory intensive workloads Single-precision – more CPU-intensive Double-precision – more memory-intensive

HPCCG – CPU intensive Palacios provides better performance than native Linux when running on the same NUMA node (1,2,4 cores), but slightly worse performance on 8 cores On 8 cores, we believe that Palacios is worst because of NUMA – the Kitten VM has no understanding of the underlying NUMA layout. Linux, however, does have that information available Palacios’ performance is most consistent which indicates that it is likely to exhibit better scalability that linux Again, while not better across the board, Palacios was indeed better in 2 scenarios, showing that it is capable of outperforming a native Linux host

HPCCG – memory intensive Only experiment in which Palacios typically performs slightly worse than native Linux – above 1 core however, results are nearly identical However, Palacios did provide lower variance than either Linux configuration – again good for scaling

Future Work Extend to actual Cray hardware with a CNL host Show definitively if this approach can work Explore the possibility that this approach can be deployed in a cloud setting to provide virtual HPC environments on commodity clouds Previously infeasible, due to the contention, noise, etc. Problems we think can be solved by the same techniques used in this work

Conclusions Palacios is capable of providing superior performance to native Linux Palacios can provide a low noise environment, even when running on a noisy Linux host While results are preliminary, they show that this approach is feasible at small scales Superior, particularly in Stream Feasible at small scales, and the consistency demonstrated in all environments is indicative that it is likely to scale well

Acknowledgments Palacios: http://www.v3vee.org/palacios Kitten: https://software.sandia.gov/trac/kitten Email: briankoco@cs.pitt.edu jacklange@cs.pitt.edu