An official website of the United States government
Traditionally, HPC workloads have been deployed in bare-metal clusters; but the advances in virtualization have led the pathway for these workloads to be deployed in virtualized clusters. However, HPC cluster administrators/providers still face challenges in terms of resource elasticity and virtual machine (VM) provisioning at large-scale, due to the lack of coordination between a traditional HPC scheduler and the VM hypervisor (resource management layer). This lack of interaction leads to low cluster utilization and job completion throughput. Furthermore, the VM provisioning delays directly impact the overall performance of jobs in the cluster. Hence, there is a need for effectively provisioning virtualized HPC clusters, which can best-utilize the physical hardware with minimal provisioning overheads.Towards this, we propose Multiverse, a VM provisioning framework, which can dynamically spawn VMs for incoming jobs in a virtualized HPC cluster, by integrating the HPC scheduler along with VM resource manager. We have implemented this framework on the Slurm scheduler along with the vSphere VM resource manager. In order to reduce the VM provisioning overheads, we use instant cloning which shares both the disk and memory with the parent VM, when compared to full VM cloning which has to boot-up a new VM from scratch. Measurements with real-world HPC workloads demonstrate that, instant cloning is 2.5× faster than full cloning in terms of VM provisioning time. Further, it improves resource utilization by up to 40%, and cluster throughput by up to 1.5×, when compared to full clone for bursty job arrival scenarios.
more »
« less
Expanding an HPC Cluster to Support the Computational Demands of Digital Pathology
The goal of this work was to design a low-cost computing facility that can support the development of an open source digital pathology corpus containing 1M images [1]. A single image from a clinical-grade digital pathology scanner can range in size from hundreds of megabytes to five gigabytes. A 1M image database requires over a petabyte (PB) of disk space. To do meaningful work in this problem space requires a significant allocation of computing resources. The improvements and expansions to our HPC (highperformance computing) cluster, known as Neuronix [2], required to support working with digital pathology fall into two broad categories: computation and storage. To handle the increased computational burden and increase job throughput, we are using Slurm [3] as our scheduler and resource manager. For storage, we have designed and implemented a multi-layer filesystem architecture to distribute a filesystem across multiple machines. These enhancements, which are entirely based on open source software, have extended the capabilities of our cluster and increased its cost-effectiveness. Slurm has numerous features that allow it to generalize to a number of different scenarios. Among the most notable is its support for GPU (graphics processing unit) scheduling. GPUs can offer a tremendous performance increase in machine learning applications [4] and Slurm’s built-in mechanisms for handling them was a key factor in making this choice. Slurm has a general resource (GRES) mechanism that can be used to configure and enable support for resources beyond the ones provided by the traditional HPC scheduler (e.g. memory, wall-clock time), and GPUs are among the GRES types that can be supported by Slurm [5]. In addition to being able to track resources, Slurm does strict enforcement of resource allocation. This becomes very important as the computational demands of the jobs increase, so that they have all the resources they need, and that they don’t take resources from other jobs. It is a common practice among GPU-enabled frameworks to query the CUDA runtime library/drivers and iterate over the list of GPUs, attempting to establish a context on all of them. Slurm is able to affect the hardware discovery process of these jobs, which enables a number of these jobs to run alongside each other, even if the GPUs are in exclusive-process mode. To store large quantities of digital pathology slides, we developed a robust, extensible distributed storage solution. We utilized a number of open source tools to create a single filesystem, which can be mounted by any machine on the network. At the lowest layer of abstraction are the hard drives, which were split into 4 60-disk chassis, using 8TB drives. To support these disks, we have two server units, each equipped with Intel Xeon CPUs and 128GB of RAM. At the filesystem level, we have implemented a multi-layer solution that: (1) connects the disks together into a single filesystem/mountpoint using the ZFS (Zettabyte File System) [6], and (2) connects filesystems on multiple machines together to form a single mountpoint using Gluster [7]. ZFS, initially developed by Sun Microsystems, provides disk-level awareness and a filesystem which takes advantage of that awareness to provide fault tolerance. At the filesystem level, ZFS protects against data corruption and the infamous RAID write-hole bug by implementing a journaling scheme (the ZFS intent log, or ZIL) and copy-on-write functionality. Each machine (1 controller + 2 disk chassis) has its own separate ZFS filesystem. Gluster, essentially a meta-filesystem, takes each of these, and provides the means to connect them together over the network and using distributed (similar to RAID 0 but without striping individual files), and mirrored (similar to RAID 1) configurations [8]. By implementing these improvements, it has been possible to expand the storage and computational power of the Neuronix cluster arbitrarily to support the most computationally-intensive endeavors by scaling horizontally. We have greatly improved the scalability of the cluster while maintaining its excellent price/performance ratio [1].
more »
« less
- Award ID(s):
- 1726188
- PAR ID:
- 10211255
- Editor(s):
- Obeid, Iyad; Selesnick, Ivan; Picone, Joseph
- Date Published:
- Journal Name:
- IEEE Signal Processing in Medicine and Biology Symposium (SPMB)
- Volume:
- 1
- Issue:
- 1
- Page Range / eLocation ID:
- 01 to 03
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Twister2 is an open‐source big data hosting environment designed to process both batch and streaming data at scale. Twister2 runs jobs in both high‐performance computing (HPC) and big data clusters. It provides a cross‐platform resource scheduler to run jobs in diverse environments. Twister2 is designed with a layered architecture to support various clusters and big data problems. In this paper, we present the cross‐platform resource scheduler of Twister2. We identify required services and explain implementation details. We present job startup delays for single jobs and multiple concurrent jobs in Kubernetes and OpenMPI clusters. We compare job startup delays for Twister2 and Spark at a Kubernetes cluster. In addition, we compare the performance of terasort algorithm on Kubernetes and bare metal clusters at AWS cloud.more » « less
-
With the wide adoption of deep neural network (DNN) models for various applications, enterprises, and cloud providers have built deep learning clusters and increasingly deployed specialized accelerators, such as GPUs and TPUs, for DNN training jobs. To arbitrate cluster resources among multi-user jobs, existing schedulers fall short, either lacking fine-grained heterogeneity awareness or hardly generalizable to various scheduling policies. To fill this gap, we propose a novel design of a task-level heterogeneity-aware scheduler, Hadar, based on an online optimization framework that can express other scheduling algorithms. Hadar leverages the performance traits of DNN jobs on a heterogeneous cluster, characterizes the task-level performance heterogeneity in the optimization problem, and makes scheduling decisions across both spatial and temporal dimensions. The primal-dual framework is employed, with our design of a dual subroutine, to solve the optimization problem and guide the scheduling design. Extensive trace-driven simulations with representative DNN models have been conducted to demonstrate that Hadar improves the average job completion time (JCT) by 3× over an Apache YARN-based resource manager used in production. Moreover, Hadar outperforms Gavel[1], the state-of-the-art heterogeneity-aware scheduler, by 2.5× for the average JCT, and shortens the queuing delay by 13% and improve FTF (Finish-Time-Fairness) by 1.5%.more » « less
-
The Sia1 scheduler efficiently assigns heterogeneous deep learning (DL) cluster resources to elastic resource-adaptive jobs. Although some recent schedulers address one aspect or another (e.g., heterogeneity or resource-adaptivity), none addresses all and most scale poorly to large clusters and/or heavy workloads even without the full complexity of the combined scheduling problem. Sia introduces a new scheduling formulation that can scale to the search-space sizes and intentionally match jobs and their configurations to GPU types and counts, while adapting to changes in cluster load and job mix over time. Sia also introduces a low- profiling-overhead approach to bootstrapping (for each new job) throughput models used to evaluate possible resource assignments, and it is the first cluster scheduler to support elastic scaling of hybrid parallel jobs. Extensive evaluations show that Sia outperforms state-of- the-art schedulers. For example, even on relatively small 44- to 64-GPU clusters with a mix of three GPU types, Sia reduces average job completion time ( JCT) by 30–93%, 99th percentile JCT and makespan by 28–95%, and GPU hours used by 12– 55% for workloads derived from 3 real-world environments. Additional experiments demonstrate that Sia scales to at least 2000-GPU clusters, provides improved fairness, and is not over-sensitive to scheduler parameter settings.more » « less
-
Accurate wait-time prediction for HPC jobs contributes to a positive user experience but has historically been a challenging task. Previous models lack the accuracy needed for confident predictions, and many were developed before the rise of deep learning. In this work, we investigate and develop TROUT, a neural network-based model to accurately predict wait times for jobs submitted to the Anvil HPC cluster. Data was taken from the Slurm Workload Manager on the cluster and transformed before performing additional feature engineering from jobs’ priorities, partitions, and states. We developed a hierarchical model that classifies job queue times into bins before applying regression, outperforming traditional methods. The model was then integrated into a CLI tool for queue time prediction. This study explores which queue time prediction methods are most applicable for modern HPC systems and shows that deep learning-based prediction models are viable solutions.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/SPMB.2018.8615614
