We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a supercomputer. Our pipeline scales multiple packages used by the EM community with minimal changes to the original source codes. We tested each step of the pipeline individually, on a workstation, a cluster, and a supercomputer. Furthermore, we can compose workflows from these operations using a Balsam database that can be triggered during the data acquisition or with the use of different front ends and control the granularity of the pipeline execution. We describe the implementation of our pipeline and modifications required to integrate and scale up existing codes. The modular nature of our environment enables diverse research groups to contribute to the pipeline without disrupting the workflow, i.e. new individual codes can be easily integrated for each step on the pipeline.
Peng Cheng Laboratory（鹏城实验室）；Tsinghua University（清华大学）；Institute of Computing Technology Chinese Academy of Sciences（中国科学院计算技术研究所）
The plethora of complex artificial intelligence (AI) algorithms and available high performance computing (HPC) power stimulates the expeditious development of AI components with heterogeneous designs. Consequently, the need for cross-stack performance benchmarking of AI-HPC systems emerges rapidly. The de facto HPC benchmark LINPACK can not reflect AI computing power and I/O performance without representative workload. The current popular AI benchmarks like MLPerf have fixed problem size therefore limited scalability. To address these issues, we propose an end-to-end benchmark suite utilizing …
University of North Carolina at Charlotte（北卡罗来纳大学夏洛特分校）；Iowa State University（爱荷华州立大学）；Oak Ridge National Laboratory（橡树岭国家实验室）
Today high-performance computing (HPC) platforms are still dominated by batch jobs. Accordingly, effective batch job scheduling is crucial to obtain high system efficiency. Existing HPC batch job schedulers typically leverage heuristic priority functions to prioritize and schedule jobs. But, once configured and deployed by the experts, such priority functions can hardly adapt to the changes of job loads, optimization goals, or system settings, potentially leading to degraded system efficiency when changes occur. To address this fundamental issue, we present RLScheduler, an automated HPC batch …
We present AccaSim, a simulator for workload management in HPC systems. Thanks to AccaSim's scalability to large workload datasets, support for easy customization, and practical automated tools to aid experimentation, users can easily represent various real HPC systems, develop novel advanced dispatchers and evaluate them in a convenient way across different workload sources. AccaSim is thus an attractive tool for conducting job dispatching research in HPC systems.
We introduce the Balsam service to manage high-throughput task scheduling and execution on supercomputing systems. Balsam allows users to populate a task database with a variety of tasks ranging from simple independent tasks to dynamic multi-task workflows. With abstractions for the local resource scheduler and MPI environment, Balsam dynamically packages tasks into ensemble jobs and manages their scheduling lifecycle. The ensembles execute in a pilot "launcher" which (i) ensures concurrent, load-balanced execution of arbitrary serial and parallel programs with heterogeneous processor requirem…
This paper describes an automated approach to handling Big Data workloads on HPC systems. We describe a solution that dynamically creates a unified cluster based on YARN in an HPC Environment, without the need to configure and allocate a dedicated Hadoop cluster. The end user can choose to write the solution in any combination of supported frameworks, a solution that scales seamlessly from a few cores to thousands of cores. This coupling of environments creates a platform for applications to utilize the native HPC solutions along with the Big Data Frameworks. The user will be provided with HPC…
The Open Knowledgebase of Interatomic Models (OpenKIM) is an NSF Science Gateway that archives fully functional computer implementations of interatomic models (potentials and force fields) and simulation codes that use them to compute material properties. Interatomic models are coupled with compatible simulation codes and executed in a fully automated manner by the OpenKIM processing pipeline, a cloud-based computation platform. The pipeline as previously introduced in the literature was insufficient to support the large-scale computations that have become necessary within the materials scienc…
Domain-Specific Languages (DSLs) improve programmers productivity by decoupling problem descriptions from algorithmic implementations. However, DSLs for High-Performance Computing (HPC) have two additional critical requirements: performance and scalability. This paper presents the automated process of generating, from abstract mathematical specifications of Computational Fluid Dynamics (CFD) problems, optimised parallel codes that perform and scale as manually optimised ones. We consciously combine within Saiph, a DSL for solving CFD problems, low-level optimisations and parallelisation strate…
The University of Chicago（芝加哥大学）；Argonne National Laboratory（阿贡国家实验室）
Mapping all the neurons in the brain requires automatic reconstruction of entire cells from volume electron microscopy data. The flood-filling network (FFN) architecture has demonstrated leading performance for segmenting structures from this data. However, the training of the network is computationally expensive. In order to reduce the training time, we implemented synchronous and data-parallel distributed training using the Horovod library, which is different from the asynchronous training scheme used in the published FFN code. We demonstrated that our distributed training scaled well up to …
Reliability is a cumbersome problem in High Performance Computing Systems and Data Centers evolution. During operation, several types of fault conditions or anomalies can arise, ranging from malfunctioning hardware to improper configurations or imperfect software. Currently, system administrator and final users have to discover it manually. Clearly this approach does not scale to large scale supercomputers and facilities: automated methods to detect faults and unhealthy conditions is needed. Our method uses a type of neural network called autoncoder trained to learn the normal behavior of a re…
Advanced electron microscopy workflows require an ecosystem of microscope instruments and computing systems possibly located at different sites to conduct remotely steered and automated experiments. Current workflow executions involve manual operations for steering and measurement tasks, which are typically performed from control workstations co-located with microscopes; consequently, their operational tempo and effectiveness are limited. We propose an approach based on separate data and control channels for such an ecosystem of Scanning Transmission Electron Microscopes (STEM) and computing s…
The increasing availability of cloud computing services for science has changed the way scientific code can be developed, deployed, and run. Many modern scientific workflows are capable of running on cloud computing resources. Consequently, there is an increasing interest in the scientific computing community in methods, tools, and implementations that enable moving an application to the cloud and simplifying the process, and decreasing the time to meaningful scientific results. In this paper, we have applied the concepts of containerization for portability and multi-cloud automated deployment…
The prevalence of scientific workflows with high computational demands calls for their execution on various distributed computing platforms, including large-scale leadership-class high-performance computing (HPC) clusters. To handle the deployment, monitoring, and optimization of workflow executions, many workflow systems have been developed over the past decade. There is a need for workflow benchmarks that can be used to evaluate the performance of workflow systems on current and future software stacks and hardware platforms. We present a generator of realistic workflow benchmark specificatio…
