How Outdated Infrastructure Will Cripple HPC

By Dr. Craig Finch

May 20, 2014

The raw compute power of HPC clusters continues to grow, driven by new parallel technologies such as many-core CPUs, GPUs, and the Xeon Phi. It is well known that writing applications to exploit massive parallelism is a significant challenge to the growth of HPC. Another challenge, which is not as widely discussed, is the increasing difficulty of managing HPC clusters. The way we approach the management and administration of high performance computing clusters is slowly strangling the field of HPC.

The practices that many HPC administrators use to manage users, operating systems, applications, and workloads have not kept pace with the growth of compute power and the size of the HPC user base. A UNIX system administrator from 1985 could step out of a time machine and go right to work managing most HPC clusters today. Because many clusters are not designed for manageability, a significant amount of an HPC administrator’s time is spent doing things that could be automated.

Administrative processes are often automated with ad hoc collections of scripts and cron jobs instead of standard tools. Management tools are often overlooked when a new cluster is built or purchased, especially in organizations that are new to HPC. Many new HPC admins start from scratch and re-invent the wheel. Tools exist to solve these problems, but few people in HPC are even aware of them. My work in commercial enterprise IT has produced a paradigm shift in the way that I view system administration. The administration of HPC clusters can be transformed by applying the thought processes and tools that are currently used in cutting-edge enterprise information technology.

The root of the problem is that we think about HPC clusters today largely in terms of raw performance (Tflops or core count), a one-dimensional metric that omits important information about a system. The Top500 ranking is an obvious example of our focus on performance. To move beyond the limits of this paradigm, a cluster should be evaluated on two dimensions: performance and systemic complexity. Factors that contribute to complexity include the diversity of hardware in the cluster, diversity of the user base, and diversity of applications that run on the cluster. I learned about these issues first-hand during the two years I spent as a system administrator of the STOKES HPC cluster at the University of Central Florida. I’ve talked to many HPC specialists from around the country, and I know these problems are not unique to my university.

In terms of raw power, STOKES is a modest HPC cluster with about 3400 compute cores. However, it is a very complex system that has grown and evolved since the first hardware was purchased in 2008. STOKES includes servers from two vendors with three generations of CPUs, GP-GPUs, Xeon Phis, three brands of Infiniband hardware, and four brands of Ethernet switches. STOKES serves over 150 active users who run high-throughput and high-performance applications in a dozen different fields of physical and social sciences and engineering. In contrast, HPC systems that are more powerful than STOKES actually may be less complex. For example, the National Oceanic and Atmospheric Administration (NOAA) has two 10,000 core, 213Tflop clusters that run “production” hurricane and weather models[1].

Finch_picThese twin systems, provided and managed by IBM, have homogeneous hardware, serve a single customer, and run a small collection of applications. Figure 1 on the left shows how performance and complexity can be visualized on a two-dimensional plot.

Hardware is one fundamental source of complexity. An HPC system which grows over the years may have servers from different manufacturers with different generations of processors and interconnect hardware. Some servers may require specific versions of an operating system or different drivers to accommodate certain hardware. As hardware diversity increases, different types of errors can occur, and monitoring becomes more complicated. The trend to include accelerator hardware, such as Xeon Phi cards and GP-GPUs, means that modern clusters are often diverse by design.

The diversity of the cluster’s user base is another major source of complexity. As HPC becomes more widely used, the user base will grow and become more diverse. While this is a sign of success for a general-purpose cluster, it leads to administrative challenges. User accounts need to be created and managed more often. There will be more requests for support, which will require more time and/or better tools for monitoring the cluster and diagnosing problems.

The diversity of applications that run on the cluster is another aspect of complexity that is often correlated with the diversity of the user base. More applications are supporting parallel processing “out of the box,” often in fields that have not traditionally used HPC. These applications often bring novice users to the cluster. They are used to a graphical desktop environment, and are unprepared for the command-line and script-based submission systems used on most clusters. “Legacy” users and applications pose a different challenge: they may depend upon specific versions of the operating system, compilers, and libraries. The user may be running a program built years ago by someone else who no longer works there, and the user may not know how to recompile it. The diversity of applications also complicates workload management. Some users run high-throughput computing applications with hundreds of single-core jobs, while others need to run a single massively parallel MPI job that consumes a significant fraction of the cluster.

Today, system administration is usually managed with the tools that were provided by the original cluster vendor. As the cluster grows, administration tools that were adequate in the beginning are no longer sufficient. System administrators gradually accumulate a collection written procedures, scripts, and cron jobs to patch the gaps in the administrative framework. This approach has significant disadvantages. The amount of labor spent on administration increases as the system outgrows its management tools. This is bad news for organizations that depend on research funding, which tends to provide “up front” funds but limited or no funding for follow-on maintenance. Custom in-house solutions are only “free” if your time is worth nothing. The reliability of the system will degrade over time, as more manual input is required to keep it running. Effective operation of the system will increasingly depend on the skill and knowledge of the local sysadmin.

The ad hoc approach to system administration is also bad for the field of HPC. Significant amounts of time are spent “re-inventing the wheel” as each department, company, or university acquires its first HPC cluster. This time is wasted in the sense that it could have been better spent on advancing the field of HPC. It also increases the difficulty of attracting and retaining personnel in the HPC field.

Fortunately, there is a better way to approach the administration of an HPC cluster. The growth of cloud computing and hyperscale data centers has driven the development of practices and tools for managing computing systems that are simply too large and complex to be managed economically using methods from the 1980s. Corporate IT departments and providers of web applications and services now manage nationwide networks of servers that rival the complexity of the largest supercomputers. At this scale, a system must be designed for management. Significant amounts of time and money can be saved if these practices and tools are applied to HPC clusters.

We need to start thinking about HPC cluster management as a framework that is built from components. Every cluster has a set of management components; each component may be a software tool, or it may be a manual process. Every HPC sysadmin is familiar with workload/resource management software. Other components of the management framework may not be so obvious. For example, your cluster does have an alerting component; it may be a software tool such as Nagios, or it may be getting emails and phone calls from users when their jobs crash. You can monitor a cluster with Ganglia, or you can log in to each node and run top. Every cluster has an administrative framework, and we need to make conscious decisions about how we are going to implement that framework.

When we do choose to automate a component of the management framework, we should commit to using industry-standard system management tools wherever possible. The more “standard” a system is, the less it will cost in the long run. It is much easier to hire staff to run a system that is built with industry-standard software tools. Unfortunately, many HPC system administrators are not familiar with the standard tools that are widely used in the enterprise IT space. HPC centers are often operated as “silos” within an organization, staffed by graduate students and faculty with backgrounds in research. Enterprise IT personnel seldom cross over into HPC, since they often lack the academic qualifications for “research” positions, and the pay in research organizations is often significantly lower than in corporate IT.

There is no “one-size-fits-all” solution to the problem of cluster management. Rather, the HPC community can advance the state of cluster administration by changing the way that we approach the subject. At a high level, those who are responsible for specifying, designing, and purchasing clusters need to start prioritizing system administration. A simple calculation of Tflops per dollar is no longer sufficient. A smaller cluster with a high degree of complexity will require a larger budget for administrative systems and configuration. The alternative is to pay for these costs down the road, when the inadequacy of the administrative tools becomes clear and “unexpected” system administration costs arise.

It is difficult to justify spending more money up-front for better management tools unless there has been an honest assessment of the cost of the cluster over its lifetime. When building or purchasing a cluster, the designer or vendor must be required to specify how the proposed cluster will implement each management component. It is important to understand that the decision “we’re not going to implement this component” usually means, “we’re going to do it manually.” That can be a valid choice, but we have to budget for the long-term cost. How will the cost change if the user count or core count increases by a factor of five over the next five years? Another option is to outsource certain functions that are not core to your mission. For example, the security aspect of many clusters is implicitly outsourced to a campus or corporate IT department, which operates a border firewall that protects the cluster from outside attacks.

In order to ask the right questions, decision makers must know what components are required to manage an HPC cluster. The HPC community can help by defining a set of standard cluster management components that will form an open specification for an HPC cluster. The exact set of components, and which components should be automated first, is open to debate. As a starting point for a broader discussion, I propose that the minimum core components required for any HPC cluster are identity management, workload management, and security. Another tier of components may be implemented manually on “personal” clusters, but become increasingly time-consuming as the number of users increases beyond the size of a small research group. These components include monitoring, alerting/notification, and configuration management. Finally, designing systems for reliability becomes critical for clusters that serve large numbers of users.

The HPC community can also help cluster designers and administrators choose standard system management tools. In order to take advantage of the ecosystem of enterprise IT management tools, HPC sysadmins need to know which tools are available, and they need information to help them choose the best tool for their needs. The open cluster specification can enumerate the most widely used tools that can be used to automate each component of a cluster. To help choose the right tool for a particular situation, the HPC community needs to publish more information about how we manage our clusters. We need to report which management tools we are using, why we are using them, and how well those tools are working for us. We also need to increase our contributions to open source projects, documentation, and standards so that other HPC sysadmins can benefit from our experience.

Commercial software, whether provided by a cluster vendor or a third-party vendor, is also an important part of cluster administration. However, even commercial tools need to “play nicely” with other software to enable a healthy HPC ecosystem. HPC-specific management tools need to offer better support for modern management features. For example, any tool that depends upon user identities should be able to authenticate against an identity server instead of requiring an administrator to create and maintain another unique identity for every user. Software tools should also be able to exchange data in a standard format (SNMP, JSON, XML, etc.) to enable centralized services such as monitoring and logging.

It’s time for the HPC community to start regarding system administration as a critical aspect of an HPC cluster. We can build better administrative frameworks by drawing on the strategies and tools developed for enterprise IT. Working together as a community, we can dramatically reduce the amount of time that is wasted on outdated, inefficient cluster management practices.

About the Author

Craig Finch is a Principal Consultant at Rootwork InfoTech LLC ( Craig started his career as a design engineer in the wireless communications sector during the rapid growth period of the late 90′s. Growing bored with the evolutionary nature of wireless technology, the end of the tech bubble provided an occasion to take a break from industry and pursue a full-time PhD in Modeling and Simulation while performing research at the NanoScience Technology Center at the University of Central Florida (UCF). Craig developed predictive computational tools and used them to design optical biosensors, microfluidic devices, and functional tissue constructs. Following his PhD, he was responsible for STOKES, the core high performance computing cluster at UCF. Dr. Finch was a co-PI on several proposals, including a funded cyberinfrastructure grant from the National Science Foundation. On the side, Craig has worked as a concert lighting designer, wrote a technical book (Sage Beginners Guide), and held leadership positions in volunteer organizations.






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