EcoRNN: Fused LSTM RNN Implementation with Data Layout Optimization

EcoRNN: Fused LSTM RNN Implementation with Data Layout Optimization

Bojian Zheng
University of Toronto
&Akshay Nair
University of Toronto
\ANDQiongsi Wu
University of Toronto
\ANDNandita Vijaykumar
Carnegie Mellon University
&Gennady Pekhimenko
University of Toronto

Long-Short-Term-Memory Recurrent Neural Network (LSTM RNN) is a state-of-the-art (SOTA) model for analyzing sequential data. Current implementations of LSTM RNN in machine learning frameworks usually either lack performance or flexibility. For example, default implementations in Tensorflow and MXNet invoke many tiny GPU kernels, leading to excessive overhead in launching GPU threads. Although cuDNN, NVIDIA’s deep learning library, can accelerate performance by around , it is closed-source and inflexible, hampering further research and performance improvements in frameworks, such as PyTorch, that use cuDNN as their backend. In this paper, we introduce a new RNN implementation called EcoRNN that is significantly faster than the SOTA open-source implementation in MXNet and is competitive with the closed-source cuDNN. We show that (1) fusing tiny GPU kernels and (2) applying data layout optimization can give us a maximum performance boost of over MXNet default and over cuDNN implementations. Our optimizations also apply to other RNN cell types such as LSTM variants and Gated Recurrent Units (GRUs). We integrate EcoRNN into MXNet Python library and open-source it to benefit machine learning practitioners.

1 Introduction

Figure 1: Left: A single-layer LSTM RNN that scans through an input sequence. Right: A zoom-in view of an LSTM cell. Both diagrams have been greatly simplified for clarity.

LSTM Hochreiter and Schmidhuber (1997) RNN (Figure 1) is one of the most important machine learning models for analyzing sequential data. It is shown to have applications in areas such as speech recognition Graves et al. (2013); Graves and Jaitly (2014), language modeling Zaremba et al. (2014); Sundermeyer et al. (2012), and machine translation Bahdanau et al. (2014); Sutskever et al. (2014). However, it is also shown to have a much lower computation throughput compared to other types of networks such as Convolutional Neural Networks (CNNs) Lei et al. (2017). Although cuDNN NVIDIA (2017b); Chetlur et al. (2014), the proprietary deep learning library owned by NVIDIA, makes several efforts to accelerate RNN training, it is closed-source and therefore carved in stone. Greff et al. (2017), who do a large-scale analysis on LSTM architectures, show that there are now at least 8 variants of this single cell type used in the machine learning community. All these, however, are impossible to implement with cuDNN and machine learning frameworks, such as PyTorch Paszke et al. (2017), that use cuDNN as their backend Goel (2017). This is possibly one of the reasons that led framework developers, such as those from Tensorflow Abadi et al. (2015) or MXNet Chen et al. (2015), to develop their own implementations Tensorflow (2018a); (incubating) (2017a). Although they win flexibility, performance is lost by around compared with cuDNN (based on our results described later in this Section and also in Section 3). The primary reason, as addressed in the previous work done by Appleyard et al. (2016), is that these open-source implementations slice the computation of "" block (shown in Figure 1), which could be done in one single GPU kernel, into multiple small GPU kernels. This slicing causes performance overhead due to continuously launching a group of GPU threads (Figure 2), which is known as the cudaLaunch function call.

Figure 2: Left: Fused implementation of statement (assuming all operations are elementwise and done in parallel). Right: Unfused implementation of the same statement. Right hand side pays twice the amount of hardware overhead compared with left hand side (highlighted in red).
Figure 3: Runtime profile comparison between Default and CuDNN

Figure 3 shows the runtime profile comparison between MXNet Default and CuDNN.111 The word Default is used to differentiate between MXNet’s own and the cuDNN implementation under the MXNet framework. For convenience, we will further refer to the former as Default and the latter as CuDNN). The profile is obtained by measuring both of them running on a 1-layer LSTM RNN with a batch size of 64, hidden dimension of 512, and sequence length of 50, for 1 iteration that includes both forward and backward passes on a Titan Xp NVIDIA (2017g) GPU card using nvprof NVIDIA (2017f), the NVIDIA profiling tool for GPU programs (Section 3.1 has a more detailed description of experimental settings). We observe that cudaLaunch time spent in the case of Default is almost that of CuDNN, and it also exceeds the amount of actual compute time (GPU Kernels in Figure 3). This negative effect also exists in the Tensorflow implementation of LSTM RNN and can be exacerbated as the number of layers or sequence length increases. Clearly, there is room for improvement by fusing kernels together to get rid of the cudaLaunch overhead.

Although Appleyard et al. (2016) managed to solve the above issue, their work, however, fails to identify the runtime bottleneck of GPU Kernels in Figure 3. In this paper, we build on this prior work to further speed up LSTM RNN by applying data layout optimization Kennedy and Kremer (1998), a technique that originates from compiler research. We introduce a new implementation called EcoRNN, which stands for Efficient Computing of LSTM RNN, and we highlight its major contributions as follows: {enumerate*}[(1)]

EcoRNN can be up to faster than MXNet Default and 50% faster than CuDNN, while making no changes to the LSTM RNN algorithm.

It has a complete design that includes both forward and backward passes, and also supports dropout Srivastava et al. (2014), a technique that has been proven to be useful to avoid overfitting.

It has been integrated into MXNet ver. 0.12.1, one of the SOTA open-source machine learning frameworks. Implementations of EcoRNN propagate from the MXNet C++ core library to the Python interface, making it directly usable to machine learning researchers.

2 Data Layout Optimization

2.1 What is Data Layout Optimization?

Figure 4: Left: Programmers’ view of GPU, where data is fed to compute units directly from main memory. Right: Real GPU with cache, where data in main memory can be stored in cache for future references.

Data layout is a term that is used to specify how a piece of data (e.g., a two-dimensional array of size ) resides in memory. A row-major data layout means that data in the same row sits together in memory ( is adjacent to ), and a column-major data layout indicates that data in the same column is contiguous ( sits next to ). The idea behind data layout optimization is that changing data layout (usually from row-major to column-major or vice versa) can result in better locality in the data access pattern (Figure 5). The reason why this is preferable is because GPUs have caches NVIDIA (2017e) that temporarily store copies of memory data (Figure 4). Caches are faster to access compared to main memory and they are designed based on the observation that, when a memory address is accessed, the same memory address or nearby addresses will likely be accessed in the near future (i.e. memory accesses should exhibit locality for caches to be useful) Hennessy and Patterson (2017). Therefore, better locality yields higher cache utilization (hit rate), which leads to faster memory accesses on average, and eventually, better runtime performance.

We make the following two observations that justify why applying data layout optimization can be beneficial in the context of LSTM RNN.

Figure 5: An example showing the effect of data layout on locality. Given the same program (for-loop on index variable embedded in for-loop on ), traversing through row-major data (left) has better locality compared with column-major data (right). The reason is because index variable changes contiguously across all loop iterations. Therefore, accesses to , which have a stride of 1, exhibit better locality compared with those to , which have a stride of .

2.2 Observation 1: Data Layout Optimization can speed up Fully-Connected (FC) layers

Figure 6: Left: . Right: . Left and right do the same amount of computation.
Figure 7: Runtime (left) and hardware utilization (right) comparison between and

Suppose that we have matrix of dimension and matrix of dimension , and we want to compare the runtimes of matrix multiply and (Figure 6). This setup mimics the FC layer of an LSTM RNN cell whose batch size is 64 and hidden dimension is 512 (2048 comes from the fact that an LSTM cell has 4 nonlinear gates). Although mathematical intuition says that those two runtimes should by no means be different from each other because and are doing exactly the same amount of computation, actual measurements disagree. Figure 7 is obtained by measuring and on a Titan Xp GPU. The matrix multiply is carried out using cuBLAS 8.0 NVIDIA (2017a), the proprietary library owned by NVIDIA for doing basic linear algebraic operations, and is used by both MXNet and cuDNN for implementing FC layers Inc. (2015). The Runtime measurements have been averaged over 100 iterations. The Cache and Compute Units bars represent the utilization percentage of the corresponding hardware resources and come directly from the nvprof tool (the Cache here means GPU -cache). We see that is almost twice as fast as under this parameter setting, and the reason is that the former has better cache utilization. Therefore, it can feed data faster into compute units, and thus ends up spending more time in actual compute rather than waiting for data to arrive from main memory.

We observe that in LSTM RNN, FC layers usually have the following properties: {enumerate*}[(1)]

, of which the dimension is given by , often has more columns than rows, because the batch size (ranging between ) is usually smaller than the hidden dimension (ranging between ) (incubating) (2017c); Hieber et al. (2017); Luong et al. (2017); Britz et al. (2017).

has more rows than columns. Since an LSTM cell has 4 gates, the ratio between ’s width and height is always 4. The aforementioned properties make usually perform better than , in terms of both cache utilization and runtime.

2.3 Observation 2: The Runtime Bottleneck of LSTM RNN is FC layers

Figure 8: Runtime breakdown by GPU kernels.222All kernel names have been abbreviated and simplified. For instance, the full name for GPU kernel is sgemm_largek_lds64, and that for is maxwell_sgemm_128x128_raggedMn_nn_splitK.Annotations are what they correspond to in Figure 1.

We continue on the previous experiment in Figure 3 and dive deeper into the GPU Kernels portion. We obtain the detailed runtime breakdown of CuDNN and the result is shown in Figure 8 (due to the fact that Default slices the "" block in Figure 1 into small pieces, its result is difficult to interpret). Figure 8 shows that more than 85% of the time spent on compute has been allocated to matrix multiplies (sgemm is the name for single-precision matrix multiply kernels in cuBLAS library NVIDIA (2017a)). Despite the fact that we do not know the exact one-to-one correspondence, it can be inferred that the top two kernels with the longest runtime come from the forward and backward passes of FC layers, and the third one performs aggregation of weight gradients along the time dimension. The annotations beside the stacked bar in Figure 8 group GPU kernels together according to their counterpart in Figure 1, which explains why FC layers in LSTM RNN should be the top candidate for optimization.

2.4 Applying Data Layout Optimization in LSTM RNN and
Generalization to Other Cell Types

The previous two observations justify why data layout optimization can be helpful in improving LSTM RNN performance. We, hence, apply this optimization by transposing the input data from into , where , , and stand respectively for batch size, sequence length, and hidden dimension, before feeding it into the network. Such transpose operation introduces almost no extra runtime cost, because input data needs to become time-major first before being sliced along the time dimension. The problem is therefore whether the data layout should be or . Runtime measurements recommend as a better choice. We implement LSTM RNN using the layout and defined this new implementation as EcoRNN.

Figure 10 shows the runtime and cache utilization comparison between Default, CuDNN, EcoRNN on the forward pass under the hyperparameter setting . The Runtime is averaged over 100 iterations, and the Cache utilization is computed as the weighted average of utilization percentage by each sgemm kernel runtime Zhu et al. (2018), which is given by


We can see from Figure 10 that performance benefits we observe at the low-level for FC layers reappear at the high-level for LSTM RNN – EcoRNN is and faster compared with Default and CuDNN respectively and the reason is because it utilizes cache resources better. We can also derive two more conclusions from Figure 10: {enumerate*}[(1)]

The cache utilization in Default is almost the same with that in CuDNN. This is a good indication that data layout optimization is orthogonal to the techniques that are currently applied in cuDNN implementation of LSTM RNN, which involves other unknown optimizations. We cannot apply data layout optimization in CuDNN directly because it is closed-source, but clearly this optimization can bring more benefits than those hidden optimizations in this hyperparameter setting.

The speedup and cache utilization comparison between CuDNN and Default in Figure 10 matches the same comparison between and in Figure 7, which not only proves the correctness of our observations, but also means that any benefits seen at the FC layers can directly translate into the level of LSTM RNN Amdahl (1967).

Although in this work we focus primarily on LSTMs, the fact that data layout optimization works on FC layers rather than the "" block in Figure 1 means that the same idea applies equally well to different LSTM variants as long as the 4 nonlinear gates are preserved (such as LSTM with peephole connections Gers and Schmidhuber (2000)), and potentially to other RNN cell types. Figure 10 does similar analysis to Figure 7, except that and are now of dimension and respectively, which mimics the FC layer of a GRU cell Cho et al. (2014) with 3 nonlinear gates. We observe that is faster than , which justifies the potential of similar data layout optimization in GRU RNN.

Figure 9: Runtime (left) and cache utilization (right) comparison between Default, CuDNN, and EcoRNN on the forward pass
Figure 10: Same comparison with Figure 7 but with and mimicking the FC layer of a GRU cell

3 Experiments and Results

3.1 Experimental Settings

All the experiments included in this paper are done on a single machine with Intel®Core™i5-3570 Intel (2012) CPU and Titan Xp NVIDIA (2017g) GPU. We have been using CUDA 8.0 NVIDIA (2017c) toolkit and cuDNN 6.0 NVIDIA (2017b) for our experiments in MXNet ver. 0.12.1 Chen et al. (2015). All runtime measurements are averaged over 101 iterations, but with the first one always discarded to avoid framework tuning or warmup overhead, and all profiling results (hardware utilization, runtime breakdown) are obtained from the nvprof tool NVIDIA (2017f). To provide fair comparison against Default and CuDNN, we integrate EcoRNN into MXNet and propagate it from MXNet’s core library to the MXNet C++ and Python interfaces.

3.2 Microbenchmark

To observe the pure benefits of EcoRNN for RNN layers, we implement a microbenchmark that uses MXNet C++ interface and only includes RNN layers (i.e. there are no other layers such as embedding or softmax). We traverse through the set of hyperparameters which is defined as the cartesian product of batch size , hidden dimension , and number of layers (we kept the sequence length fixed at 50 as we observe in our experiments that runtime always scales linearly with respect to sequence length). Figure 11 shows the results of runtime comparison on the microbenchmark between Default, CuDNN, and EcoRNN. We observe that EcoRNN is always significantly better than Default and in most cases better than CuDNN. Even in a few cases where CuDNN slightly outperforms EcoRNN, the performance difference is below 20%. We believe this happens when CuDNN’s optimizations that are aimed at multi-layer LSTM RNN outweigh the benefits of data layout optimization.

Figure 11: Runtime comparison on microbenchmark between Default, CuDNN, and EcoRNN

3.3 Word-Level Language-Modeling Benchmark

Performance benefits that we observe at the C++ level are helpful to estimate the potential speedup, but machine learning researchers usually use high-level programming languages such as Python or R when building RNN models. To see the performance benefits we can get from EcoRNN in this context, we integrate it into the Python interface and test it on the word-level language modeling task in the MXNet repository (incubating) (2017c, d) on the Penn TreeBank (PTB) Zaremba et al. (2014) and Wikitext-2 Merity (2016) datasets. To avoid picking hyperparameter settings that are biased towards EcoRNN, we keep the default set of hyperparameters that is chosen by MXNet developers ( denotes the input dropout probability of LSTM cells).

We verify the correctness of EcoRNN by plotting training and validation quality versus the global number of training steps and training checkpoints respectively. The quality is measured by perplexity (lower perplexity means better quality). The first two graphs in Figure 12 show that the training curve of EcoRNN almost completely overlaps with that of Default and CuDNN. Although all three implementations are the same from the algorithmic perspective, MXNet speedometer (incubating) (2017b) tells us that they are different in terms of speed. The rightmost graph in Figure 12 demonstrates that EcoRNN is and faster than Default and CuDNN respectively under this hyperparameter selection. Table 1 and Figure 13 expands the scope of the evaluation by testing on other set of hyperparameters, of which are suggested by MXNet developers (incubating) (2017d) and are what we added to complete the sweep (other hyperparameters are kept unchanged, except for the dropout probability which scales accordingly with ). We observe that across all the hyperparameters, EcoRNN does equally well with Default and CuDNN in terms of final achieved test perplexity, yet it clearly has the advantage of better training throughput compared with both Default and CuDNN in all but a few cases where performance difference is minimal (within 20%).

Figure 12: Measurements of training perplexity (left), validation perplexity (middle), and throughput (right) as training progresses on the PTB dataset
Hidden Dimension 200 256 512 650 1024 1500
Test Perplexity Default 109.97 103.02 92.80 89.93 88.32 85.66
EcoRNN 107.40 99.80 89.90 87.41 86.45 84.47
Table 1: Final achieved test perplexities (lower means better) by Default and EcoRNN on Wikitext-2 under different hidden dimension. These also match what are claimed in the MXNet repository (incubating) (2017d).
(a) PTB
(b) Wikitext-2
Figure 13: Average throughput on PTB (left) and Wikitext-2 (right) under different hidden dimension. The throughput standard deviation is plotted on top of the average value, but it is almost negligible.

3.4 Correlation between Microbenchmark and Real Application

Some RNN models (e.g., Sockeye Hieber et al. (2017)) have an argument -fused or other equivalents that indicate the switch between the Default and CuDNN implementations, which hence require manual effort from both the model users and the model programmers side. We argue that such switching should be done automatically for machine learning users and it is part of our future plan to build a runtime tool (shown in Figure 14) on top of the microbenchmark that selects the best LSTM RNN implementation depending on the hyperparameter selection. To achieve this, the microbenchmark must be representative of the actual workload. We compute the correlation coefficient between (where stands for the runtime on microbenchmark) and average throughput measurements in Figure 13 and the results are shown in Table 2. We observe that the microbenchmark runtime is highly correlated with the throughput in both the language modeling task of PTB and that of Wikitext-2 and can therefore serve as an efficient predictor for selecting the best LSTM RNN implementation.

Figure 14: Runtime tool that automatically selects between different backend implementations depending on microbenchmark measurements
Table 2: Correlation coefficient between and average throughput on different dataset Dataset PTB Wikitext-2 0.971 0.950

4 Related Works

EcoRNN is an open-source LSTM RNN implementation that does not impose any restrictions either at the software level (hyperparameters) or at the hardware level (CPU and GPU). Diamos et al. (2016) (Persistent RNN) show that they can achieve substantial speedup by using persistent computational kernels that exploit the GPU’s inverted memory hierarchy, however, their implementation puts significant restrictions on its users. For example, the number of RNN layers must be a multiple of 4, the input data must be 16-byte aligned, and only limited GPU hardware is supported Research (2016). All these make their implementation a less desirable design for machine learning developers.

EcoRNN also makes no changes to the LSTM RNN algorithm. This is in contrast to those approaches taken by some machine learning researchers, who try to address the inefficiency of LSTM RNN from the algorithmic perspective by either getting rid of the RNN components completely (e.g., Transformer Vaswani et al. (2017), ByteNet Kalchbrenner et al. (2016), and PixelCNN van den Oord et al. (2016)) or simplifying the RNN architecture to speed up computation (e.g., RAN Lee et al. (2017), T-RNN Balduzzi and Ghifary (2016), and Miao et al. (2016)) or relieving the burden on recurrent connections to improve model parallelism (e.g., QRNN Bradbury et al. (2016) and SRU Lei et al. (2017)). These approaches are mostly orthogonal to EcoRNN and can be used in conjunction with our approach.

Compiler optimization techniques that were previously developed for high performance computing are important for achieving peak performance in machine learning workloads (such as kernel fusion Bacon et al. (1994); Padua and Wolfe (1986) and data layout transformation Kennedy and Kremer (1998)). Many researchers introduce new compiler frameworks that target DNN workloads, such as XLA Tensorflow (2018b), TVM Chen et al. (2018), Tensor Comprehensions Vasilache et al. (2018), DLVM Wei et al. (2017), nGraph Cyphers et al. (2018), and Glow Rotem et al. (2018). Unfortunately, all prior works either do not have performance evaluations Tensorflow (2018b); Wei et al. (2017); Cyphers et al. (2018) or only have evaluations that are based on Multi-Layer Perceptrons (MLP) Minsky and Papert (2017)Vasilache et al. (2018) and CNN models (such as Resnet He et al. (2015), VGG Simonyan and Zisserman (2014), and MobileNet Howard et al. (2017)) Chen et al. (2018); Vasilache et al. (2018); Rotem et al. (2018). We aim at integrating our optimizations as a part of the existing compiler frameworks and push for optimizations beyond those that are specific for MLP and CNN models.

5 Conclusion and Discussion

In this paper, we introduce EcoRNN, a new implementation of LSTM RNN with kernel fusion and data layout optimization. We show the potential of those two optimizations in multiple SOTA machine learning frameworks and RNN cell types other than LSTM. EcoRNN is always significantly better than the MXNet Default, and also the closed-source CuDNN implementations under most hyperparameter settings. We develop a microbenchmark that consists of pure LSTM RNNs and demonstrate that it is representative of the actual workload as the runtime on the microbenchmark is highly correlated with the average throughput measurements reported by MXNet speedometer.

The successful application of data layout optimization in LSTM RNN gives rise to the question as to whether or not it is universally applicable to all FC layers, or matrix multiplies in general. Matrix multiplies are ubiquitous in machine learning models, which is one of the reasons why companies such as Google and NVIDIA introduce hardware dedicated specifically for them Jouppi et al. (2017); NVIDIA (2017d). In this paper, we show how data layout optimization can give a speedup on matrix multiplies. However, applying it universally can be challenging. Figure 15 (left) explains the reason – having a single piece of data and matrix multiplies can already give us a total number of possible execution paths to consider, under the condition that those matrix multiplies are all different in terms of dimensions of matrices. However, if all matrix multiplies are the same, the NP-complete problem will be reduced to simply selecting between either row-major or column-major (i.e. a binary problem, shown in Figure 15 (right)), which is exactly the case of LSTM RNN and other recurrent models, where all FC layers share the same dimension across different layers and time steps.

Figure 15: Left: Data layout optimization problem for a program working on a single two-dimensional array that is needed by matrix multiplies. To complete execution, the program must follow the paths to go from start to end, of which some have an associated cost for remapping ’s data layout. Right: Special case where all matrix multiples are the same in terms of dimensions. No remapping is needed as the optimal layout for one kernel remains optimal for the rest.

6 Acknowledgements

We really want to express our sincere gratitude to Professor Roger Grosse, Andrew Pelegris, Shang (Sam) Wang from the University of Toronto for kindly giving us feedback on this paper.


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