Section: Application Domains
Integration of High Performance Computing and Data Analytics
Data produced by large simulations are traditionally handled by an I/O layer that moves them from the compute cores to the file system. Analysis of these data are performed after reading them back from files, using some domain specific codes or some scientific visualisation libraries like VTK. But writing and then reading back these data generates a lot of data movements and puts under pressure the file system. To reduce these data movements, the in situ analytics paradigm proposes to process the data as closely as possible to where and when the data are produced. Some early solutions emerged either as extensions of visualisation tools or of I/O libraries like ADIOS. But significant progresses are still required to provide efficient and flexible high performance scientific data analysis tools. Integrating data analytics in the HPC context will have an impact on resource allocation strategies, analysis algorithms, data storage and access, as well as computer architectures and software infrastructures. But this paradigm shift imposed by the machine performance also sets the basis for a deep change on the way users work with numerical simulations. The traditional workflow needs to be reinvented to make HPC more user-centric, more interactive and turn HPC into a commodity tool for scientific discovery and engineering developments. In this context DataMove aims at investigating programming environments for in situ analytics with a specific focus on task scheduling in particular, to ensure an efficient sharing of resources with the simulation.
Programming Model and Software Architecture
In situ creates a tighter loop between the scientist and her/his simulation. As such, an in situ framework needs to be flexible to let the user define and deploy its own set of analysis. A manageable flexibility requires to favor simplicity and understandability, while still enabling an efficient use of parallel resources. Visualization libraries like VTK or Visit, as well as domain specific environments like VMD have initially been developed for traditional post-mortem data analysis. They have been extended to support in situ processing with some simple resource allocation strategies but the level of performance, flexibility and ease of use that is expected requires to rethink new environments. There is a need to develop a middleware and programming environment taking into account in its fundations this specific context of high performance scientific analytics.
Similar needs for new data processing architectures occurred for the emerging area of Big Data Analytics, mainly targeted to web data on cloud-based infrastructures. Google Map/Reduce and its successors like Spark or Stratosphere/Flink have been designed to match the specific context of efficient analytics for large volumes of data produced on the web, on social networks, or generated by business applications. These systems have mainly been developed for cloud infrastructures based on commodity architectures. They do not leverage the specifics of HPC infrastructures. Some preliminary adaptations have been proposed for handling scientific data in a HPC context. However, these approaches do not support in situ processing.
Following the initial development of FlowVR, our middleware for in situ processing, we will pursue our effort to develop a programming environment and software architecture for high performance scientific data analytics. Like FlowVR, the map/reduce tools, as well as the machine learning frameworks like TensorFlow, adopted a dataflow graph for expressing analytics pipe-lines. We are convinced that this dataflow approach is both easy to understand and yet expresses enough concurrency to enable efficient executions. The graph description can be compiled towards lower level representations, a mechanism that is intensively used by Stratosphere/Flink for instance. Existing in situ frameworks, including FlowVR, inherit from the HPC way of programming with a thiner software stack and a programming model close to the machine. Though this approach enables to program high performance applications, this is usually too low level to enable the scientist to write its analysis pipe-line in a short amount of time. The data model, i.e. the data semantics level accessible at the framework level for error check and optimizations, is also a fundamental aspect of such environments. The key/value store has been adopted by all map/reduce tools. Except in some situations, it cannot be adopted as such for scientific data. Results from numerical simulations are often more structured than web data, associated with acceleration data structures to be processed efficiently. We will investigate data models for scientific data building on existing approaches like Adios or DataSpaces.
To alleviate the I/O bottleneck, the in situ paradigm proposes to start processing data as soon as made available by the simulation, while still residing in the memory of the compute node. In situ processings include data compression, indexing, computation of various types of descriptors (1D, 2D, images, etc.). Per se, reducing data output to limit I/O related performance drops or keep the output data size manageable is not new. Scientists have relied on solutions as simple as decreasing the frequency of result savings. In situ processing proposes to move one step further, by providing a full fledged processing framework enabling scientists to more easily and thoroughly manage the available I/O budget.
The most direct way to perform in situ analytics is to inline computations directly in the simulation code. In this case, in situ processing is executed in sequence with the simulation that is suspended meanwhile. Though this approach is direct to implement and does not require complex framework environments, it does not enable to overlap analytics related computations and data movements with the simulation execution, preventing to efficiently use the available resources. Instead of relying on this simple time sharing approach, several works propose to rely on space sharing where one or several cores per node, called helper cores, are dedicated to analytics. The simulation responsibility is simply to handle a copy of the relevant data to the node-local in situ processes, both codes being executed concurrently. This approach often lead to significantly beter performance than in-simulation analytics.
For a better isolation of the simulation and in situ processes, one solution consists in offloading in situ tasks from the simulation nodes towards extra dedicated nodes, usually called staging nodes. These computations are said to be performed in-transit. But this approach may not always be beneficial compared to processing on simulation nodes due to the costs of moving the data from the simulation nodes to the staging nodes.
FlowVR enables to mix these different resources allocation strategies for the different stages of an analytics pile-line. Based on a component model, the scientist designs analytics workflows by first developing processing components that are next assembled in a dataflow graph through a Python script. At runtime the graph is instantiated according to the execution context, FlowVR taking care of deploying the application on the target architecture, and of coordinating the analytics workflows with the simulation execution.
But today the choice of the resource allocation strategy is mostly ad-hoc and defined by the programmer. We will investigate solutions that enable a cooperative use of the resource between the analytics and the simulation with minimal hints from the programmer. In situ processings inherit from the parallelization scale and data distribution adopted by the simulation, and must execute with minimal perturbations on the simulation execution (whose actual resource usage is difficult to know a priori). We need to develop adapted scheduling strategies that operate at compile and run time. Because analysis are often data intensive, such solutions must take into consideration data movements, a point that classical scheduling strategies designed first for compute intensive applications often overlook. We expect to develop new scheduling strategies relying on the methodologies developed in Section 4.1.5. Simulations as well as analysis are iterative processes exposing a strong spatial and temporal coherency that we can take benefit of to anticipate their behavior and then take more relevant resources allocation strategies, possibly based on advanced learning algorithms or as developed in Section 4.1.
In situ analytics represent a specific workload that needs to be scheduled very closely to the simulation, but not necessarily active during the full extent of the simulation execution and that may also require to access data from previous runs (stored in the file system or on specific burst-buffers). Several users may also need to run concurrent analytics pipe-lines on shared data. This departs significantly from the traditional batch scheduling model, motivating the need for a more elastic approach to resource provisioning. These issues will be conjointly addressed with research on batch scheduling policies (Section 4.1).
Co-Design with Data Scientists
Given the importance of users in this context, it is of primary importance that in situ tools be co-designed with advanced users, even if such multidisciplinary collaborations are challenging and require constant long term investments to learn and understand the specific practices and expectations of the other domain.
We will tightly collaborate with scientists of some application domains, like molecular dynamics or fluid simulation, to design, develop, deploy and assess in situ analytics scenarios, as already done with Marc Baaden, a computational biologist from LBT.
We recently extended our collaboration network. We started in 2015 a PhD co-advised with CEA DAM to investigate in situ analytics scenarios in the context of atomistic material simulations. CEA DAM is a French energy lab hosting one of the largest european supercomputer. They gather physicists, numerical scientists as well as high performance computer engineers, making it a very interesting partner for developing new scientific data analysis solutions. We also got a national grant (2015-2018) to compute in situ statistics for multi-parametric parallel studies with the research department of French power company EDF. In this context we collaborate with statisticians and fluid simulation experts to define in situ scenarios, revisit the statistic operators to be amenable to in situ processing, and define an adapted in situ framework.