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1. MemHC: An Optimized GPU Memory Management Framework for Accelerating Many-body Correlation

   https://doi.org/10.1145/3506705  

   Wang, Qihan ; Peng, Zhen ; Ren, Bin ; Chen, Jie ; Edwards, Robert G. ( June 2022 , ACM Transactions on Architecture and Code Optimization)

   The many-body correlation function is a fundamental computation kernel in modern physics computing applications, e.g., Hadron Contractions in Lattice quantum chromodynamics (QCD). This kernel is both computation and memory intensive, involving a series of tensor contractions, and thus usually runs on accelerators like GPUs. Existing optimizations on many-body correlation mainly focus on individual tensor contractions (e.g., cuBLAS libraries and others). In contrast, this work discovers a new optimization dimension for many-body correlation by exploring the optimization opportunities among tensor contractions. More specifically, it targets general GPU architectures (both NVIDIA and AMD) and optimizes many-body correlation’s memory management by exploiting a set of memory allocation and communication redundancy elimination opportunities: first, GPU memory allocation redundancy : the intermediate output frequently occurs as input in the subsequent calculations; second, CPU-GPU communication redundancy : although all tensors are allocated on both CPU and GPU, many of them are used (and reused) on the GPU side only, and thus, many CPU/GPU communications (like that in existing Unified Memory designs) are unnecessary; third, GPU oversubscription: limited GPU memory size causes oversubscription issues, and existing memory management usually results in near-reuse data eviction, thus incurring extra CPU/GPU memory communications. Targeting these memory optimization opportunities, this articlemore »proposes MemHC, an optimized systematic GPU memory management framework that aims to accelerate the calculation of many-body correlation functions utilizing a series of new memory reduction designs. These designs involve optimizations for GPU memory allocation, CPU/GPU memory movement, and GPU memory oversubscription, respectively. More specifically, first, MemHC employs duplication-aware management and lazy release of GPU memories to corresponding host managing for better data reusability. Second, it implements data reorganization and on-demand synchronization to eliminate redundant (or unnecessary) data transfer. Third, MemHC exploits an optimized Least Recently Used (LRU) eviction policy called Pre-Protected LRU to reduce evictions and leverage memory hits. Additionally, MemHC is portable for various platforms including NVIDIA GPUs and AMD GPUs. The evaluation demonstrates that MemHC outperforms unified memory management by \( 2.18\times \) to \( 10.73\times \) . The proposed Pre-Protected LRU policy outperforms the original LRU policy by up to \( 1.36\times \) improvement. 1« less
2. UNIT: Unifying Tensorized Instruction Compilation

   https://doi.org/10.1109/CGO51591.2021.9370330  

   Weng, Jian ; Jain, Animesh ; Wang, Jie ; Wang, Leyuan ; Wang, Yida ; Nowatzki, Tony ( February 2021 , 2021 IEEE/ACM International Symposium on Code Generation and Optimization (CGO))

   Because of the increasing demand for intensive computation in deep neural networks, researchers have developed both hardware and software mechanisms to reduce the compute and memory burden. A widely adopted approach is to use mixed precision data types. However, it is hard to benefit from mixed precision without hardware specialization because of the overhead of data casting. Recently, hardware vendors offer tensorized instructions specialized for mixed-precision tensor operations, such as Intel VNNI, Nvidia Tensor Core, and ARM DOT. These instructions involve a new computing idiom, which reduces multiple low precision elements into one high precision element. The lack of compilation techniques for this emerging idiom makes it hard to utilize these instructions. In practice, one approach is to use vendor-provided libraries for computationally-intensive kernels, but this is inflexible and prevents further optimizations. Another approach is to manually write hardware intrinsics, which is error-prone and difficult for programmers. Some prior works tried to address this problem by creating compilers for each instruction. This requires excessive efforts when it comes to many tensorized instructions. In this work, we develop a compiler framework, UNIT, to unify the compilation for tensorized instructions. The key to this approach is a unified semantics abstraction which makesmore »the integration of new instructions easy, and the reuse of the analysis and transformations possible. Tensorized instructions from different platforms can be compiled via UNIT with moderate effort for favorable performance. Given a tensorized instruction and a tensor operation, UNIT automatically detects the applicability of the instruction, transforms the loop organization of the operation, and rewrites the loop body to take advantage of the tensorized instruction. According to our evaluation, UNIT is able to target various mainstream hardware platforms. The generated end-to-end inference model achieves 1.3 x speedup over Intel oneDNN on an x86 CPU, 1.75x speedup over Nvidia cuDNN on an Nvidia GPU, and 1.13x speedup over a carefully tuned TVM solution for ARM DOT on an ARM CPU.« less
3. Exploiting Computation Reuse for Stencil Accelerators

   Chi, Yuze ; Cong, Jason ( July 2020 , Proceedings of the 57th Design Automation Conference (DAC 2020), San Francisco, CA, July 19-23, 2020.)

   Stencil kernel is an important type of kernel used extensively in many application domains. Over the years, researchers have been studying the optimizations on parallelization, communication reuse, and computation reuse for various target platforms. However, challenges still exist, especially on the computation reuse problem for accelerators, due to the lack of complete design-space exploration and effective design-space pruning. In this paper, we present solutions to the above challenges for a wide range of stencil kernels (i.e., stencil with reduction operations), where the computation reuse patterns are extremely flexible due to the commutative and associative properties. We formally define the complete design space, based on which we present a provably optimal dynamic programming algorithm and a heuristic beam search algorithm that provides near-optimal solutions under an architecture-aware model. Experimental results show that for synthesizing stencil kernels to FPGAs, compared with state-of-the-art stencil compiler without computation reuse capability, our proposed algorithm can reduce the look-up table (LUT) and digital signal processor (DSP) usage by 58.1% and 54.6% on average respectively, which leads to an average speedup of 2.3× for compute-intensive kernels, outperforming the latest CPU/GPU results.
4. Issues in the Reproducibility of Deep Learning Results

   https://doi.org/10.1109/SPMB47826.2019.9037840  

   Jean-Paul, S. ; Elseify, T. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. ; Selesnik, I. ; Picone, J. (Ed.)

   The Neuronix high-performance computing cluster allows us to conduct extensive machine learning experiments on big data [1]. This heterogeneous cluster uses innovative scheduling technology, Slurm [2], that manages a network of CPUs and graphics processing units (GPUs). The GPU farm consists of a variety of processors ranging from low-end consumer grade devices such as the Nvidia GTX 970 to higher-end devices such as the GeForce RTX 2080. These GPUs are essential to our research since they allow extremely compute-intensive deep learning tasks to be executed on massive data resources such as the TUH EEG Corpus [2]. We use TensorFlow [3] as the core machine learning library for our deep learning systems, and routinely employ multiple GPUs to accelerate the training process. Reproducible results are essential to machine learning research. Reproducibility in this context means the ability to replicate an existing experiment – performance metrics such as error rates should be identical and floating-point calculations should match closely. Three examples of ways we typically expect an experiment to be replicable are: (1) The same job run on the same processor should produce the same results each time it is run. (2) A job run on a CPU and GPU should producemore »identical results. (3) A job should produce comparable results if the data is presented in a different order. System optimization requires an ability to directly compare error rates for algorithms evaluated under comparable operating conditions. However, it is a difficult task to exactly reproduce the results for large, complex deep learning systems that often require more than a trillion calculations per experiment [5]. This is a fairly well-known issue and one we will explore in this poster. Researchers must be able to replicate results on a specific data set to establish the integrity of an implementation. They can then use that implementation as a baseline for comparison purposes. A lack of reproducibility makes it very difficult to debug algorithms and validate changes to the system. Equally important, since many results in deep learning research are dependent on the order in which the system is exposed to the data, the specific processors used, and even the order in which those processors are accessed, it becomes a challenging problem to compare two algorithms since each system must be individually optimized for a specific data set or processor. This is extremely time-consuming for algorithm research in which a single run often taxes a computing environment to its limits. Well-known techniques such as cross-validation [5,6] can be used to mitigate these effects, but this is also computationally expensive. These issues are further compounded by the fact that most deep learning algorithms are susceptible to the way computational noise propagates through the system. GPUs are particularly notorious for this because, in a clustered environment, it becomes more difficult to control which processors are used at various points in time. Another equally frustrating issue is that upgrades to the deep learning package, such as the transition from TensorFlow v1.9 to v1.13, can also result in large fluctuations in error rates when re-running the same experiment. Since TensorFlow is constantly updating functions to support GPU use, maintaining an historical archive of experimental results that can be used to calibrate algorithm research is quite a challenge. This makes it very difficult to optimize the system or select the best configurations. The overall impact of all of these issues described above is significant as error rates can fluctuate by as much as 25% due to these types of computational issues. Cross-validation is one technique used to mitigate this, but that is expensive since you need to do multiple runs over the data, which further taxes a computing infrastructure already running at max capacity. GPUs are preferred when training a large network since these systems train at least two orders of magnitude faster than CPUs [7]. Large-scale experiments are simply not feasible without using GPUs. However, there is a tradeoff to gain this performance. Since all our GPUs use the NVIDIA CUDA® Deep Neural Network library (cuDNN) [8], a GPU-accelerated library of primitives for deep neural networks, it adds an element of randomness into the experiment. When a GPU is used to train a network in TensorFlow, it automatically searches for a cuDNN implementation. NVIDIA’s cuDNN implementation provides algorithms that increase the performance and help the model train quicker, but they are non-deterministic algorithms [9,10]. Since our networks have many complex layers, there is no easy way to avoid this randomness. Instead of comparing each epoch, we compare the average performance of the experiment because it gives us a hint of how our model is performing per experiment, and if the changes we make are efficient. In this poster, we will discuss a variety of issues related to reproducibility and introduce ways we mitigate these effects. For example, TensorFlow uses a random number generator (RNG) which is not seeded by default. TensorFlow determines the initialization point and how certain functions execute using the RNG. The solution for this is seeding all the necessary components before training the model. This forces TensorFlow to use the same initialization point and sets how certain layers work (e.g., dropout layers). However, seeding all the RNGs will not guarantee a controlled experiment. Other variables can affect the outcome of the experiment such as training using GPUs, allowing multi-threading on CPUs, using certain layers, etc. To mitigate our problems with reproducibility, we first make sure that the data is processed in the same order during training. Therefore, we save the data from the last experiment and to make sure the newer experiment follows the same order. If we allow the data to be shuffled, it can affect the performance due to how the model was exposed to the data. We also specify the float data type to be 32-bit since Python defaults to 64-bit. We try to avoid using 64-bit precision because the numbers produced by a GPU can vary significantly depending on the GPU architecture [11-13]. Controlling precision somewhat reduces differences due to computational noise even though technically it increases the amount of computational noise. We are currently developing more advanced techniques for preserving the efficiency of our training process while also maintaining the ability to reproduce models. In our poster presentation we will demonstrate these issues using some novel visualization tools, present several examples of the extent to which these issues influence research results on electroencephalography (EEG) and digital pathology experiments and introduce new ways to manage such computational issues.« less
5. Offload Annotations: Bringing Heterogeneous Computing to Existing Libraries and Workloads

   Yuan, Gina ; Palkar, Shoumik ; Narayanan, Deepak ; and Zaharia, Matei. ( July 2020 , USENIX ATC 2020)

   As specialized hardware accelerators such as GPUs become increasingly popular, developers are looking for ways to target these platforms with high-level APIs. One promising approach is kernel libraries such as PyTorch or cuML, which provide interfaces that mirror CPU-only counterparts such as NumPy or Scikit-Learn. Unfortunately, these libraries are hard to develop and to adopt incrementally: they only support a subset of their CPU equivalents, only work with datasets that fit in device memory, and require developers to reason about data placement and transfers manually. To address these shortcomings, we present a new approach called offload annotations (OAs) that enables heterogeneous GPU computing in existing workloads with few or no code modifications. An annotator annotates the types and functions in a CPU library with equivalent kernel library functions and provides an offloading API to specify how the inputs and outputs of the function can be partitioned into chunks that fit in device memory and transferred between devices. A runtime then maps existing CPU functions to equivalent GPU kernels and schedules execution, data transfers and paging. In data science workloads using CPU libraries such as NumPy and Pandas, OAs enable speedups of up to 1200⇥ and a median speedup of 6.3⇥more »by transparently offloading functions to a GPU using existing kernel libraries. In many cases, OAs match the performance of handwritten heterogeneous implementations. Finally, OAs can automatically page data in these workloads to scale to datasets larger than GPU memory, which would need to be done manually with most current GPU libraries.« less