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GPU Tuning Guide and Performance Comparison

How It Works?

In LightGBM, the main computation cost during training is building the feature histograms. We use an efficient algorithm on GPU to accelerate this process. The implementation is highly modular, and works for all learning tasks (classification, ranking, regression, etc). GPU acceleration also works in distributed learning settings. GPU algorithm implementation is based on OpenCL and can work with a wide range of GPUs.

Supported Hardware

We target AMD Graphics Core Next (GCN) architecture and NVIDIA Maxwell and Pascal architectures. Most AMD GPUs released after 2012 and NVIDIA GPUs released after 2014 should be supported. We have tested the GPU implementation on the following GPUs:

  • AMD RX 480 with AMDGPU-pro driver 16.60 on Ubuntu 16.10
  • AMD R9 280X (aka Radeon HD 7970) with fglrx driver 15.302.2301 on Ubuntu 16.10
  • NVIDIA GTX 1080 with driver 375.39 and CUDA 8.0 on Ubuntu 16.10
  • NVIDIA Titan X (Pascal) with driver 367.48 and CUDA 8.0 on Ubuntu 16.04
  • NVIDIA Tesla M40 with driver 375.39 and CUDA 7.5 on Ubuntu 16.04

Using the following hardware is discouraged:

  • NVIDIA Kepler (K80, K40, K20, most GeForce GTX 700 series GPUs) or earlier NVIDIA GPUs. They don't support hardware atomic operations in local memory space and thus histogram construction will be slow.
  • AMD VLIW4-based GPUs, including Radeon HD 6xxx series and earlier GPUs. These GPUs have been discontinued for years and are rarely seen nowadays.

How to Achieve Good Speedup on GPU

  1. You want to run a few datasets that we have verified with good speedup (including Higgs, epsilon, Bosch, etc) to ensure your setup is correct. If you have multiple GPUs, make sure to set gpu_platform_id and gpu_device_id to use the desired GPU. Also make sure your system is idle (especially when using a shared computer) to get accuracy performance measurements.
  2. GPU works best on large scale and dense datasets. If dataset is too small, computing it on GPU is inefficient as the data transfer overhead can be significant. For dataset with a mixture of sparse and dense features, you can control the sparse_threshold parameter to make sure there are enough dense features to process on the GPU. If you have categorical features, use the categorical_column option and input them into LightGBM directly; do not convert them into one-hot variables. Make sure to check the run log and look at the reported number of sparse and dense features.
  3. To get good speedup with GPU, it is suggested to use a smaller number of bins. Setting max_bin=63 is recommended, as it usually does not noticeably affect training accuracy on large datasets, but GPU training can be significantly faster than using the default bin size of 255. For some dataset, even using 15 bins is enough (max_bin=15); using 15 bins will maximize GPU performance. Make sure to check the run log and verify that the desired number of bins is used.
  4. Try to use single precision training (gpu_use_dp=false) when possible, because most GPUs (especially NVIDIA consumer GPUs) have poor double-precision performance.

Performance Comparison

We evaluate the training performance of GPU acceleration on the following datasets:

Data Task Link #Examples #Features Comments
Higgs Binary classification link1 10,500,000 28 use last 500,000 samples as test set
Epsilon Binary classification link2 400,000 2,000 use the provided test set
Bosch Binary classification link3 1,000,000 968 use the provided test set
Yahoo LTR Learning to rank link4 473,134 700 set1.train as train, set1.test as test
MS LTR Learning to rank link5 2,270,296 137 {S1,S2,S3} as train set, {S5} as test set
Expo Binary classification (Categorical) link6 11,000,000 700 use last 1,000,000 as test set

We used the following hardware to evaluate the performance of LightGBM GPU training. Our CPU reference is a high-end dual socket Haswell-EP Xeon server with 28 cores; GPUs include a budget GPU (RX 480) and a mainstream (GTX 1080) GPU installed on the same server. It is worth mentioning that the GPUs used are not the best GPUs in the market; if you are using a better GPU (like AMD RX 580, NVIDIA GTX 1080 Ti, Titan X Pascal, Titan Xp, Tesla P100, etc), you are likely to get a better speedup.

Hardware Peak FLOPS Peak Memory BW Cost (MSRP)
AMD Radeon RX 480 5,161 GFLOPS 256 GB/s $199
NVIDIA GTX 1080 8,228 GFLOPS 320 GB/s $499
2x Xeon E5-2683v3 (28 cores) 1,792 GFLOPS 133 GB/s $3,692

During benchmarking on CPU we used only 28 physical cores of the CPU, and did not use hyper-threading cores, because we found that using too many threads actually makes performance worse. The following shows the training configuration we used:

max_bin = 63
num_leaves = 255
num_iterations = 500
learning_rate = 0.1
tree_learner = serial
task = train
is_training_metric = false
min_data_in_leaf = 1
min_sum_hessian_in_leaf = 100
ndcg_eval_at = 1,3,5,10
sparse_threshold=1.0
device = gpu
gpu_platform_id = 0
gpu_device_id = 0
num_thread = 28

We use the configuration shown above, except for the Bosch dataset, we use a smaller learning_rate=0.015 and set min_sum_hessian_in_leaf=5. For all GPU training we set sparse_threshold=1, and vary the max number of bins (255, 63 and 15). The GPU implementation is from commit 0bb4a82 of LightGBM, when the GPU support was just merged in.

The following table lists the accuracy on test set that CPU and GPU learner can achieve after 500 iterations. GPU with the same number of bins can achieve a similar level of accuracy as on the CPU, despite using single precision arithmetic. For most datasets, using 63 bins is sufficient.

  CPU 255 bins CPU 63 bins CPU 15 bins GPU 255 bins GPU 63 bins GPU 15 bins
Higgs AUC 0.845612 0.845239 0.841066 0.845612 0.845209 0.840748
Epsilon AUC 0.950243 0.949952 0.948365 0.950057 0.949876 0.948365
Yahoo-LTR NDCG1 0.730824 0.730165 0.729647 0.730936 0.732257 0.73114
Yahoo-LTR NDCG3 0.738687 0.737243 0.736445 0.73698 0.739474 0.735868
Yahoo-LTR NDCG5 0.756609 0.755729 0.754607 0.756206 0.757007 0.754203
Yahoo-LTR NDCG10 0.79655 0.795827 0.795273 0.795894 0.797302 0.795584
Expo AUC 0.776217 0.771566 0.743329 0.776285 0.77098 0.744078
MS-LTR NDCG1 0.521265 0.521392 0.518653 0.521789 0.522163 0.516388
MS-LTR NDCG3 0.503153 0.505753 0.501697 0.503886 0.504089 0.501691
MS-LTR NDCG5 0.509236 0.510391 0.507193 0.509861 0.510095 0.50663
MS-LTR NDCG10 0.527835 0.527304 0.524603 0.528009 0.527059 0.524722
Bosch AUC 0.718115 0.721791 0.716677 0.717184 0.724761 0.717005

We record the wall clock time after 500 iterations, as shown in the figure below:

./_static/images/gpu-performance-comparison.png

When using a GPU, it is advisable to use a bin size of 63 rather than 255, because it can speed up training significantly without noticeably affecting accuracy. On CPU, using a smaller bin size only marginally improves performance, sometimes even slows down training, like in Higgs (we can reproduce the same slowdown on two different machines, with different GCC versions). We found that GPU can achieve impressive acceleration on large and dense datasets like Higgs and Epsilon. Even on smaller and sparse datasets, a budget GPU can still compete and be faster than a 28-core Haswell server.

Memory Usage

The next table shows GPU memory usage reported by nvidia-smi during training with 63 bins. We can see that even the largest dataset just uses about 1 GB of GPU memory, indicating that our GPU implementation can scale to huge datasets over 10x larger than Bosch or Epsilon. Also, we can observe that generally a larger dataset (using more GPU memory, like Epsilon or Bosch) has better speedup, because the overhead of invoking GPU functions becomes significant when the dataset is small.

Datasets Higgs Epsilon Bosch MS-LTR Expo Yahoo-LTR
GPU Memory Usage (MB) 611 901 1067 413 405 291

Further Reading

You can find more details about the GPU algorithm and benchmarks in the following article:

Huan Zhang, Si Si and Cho-Jui Hsieh. GPU Acceleration for Large-scale Tree Boosting. SysML Conference, 2018.