HPC in the cloud
Cloud Computing for Research Computing
I freely admit that I scoffed at the use of cloud computing to solve traditional HPC problems when it started coming into vogue. The idea of taking perfectly good hardware and layering virtualization on top of it with a new set of tools and APIs – in a data center that I didn't control or have access to – seemed abhorrent. As I saw HPC morphing into research computing, though, I began to realize that cloud computing is a tool for solving problems that I could not easily solve before.
The first example – in which the users need a massive number of cores and need them to run at the same time – can be solved by classic HPC systems with a large number of cores, a reasonably fast network for data traffic (10GigE), and the associated clustering software. Job arrays can be written to start and schedule 25,000 jobs. With a general-purpose cluster, jobs that have to run at the same time will likely have to wait for a large number of nodes to finish their jobs before enough cores are free to launch the queued jobs. For potentially long periods of time, the nodes will be idle, wasting CPU time waiting for cores to become available. Couple this with the short period of time users need the cores, and you have even more wasted CPU cycles. Many HPC centers have struggled with this inefficient scenario.
Perhaps a more efficient way of providing resources for these researchers and their workload is to take a standard server, virtualize it, and oversubscribe the server, providing more virtual machines (VMs) than the server has physical cores. For example, a four-socket server that has 16 cores per socket has a total of 64 cores per server, and you can run perhaps 128 or 256 VMs on the system as long as each VM has enough memory to run the application. Remember that for this type of workload, performance is not the most important metric. If, by virtualizing the server, you lose 10% to 30% in performance, you are not really negatively affecting the research. In fact, you might be enhancing the research because you can easily provide enough resources in a short period of time without wasting CPU cycles waiting for the physical cores to be available. Moreover, virtualizing the server allows a much smaller number of physical servers to be purchased to meet the needs of these workloads.
Another possibility is to push these workloads into the cloud. Because performance is not the most important concern, cloud computing resources could be very appropriate. The researchers don't need a large number of cores all of the time in this scenario, so buying dedicated hardware, even if it is virtualized, might not be the most efficient use of resources. Also, don't forget that many of these workloads don't do a great deal of I/O, so data movement to and from the cloud could have very little effect on performance. Running these applications in the cloud (e.g., Amazon or Google) might be a much more cost effective approach than providing local resources, even if they are virtualized.
Recently, Cycle Computing  announced that they started up 10,600 VM instances  inside Amazon EC2. It took two hours to configure the instances and nine hours to run (a total of 11 hours) and cost US$ 4,362. This is $0.4115 per instance for 11 hours, or $0.037 per instance per hour.
For the researcher that needs to run 25,000 instances at the same time, on the basis of Cycle's experience, I'll assume it takes two hours to start up these instances. I'll also assume it takes 15 minutes to run the application if all jobs start at the same time (0.25 hours). The total time is 2.25 hours for 25,000 instances. At a price of $0.037 per instance per hour, the resulting total cost is US$ 2,081.25. Now, assume that the researchers do this three times a week for an entire year (a total of 156 runs). The total for the year is then US$ 324,675. At first blush, this seems like enough money to buy your own on-premises system using oversubscribed virtualized machines. Or is it?
For comparison, assume the building block is a four-socket AMD node with 16 cores per socket (64 physical cores). Also assume that you oversubscribe the physical cores 3:1, producing 192 VMs per physical server. Furthermore, assume that each VM needs at least 2GB of memory, resulting in about 512GB of memory per node.
Using Dell's handy online configuration tool , I configured a 2U server that meets the specifications and has a price of about US$ 14,500. The power usage  for such a node under load is about 992W (almost 1kW), and the idle load is 434W. Assuming power is $0.14/kW, the power cost for a single system is about US$ 535 (8,721 hours at idle, 39 hours at peak load). Therefore, the cost to buy and operate a single node over one year is roughly US$ 15,000. Using the yearly cost from the Cycle Computing example, you can afford to buy roughly 21 systems. Using 192 VMs per server, you only end up with 4,032 VMs, whereas with Cycle Computing, you get 25,000 instances, even including the two hours to configure all of them when they are needed.
To match the number of VMs needed (25,000), you need about 131 servers. The purchase cost for these is US$ 1,899,500. The yearly power bill is US$ 65,500. Over one year, this works out to a total of US$ 1,965,000. Over three years, the total is US$ 2,096,000. On the other hand, using cloud computing via Cycle Computing, the price for one year is US$ 324,675; over the three years, the price is about US$ 974,025. Cloud computing works out to half the cost of a dedicated system for these workloads.
This is a very simplified analysis because you could argue that the idle systems could run someone else's jobs, but the point of the comparison is to determine whether it is better to buy dedicated systems to run 25,000 jobs at the same time, 156 times a year, using virtualized systems or to use the cloud. I think this rudimentary comparison still shows that this particular workload is more efficient in the cloud than using on-premise resources, even with oversubscribed virtual machines.
Although the title of this article is about HPC in the cloud, it's really about two things: the evolution of HPC into research computing and how cloud computing can be used to solve research computing problems. At first, it was fairly easy to dismiss cloud computing for traditional HPC workloads. The "HP," after all, stands for "high performance," and doing anything to reduce performance is counterproductive. You are paying more and getting less. However, new workloads are being added to HPC all the time that might be very different from the classic MPI applications in HPC and have different characteristics. The amount of computation in these new workloads is increasing at an alarming rate – so much so, that I think HPC is giving way to RC (research computing).
In this article, I gave two examples of new workloads that are helping to morph HPC into RC. The first example is an application class that needs to run on thousands of cores serially, doesn't run very long, and doesn't go a great deal of I/O, but all instances of the application need to run at the same time. The applications are varied, but they share these common aspects, particularly the need to run all the applications at about the same time.
Until a few years ago, I didn't hear too much about these applications, but in recent years, they've become more and more common at HPC centers. Improving the per-core performance will not help overall productivity because the applications run so quickly. What really improves productivity is running all instances of the application at the same time. This makes the researcher much more productive than having just a few applications run at a time.
In the second example, applications run on the web are being used for data post-processing, as well as data creation. These applications need web servers on which to share and investigate data and research results. In the past, these applications had to be run on IT department web servers, although they are really RC applications, and the IT departments don't really know how to handle these requests because their mission is a bit different. Consequently, these applications are increasingly run by the research computing team.
The second theme of this article is that many of the workloads in RC can be tackled by cloud computing that is not necessarily on-premises (rather, in the public cloud). The characteristics of some of the workloads are such that putting them in the cloud can save money relative to running them on traditional HPC hardware, and in many cases, it can save time because you can spin up very quickly a large set of resources larger than anything you might have in the HPC center. Moreover, moving these workloads to the cloud can also make your traditional HPC systems more efficient because you do not have large applications blocking the queues.
I consider cloud computing a tool or technique for solving research computing problems. Nothing more or less. It's not a panacea, nor should it be ignored. Issues that must be addressed include data movement and security, but it also can save you money and make your traditional HPC resources stretch further. If you examine your workloads and their characteristics carefully, I think you will be surprised how many can be run easily in the cloud.
- nanoHUB: https://nanohub.org/
- Galaxy: http://galaxyproject.org/
- Cycle Computing: http://www.cyclecomputing.com/
- Cycle Computing spins up 10,600 instances in Amazon's cloud: http://www.networkworld.com/news/2013/020713-cycle-computing-266512.html
- Dell configuration tool: http://configure.us.dell.com/dellstore/config.aspx?oc=bemtx5b&model_id=poweredge-r815&c=us&l=en&s=bsd&cs=04
- Dell Energy Smart Solution Advisor: http://essa.us.dell.com/DellStarOnline/DCCP.aspx?c=us&l=en&s=corp&Template=6945c07e-3be7-47aa-b318-18f9052df893
Buy this article as PDF
Both projects help organizations build their own containerized systems.
Mark Shuttleworth has resumed the position of CEO of Canonical.
Microsoft's open source code hosting platform CodePlex will come to an end after a more than 10-year stint.
Comes with Gnome 3.24
The bug was introduced back in 2009 and has been lurking around all this time.
The new release deprecates the sshd_config UsePrivilegeSeparation option.
Lives on as a community project
Five new systems join Dell XPS 13 Developer Edition that come with Ubuntu pre-installed.
The Skype Linux client now has almost the same capabilities that it enjoys on other platforms.
At CeBIT 2017, OpenStack Day will offer a wide range of lectures and discussions.