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MrBayes tgMC3: A Tight GPU Implementation of MrBayes

  • Cheng Ling ,

    c.ling@giat.ac.cn (CL); wfshi.tsmc@gmail.com (WS)

    Affiliation Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China

  • Tsuyoshi Hamada,

    Affiliation Department of Computer and Information Science, Nagasaki University, Nagasaki, Japan

  • Jianing Bai,

    Affiliation Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China

  • Xianbin Li,

    Affiliations Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China, University of Chinese Academy of Sciences, Beijing, China

  • Douglas Chesters,

    Affiliations Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China, Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

  • Weimin Zheng,

    Affiliation Guangzhou Institute of Advanced Technology, Chinese Academy of Science, Guangzhou, China

  • Weifeng Shi

    c.ling@giat.ac.cn (CL); wfshi.tsmc@gmail.com (WS)

    Affiliation School of Basic Medical Sciences, Taishan Medical College, Taian, Shandong, China

MrBayes tgMC3: A Tight GPU Implementation of MrBayes

  • Cheng Ling, 
  • Tsuyoshi Hamada, 
  • Jianing Bai, 
  • Xianbin Li, 
  • Douglas Chesters, 
  • Weimin Zheng, 
  • Weifeng Shi
PLOS
x

Abstract

MrBayes is model-based phylogenetic inference tool using Bayesian statistics. However, model-based assessment of phylogenetic trees adds to the computational burden of tree-searching, and so poses significant computational challenges. Graphics Processing Units (GPUs) have been proposed as high performance, low cost acceleration platforms and several parallelized versions of the Metropolis Coupled Markov Chain Mote Carlo (MC3) algorithm in MrBayes have been presented that can run on GPUs. However, some bottlenecks decrease the efficiency of these implementations. To address these bottlenecks, we propose a tight GPU MC3 (tgMC3) algorithm. tgMC3 implements a different architecture from the one-to-one acceleration architecture employed in previously proposed methods. It merges multiply discrete GPU kernels according to the data dependency and hence decreases the number of kernels launched and the complexity of data transfer. We implemented tgMC3 and made performance comparisons with an earlier proposed algorithm, nMC3, and also with MrBayes MC3 under serial and multiply concurrent CPU processes. All of the methods were benchmarked on the same computing node from DEGIMA. Experiments indicate that the tgMC3 method outstrips nMC3 (v1.0) with speedup factors from 2.1 to 2.7×. In addition, tgMC3 outperforms the serial MrBayes MC3 by a factor of 6 to 30× when using a single GTX480 card, whereas a speedup factor of around 51× can be achieved by using two GTX 480 cards on relatively long sequences. Moreover, tgMC3 was compared with MrBayes accelerated by BEAGLE, and achieved speedup factors from 3.7 to 5.7×. The reported performance improvement of tgMC3 is significant and appears to scale well with increasing dataset sizes. In addition, the strategy proposed in tgMC3 could benefit the acceleration of other Bayesian-based phylogenetic analysis methods using GPUs.

Introduction

In biology, the evolutionary relationships between groups of organisms or families of related genes and proteins can be inferred from the pattern of states at homologous characters, and represented as a tree structure. A number of algorithms have been developed to construct phylogenetic trees, such as Neighbour-Joining (NJ) [1] or Maximum Parsimony [2], whereas methods that implement a model of sequence evolution, such as Maximum Likelihood [3] and Bayesian inference [4], are more computationally demanding [5]. MrBayes [6] is a popular tool that implements the Metropolis Coupled Markov Chain Monte Carlo (MC3) sampling method for Bayesian inference of phylogeny. Since each chain in MC3 runs more or less independently, MrBayes is well suited to parallel implementation on multi-core systems as an approach to reduce computation time.

The programmable Graphics Processing Units (GPUs) have become very powerful many-core processors, driven by demand from various graphical, computational and engineering applications. Current GPUs can attain a peak float-point throughput of up to 3250 GFlop/s per chip, which is higher than that of the fastest CPU by a factor of over 10. Moreover, recent GPUs support Compute Unified Device Architecture (CUDA) [7], which allows users to develop a wide range of applications under a high-level, general-purpose programming model. Such a general-purpose GPU computing (GPGPU) model significantly improves development productivity as it follows the traditional software programming flow. CUDA is the programming environment for NVIDIA GPUs. CUDA C is an extension of C programming language and follows an SPMD execution model with a thread as the basic unit for parallel computations. Tens of thousands of threads can be launched concurrently, all executing the same program, but on different data packets. Threads in the same block can share data using fast on-chip memory (shared memory). Threads in different blocks can only share data using relatively slow on-board memory (global memory) on a GPU card. During execution, every 32 threads in a block (a warp) follow exactly the same instruction schedule.

To increase efficiency of GPU implementation of MrBayes MC3, we propose a new implementation architecture, tgMC3. A performance comparison between tgMC3, BEAGLE-based MrBayes MC3 [8], nMC3 (v1.0) [9], nMC3 (v2.1, the latest version so far), as well as the multi-core parallel MrBayes MC3, is performed.

Approach

Overview of MrBayes MC3

MrBayes MC3 is a computer package for the Bayesian inference of phylogeny, which has a command-line interface and performs phylogenetic analysis under various evolutionary models. For the purpose of a standardized evaluation against other implementations, we used MrBayes v3.1.2 (unless stated otherwise) under a commonly applied model which is set using the following command:

A detailed description of MrBayes MC3 settings can be found elsewhere [10], but briefly, this model allows gamma distributed variation in the rate of substitution over sites [11], with six substitution rate parameters, four base frequencies, and a proportion of invariable positions. Both the sampling frequency and the diagnosis frequency were set to 1000. The total number of generations for each dataset in our experiments can be found in section 4. For each dataset, two independent runs were performed, each with four Markov chains (three heated chains and one cold chain). Multiple chains can be used for fast mixing [12]. For individual run, each chain is operated one by one as depicted in Figure 1. We let TN denote the initial tree of chain N, denote the new group of trees modified from by proposed moves in iteration j, denote the seed value of chain N in iteration j and Q denote whether the move is aborted.

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Figure 1. The flow diagram of MrBayes MC3.

The gray box indicates the detailed operation of each procedure, and the arrow indicates the required parameters in a given procedure.

https://doi.org/10.1371/journal.pone.0060667.g001

For each chain, we let M denote the mutation matrix, Dz denote the DNA data at site z, Lz denote the number of site z, Pj denote the proportion of invariable sites and denote the base frequency of character state in DNA sequence in iteration j, where m∈{A, C, G, T}. The computation order of nodes in MrBayes MC3 uses the recursive algorithm [3]. In each procedure, the parameter Q needs to be verified in advance.

Since Markov chains in MrBayes MC3 are scheduled serially, and the run-time of each tree can be considered identical, the elapsed time can be regarded proportional to the number of chains. In addition, the number of unobserved tree nodes in an arbitrary tree topology and the computations of conditional likelihood probabilities of non-terminal node in each chain can be deemed as constant and performed independently.

Overview of Parallel MrBayes MC3 on GPUs

To our knowledge, the first parallel version of MrBayes MC3 was gMC3 [13], [14]. Since the transfer of the transition probability (tip) matrix between CPU and GPU is very frequently, it meets a large transfer overhead. Based on the gMC3, an improved parallel version of MrBayes MC3 was proposed (nMC3 [9]). In the initial version of nMC3, the authors decreased the frequency of tip matrix uploading and made both the CPU and GPU perform computations in parallel. This results in improved overlap in CPU-GPU data communication. In addition, site likelihood computation was performed in parallel by GPUs, which gives a delay in GPU to CPU transfer and decreases the amount of data transferred. Further speedups were achieved as a result of these modifications. In subsequent versions of nMC3, the authors optimized the stream order and thread parallelization strategy for large datasets. However, these various nMC3 implementations all used traditional one-to-one acceleration architecture, thus giving complex kernel launches. For the purpose of avoiding redundant computations and data transfer, we propose a new improved architecture for applying MrBayes MC3 to GPUs. Furthermore, Ayres and colleagues implemented an open API library, BEAGLE, to speed up likelihood calculations [8]. The BEAGLE library is now supported in MrBayes (v3.2.1), and is also included in this article for the performance comparisons.

Design and Implementation

1. The MrBayes nMC3 Method

The two most time-consuming aspects of MrBayes MC3 are the calculation of tip, and the calculation of clp. Since the implementation of the former on GPUs is identical in both tgMC3 and nMC3, we will not introduce this process here (for more details, see [9]).

Whereas GPU computation of clp under nMC3 is as follows. We assume that the transition probability matrix for each non-terminal node has already been calculated and transferred to GPU memory. As in Figure 2, the implementation architecture of nMC3 can be grouped into five modules according to the associated procedures in MrBayes MC3, with each module implemented by a single kernel which is labeled in a rectangle by dashed line. We will first introduce the essential function of each kernel, and then give the potentially redundant procedures in nMC3 by discussing the data relevance among the kernels.

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Figure 2. GPU implementation architecture in nMC3.

Each module is implemented by a single kernel which is labeled in a rectangle by dashed line.

https://doi.org/10.1371/journal.pone.0060667.g002

kernel1.

Transform tip matrix of non-terminal nodes and pad the transformed matrix (prelike matrix) with new tip for ambiguity data in parallel by GPU threads. Not all non-terminal nodes need to perform the procedure, as some of them may not have terminal node.

kernel2.

Load tip or prelike matrix from global memory to shared memory, in addition to terminal states or clp of its descendents, and distribute the computation of clp among threads. The computed clp values need to be saved in global memory iteratively until reaching the root node.

kernel3.

If the parameter scalarsSet of the node is activated, the lnscaler value of each site belonging to the node should be subtracted by old scaler, with kernel 3 used to implement this function. In the mean time, the CPU process flips the scalersSet bit alongside the GPU.

kernel4.

For a scaler node, MrBayes MC3 stipulates the maximum clp within each residue as the scaler of the residue, which is achieved simply by traversing all clp. The new scaler is then divided by all clp of that residue. The kernel employs multiple threads to traverse the corresponding clp and scale them in parallel, which requires reloading clp from global memory. Similarly, alongside the GPU, the CPU process flips the scalersSet bit.

kernel5.

The kernel computes the clp of a root node, which requires the following new parameters: proportion of invariable sites, state frequencies and the weight of each site.

Kernels 3 and 4 may not occur in some non-terminal nodes. Therefore, if the node is non-scaling, only kernels 1, 2 and 5 will be implemented for a root node, and 1, 2 will be implemented for down nodes. Otherwise, the number of kernels for root and down node is 5 and 4, respectively. Besides, kernels 3 and 4 are two independent procedures. The bit switch operation of the former will not affect the computation of the latter, and the updated value only affects the computation of the new tree sample in the next generation. Therefore, kernels 3 and 4 can be merged into one module and the bit switch operations can be stacked and implemented together by CPU processes after these modules. Moreover, new parameters in kernel 5 can be calculated in advance and merged in kernel 2 for computing likelihoods of the root node.

2. An Improved GPU Implementation of MrBayes MC3

Since the computation of clp can be regarded as a pipeline of several sequential steps, we put forward a tight GPU implementation of MrBayes MC3, tgMC3. The pseudo-code description of the clp computation for an arbitrary down node can be found in Figure 3. The single tight kernel integrates all kernel functions in earlier applications on GPUs. In tgMC3, we do not use global kernels to perform each function, but use device function in the kernel to process each step. The concise and explicit architecture of tgMC3 is illustrated in Figure 4. The major advantages of tgMC3 over nMC3 are listed below:

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Figure 3. Pseudo code of computing the conditional likelihood probability of down nodes implemented in tgMC3.

https://doi.org/10.1371/journal.pone.0060667.g003

  • By analyzing data dependencies in MrBayes MC3, tgMC3 integrates multiple functions into a single tight GPU kernel, instead of using several discrete kernels, hence decreasing the complexity of kernel launching. Just one kernel is sufficient for likelihood computation of both down and root nodes. This is particularly useful for large datasets having a relatively small amount of unique sites.
  • In step 1, for terminal nodes, nMC3 loads tip and the transition probability for ambiguity data initially into a prelike matrix, and then re-load the prelike matrix from global memory into shared memory for likelihoods computation. However, this is a redundant process on GPUs, which we have improved here. A direct multi-threaded data transfer of tip matrices is proposed in the tgMC3 method.
  • For scaling nodes, the nMC3 method accelerates steps 3 and 4 by two individual GPU kernels. However, the scaled data and scaler are closely connected with conditional likelihoods from step 2. Therefore, combined with the original down node types, a scaler shortcut is calculated by scaler parameters for the purpose of integrating these steps without adding branches, and the final number of down node kernel type is expanded from 4 to 16. These modifications improve the scaling node procedures on GPUs.

2.1 A direct read of transition probability matrix.

In MrBayes MC3, in the jth generation of Markov chain i, on the newly proposed tree topology T, for non-terminal node k, site l, discrete rate r and nucleotide m, where m∈{A, C, G, T}, before computing a conditional likelihood probability clpm = clP(T, k, l, r, m) of the node, the corresponding transition probability matrices tip for terminal node descendents should be transformed. Since each non-terminal node has two child nodes which are either terminal or non-terminal, non-terminal node can be classified into 4 groups. MrBayes MC3 assesses the combinations of the node, and labels the node as one of down_0, down_1, down_2 or down_3. The computation of clp is then distributed to the relevant pass.

In the nMC3 algorithm, the procedure described above is split into two sections by first accelerating the transformation of tip matrices to prelike matrices, and then accelerates the computation of clp. These accelerations are implemented by two separate kernels. Assuming that both the left and right children of a node are terminal, i.e. the node belongs to down_3, tipL and tipR matrices need to be transformed into prelikeL and prelikeR matrices. For this, the implementation requires two global memory reads and writes. Since prelike matrices are in use in the computation of clp, one additional global memory read is needed.

In the tgMC3 algorithm, to compute clp = CLP(T, k, l, r, m) over all l, r and m at non-terminal node k on the newly proposed tree topology T, nodes will be distributed into the relevant down_x, x∈ {0, 1, 2, 3} after assessment. The implementation is performed by transforming the tipL and tipR matrices to prelikeL and prelikeR matrices in shared memory directly for the computation of clp, instead of loading from global memory repeatedly. Hence, the whole procedure is performed within the same kernel on GPUs.

2.2 One tight kernel versus multiple discrete kernels.

Some non-terminal nodes are specified to be scaled after the clp of these nodes are computed. In MrBayes MC3, scaling is performed either by subtracting the value of the old scaler or adding the new scaler to the lnScaler variable, or both steps are performed successively. These steps are followed by two bit switch operations. These operations actually block the scaling being performed in the same kernel on GPUs in the nMC3 algorithm. As explained in section 3.1, these steps are independent and the bit switch operation of step 1 will not affect the input variables of step 2. Hence they can be grouped and performed after the two steps. Experimental results confirm that the accuracy of the results is not changed by porting these codes (Table S1). This principle is adopted for our tgMC3 algorithm. Since the two steps may not occur on the same node, simply including these steps in the kernel will result in redundant branch judgments for GPU threads. Therefore, we develop a shortcut list helping the CPU decide which tight GPU kernel to be launched (Table 1), where the values of S and N represent whether scalersSet or scalerNode is activated. T denotes the shortcut for each type of down node, i.e. a secondary classification of down nodes. With these improvements, a union implementation scheme is established so that the whole implementation architecture employs just one tight GPU kernel. This not only decreases the CPU-GPU communication overhead, but also affords new implementation architecture to avoid redundant data transfers. In particular, the tight GPU kernel is extremely useful for clp, as shared memory and registers can be fully utilized, instead of repeatedly loading the data from global memory.

Table 2 presents the data transfer complexity of the major parameters in the GPU-based implementation of MrBayes MC3, where the read and write operations on global memory are separately counted. Since the types of node and the scaler state are indeterminate, it is not feasible to calculate a completely accurate value. Hence, the statistics of data transfers are established in the case that each non-terminal node is composed of a terminal node and a non-terminal node descendent, and that all nodes are scaling-node. If the size per transfer is normalized to 1, transfer complexity can be decreased from O(4(N-2)+5) to O(2(N-2)+2) for clp, from O(3(N-2)+3) to O(N-1) for tip and from O(4(N-2)+4) to O(2(N-2)+2) for lnscaler. However, we will not claim that the improved method can achieve such improvements in practice, and the aim of such a comparison is primarily to highlight the differences between tgMC3 and nMC3.

2.3 Intra-task parallelization versus Inter-task parallelization.

The proposed algorithm is implemented by two task parallelization strategies. The difference between these strategies is whether the computation of an individual nucleotide residue is performed by a single thread or by multiple threads. An intra-task parallelization strategy is normally used to process relatively short nucleotide sequences in order to utilize GPU resources to the greatest extent, whereas shared memory is commonly exploited for faster accession of data. The inter-task parallelization method is normally used to process relatively long nucleotide sequence, as the overlap of memory access is higher, which also reduces costs on dispatching threads. In the specified evolutionary model, 16 elements for each nucleotide need to be calculated in total, which is separated into 4 sets, each with four values corresponding to the A, C, G, T nucleotide states. In nMC3 (v1.0), this is performed by a single parallelization strategy, the so-called Intra-task parallelization method, where the computation of each nucleotide residue is completed by 16 threads. In nMC3 (v2.1), the situation appears quite complicated, as the module for computing clp (kernel 2) is performed by mixed parallelization strategies (Figure 2), where the inter-task parallelization strategy is directed against long sequences and the intra-task parallelization strategy is directed against short sequences. The module for scaling nodes (kernel 4) is performed simply using the inter-task parallelization strategy. The parallelization strategy used in version 1.0 is suitable for short sequences, since if there are only a few nucleotide residues, increased thread allocation makes efficient use of GPU resources, although there is cost in terms of coordination among threads. The fact that version 1.0 adopts a reduction method to find the maximum clp value of each nucleotide residue in module 4 results in 50% of threads working in an idle state during each iteration. Nonetheless, Intra-task parallelization is still more preferred than Inter-task parallelization on the implementation of relatively short sequences. For version 2.1, module 4 can be performed by two parallelization strategies, which we improved here. Therefore, tgMC3 contains two parallelization strategies, and a threshold value regarding to the choice of parallelization strategy is empirically defined before running.

Experiments

1. Experimental Environments

All experiments were benchmarked on the same computing node of DEGIMA (Destination for Gpu intensive MAchine) [15], built by one of the authors of this article (TH) for high performance computing research in Nagasaki University. The process technology of the CPU used in [9] is less current than the GTX 480 card, and hence we used a relatively advanced processor based on 32 nm process technology for equivalent comparisons. The details of experimental environments are listed in Table 3. The gcc version 4.4.4 with the –O3 and Wall flag was used for compiling MrBayes MC3, as well as the CPU-side code of tgMC3, nMC3 and BEAGLE-based MrBayes. The GPU-side code of tgMC3, nMC3 and BEAGLE-based MrBayes MC3 were compiled using CUDA Toolkit, version 4.2. CUDA_INSTALL_PATH and SDK_INSTALL_PATH should be imported to environment before making the codes, more details can be found in the user manual of tgMC3 (File S1).

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Table 3. The experimental environments of host and device in the proposed method.

https://doi.org/10.1371/journal.pone.0060667.t003

2. Datasets

The nucleotide datasets used in experiments can be placed into three categories according to their unique sites: short (datasets 1 and 2), medium (dataset 3) and long sequence length (datasets 4 and 5). We briefly list them below, and the details of these datasets can be found in [16][18].

Dataset 1: A group of Trichophora 18S rDNA including 26 taxa.

Dataset 2: A group of Euhemiptera 18S rDNA including 33 taxa.

Dataset 3: A group of metazoan 18S rDNA including 111 taxa.

Dataset 4: A group of eukaryotic 18S rDNA including 234 taxa.

Dataset 5: A group of 23 - 28S rDNA from Bacteria, Archaea, and Eukaryota including 288 taxa.

3. Results

3.1 Run-time.

The run-time gives elapsed time for the whole analysis. Table 4 presents the run-time required to analyze the datasets on the platforms described in Section 4.2 with 1) serial MrBayes MC3 using one CPU process, 2) MrBayes MC3 using two concurrent CPU processes, 3) BEAGLE-based MrBayes MC3 using one GTX 480 card, 4) nMC3 (v1.0 and 2.1) using one GTX 480 card, 5) tgMC3 using either one GPU or two GPUs. From Table 4 we can see that tgMC3 takes the least time in our test.

3.2 Speedup.

We made the following definitions:

  1. The b-m speedup is the number of times faster that BEAGLE-based MrBayes MC3 using one CPU process and one GPU device performs when compared with MrBayes MC3 implemented by either one CPU process or two concurrent CPU processes.
  2. The n-m speedup is the number of times faster that the nMC3 (v2.1) algorithm using one CPU process and one GPU device performs when compared with MrBayes MC3 implemented by either one CPU process or two concurrent CPU processes.
  3. The t-m speedup is the number of times faster that the tgMC3 algorithm using one CPU process and one GPU device performs when compared with MrBayes MC3 implemented by either one CPU process or two concurrent CPU processes.

Table 5 presents the speedups, computed from the data in Table 4. The tgMC3 method outperforms the serial MrBayes MC3 by a factor between 6 to 30 times when using a single GTX480 card, whereas a speedup factor around 51 times can be achieved by using two GTX 480 cards on relatively long sequences (Table 4). The number of times faster between each GPU-based MrBayes MC3 can also be computed from Table 4. Experiments indicate that the tgMC3 method outstrips nMC3 (v1.0) with speedup factors from 2.1 to 2.7 times and nMC3 (v2.1) from 1.2 to 1.7 times. Moreover, tgMC3 outperforms the BEAGLE-lib based method from 3.7 to 5.7 times. For all the five test datasets, tgMC3 always achieves the greatest speedup factor when using one core or two cores (Table 5).

3.3 Scalability.

The sequence length discussed in this section is the number of unique sites per dataset, as opposed to the complete length of sequences, since only unique sites affect the computation complexity in MrBayes MC3. We normalized the speedup comparisons of the GPU-based implementation of MrBayes MC3 to serial MrBayes MC3. Figures 5 and 6 illustrate the speedup comparisons between these methods when using the first N taxa of datasets 4 and 5. These datasets are composed of relatively long sequences, with 1790 nt and 3386 nt. From these figures, it is apparent that the speedup factors of tgMC3 and nMC3 (v2.1) show better scalability than the remaining methods. In particular, tgMC3 runs at least 1.2 times faster than nMC3 (v2.1). Figure 7 illustrates the speedup of a group of simulated datasets composed of 60 taxa, which were generated with Seq-Gen version 1.3.2 [19], consisting L unique sites. In each case, we run serial MrBayes MC3, BEAGLE, nMC3 (v1.0), nMC3 (v2.1) and tgMC3 for 10000 generations. The speedup of each GPU-version of MrBayes MC3 is normalized by the run-time of serial MrBayes MC3. Likewise, tgMC3 outperforms other methods and shows the best scalability as sequence length is increased (Figure 7).

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Figure 5. Speedup comparisons between BEAGLE, nMC3(v1.0), nMC3(v2.1) and tgMC3 on the first N taxa in dataset 4, where N∈ {40, 60, …, 220}.

https://doi.org/10.1371/journal.pone.0060667.g005

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Figure 6. Speedup comparisons between, BEAGLE, nMC3(v1.0), nMC3(v2.1) and tgMC3 on the first N taxa in dataset 5, where N∈ {40, 60, …, 220}.

https://doi.org/10.1371/journal.pone.0060667.g006

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Figure 7. Speedup comparisons between BEAGLE, nMC3(v1.0), nMC3(v2.1) and tgMC3 on a group of 60 taxa, consisting L unique sites, where L∈ {1000, 2000, …, 10000}.

https://doi.org/10.1371/journal.pone.0060667.g007

Discussion

While there have been a number of versions of MrBayes MC3 accelerated with GPUs, several bottlenecks still exist. Firstly, data transfer can impose a substantial overhead in GPU-CPU heterogeneous computing for MrBayes MC3 if calculation times are not well synchronized. Secondly, the adoption of several CUDA kernels to accelerate each sub-function in MrBayes MC3 can be inefficient. The use of multiple CUDA kernels may reduce speedup as there are redundant global memory accesses between kernels. Thirdly, the size of the input data influences the degree of acceleration, particularly with insufficient computational load reducing the efficiency of GPU hardware usage. Previous methods fail to take these into account.

To address these bottlenecks and further accelerate MrBayes MC3 on GPUs, we propose a tight GPU MC3 (tgMC3) algorithm with three key features; i) the algorithm applies a tight GPU kernel to avoid data transfer overhead between CPU and GPU; ii) it encapsulates conditional likelihood probability estimation in a single CUDA kernel, also reducing the run-time consumed on GPU device memory access; iii) it employs two different task parallelization strategies to make full use of GPU hardware resources. Thus, tgMC3 can outperform the serial MrBayes MC3 by considerable speedup factors on empirical and simulated datasets.

Figures 5 and 6 illustrate that the outperformance of tgMC3 compared to other acceleration methods with datasets of various size, although the scalability is similar to nMC3 (v2.1) for long sequences. tgMC3 and nMC3 (v2.1) also show similar scalability with the increase of alignment length (Figure 7). The reason is associated with the task parallelization strategies. In tgMC3, two different task parallelization strategies are used to accelerate the computation of clp. Intra-task parallelization is used for short and medium alignments, with the aim to fully utilize GPU resources by allocating as many threads as possible, whereas inter-task parallelization is performed for long sequences to avoid redundant computation. An alignment length threshold is defined to select amongst these two strategies. However, in nMC3 (v2.1), only inter-task parallelization is adopted. As datasets 4 (results shown in Figure 5) and 5 (results shown in Figure 6) are composed of long sequences, both tgMC3 and nMC3 (v2.1) apply the same strategy, inter-task parallelization. This accounts for similar performance with increasing alignment length.

As can be seen from Table 4, the performance of the BEAGLE-based (1 GPU) implementation and MrBayes MC3 (1 CPU core) is very similar when using dataset 1. Performance differs for all remaining datasets, with BEAGLE running in a much shorter time. While a GPU has many cores, the frequency of each core is relatively low. In cases where there is a small amount of data for computation, there is no advantage for parallel computing compared with serial computing. In addition, CPU-GPU data transfer could be a big overhead. If there is not enough data within each CUDA kernel or the data transfer frequency is continual, GPU-based heterogeneous computing is not a good option. BEAGLE-based implementation only parallelizes the computation of conditional likelihood probability, while the chains are still scheduled serially. Therefore, it cannot achieve much speedup on datasets with short alignments as there is insufficient computation load. When the alignment length increases, higher speedup can be achieved by BEAGLE. This also can be seen from the performance of other GPU-based implementations.

The experimental results show that the proposed tgMC3 algorithm achieves increasing speedup as the number of unique sites increases, compared with serial GPU-based MrBayes MC3. In addition, tgMC3 outperforms other GPU-based MrBayes MC3, by a speedup factor of 3.7–5.7 times to the BEAGLE-based method, and 2.1–2.7 times to the nMC3 algorithm (v1.0). Moreover, the tgMC3 algorithm achieves a speedup factor of up to 1.7 times compared with nMC3 (v2.1). A minimum speedup factor of 1.2 times can be achieved when computing sufficiently long sequences.

Conclusions

We presented an accelerated implementation of MrBayes MC3 by employing an encapsulated GPU-based implementation architecture, tgMC3. Besides the acceleration strategies implemented in nMC3, the proposed tgMC3 further reduces the run-time of MrBayes MC3 by decreasing data transfer overhead, and accelerating the computation of conditional likelihood probabilities of sampling trees by two different task parallelization strategies. A number of empirical and simulated datasets are used to assess the speedup and scalability of the algorithm. The experiments indicate that one GTX 480 card can improve the performance of serial MrBayes MC3 running on a start-of-the-art general purpose processor by a factor of 6 for datasets with short sequences, and up to roughly 30 for datasets with long sequences. Moreover, tgMC3 outperforms the nMC3 algorithm (v1.0) from 2.1 to 2.7 times and the latest version (v2.1) from 1.2 to 1.7 times depending on the alignment length. In addition, tgMC3 shows similar scalability to the nMC3 algorithm (v2.1), with increasing data size and alignment length. To conclude, tgMC3 achieves better acceleration than previously proposed GPU-based optimization strategies of MrBayes MC3. In particular, our method could benefit the acceleration of the latest version of MrBayes (v3.2.1) and other Bayesian-based methods for phylogenetic analysis.

Supporting Information

Table S1.

Split frequency comparisons after resolving scaler code.

https://doi.org/10.1371/journal.pone.0060667.s002

(XLSX)

Acknowledgments

The authors would like to express their thanks to Xiaoguang Liu and Qiang Xie for their helpful comments on the nMC3 algorithm, Hongju Xia for providing valuable parallelization strategy, Hehui Zou for his assistance on writing the article.

Availability: An open source MrBayes tgMC3 (GNU GPL v.2) is available from: http://code.google.com/p/a-tight-gpu-implementation-of-mrbayes/

Author Contributions

Conceived and designed the experiments: CL WS. Performed the experiments: CL TH JB XL WZ WS. Analyzed the data: CL JB XL WS DC. Wrote the paper: CL TH WS DC.

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