SWAPHI - Smith-Waterman Algorithm on Intel Xeon Phi Coprocessors

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• Introduction
• Downloads
• Citations
• Parameters
• Installation and Usage
• Change Log
• Contact

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© 2013 Yongchao Liu

Introduction

SWAPHI is the first parallel algorithm to accelerate the Smith-Waterman protein database search on Intel Xeon Phi coprocessors (with affine gap penalty and only using Xeon Phis). By searching against the UniProtKB/TrEMBL database (comprising 13,208,986,710 amino acids in 41,451,118 sequences, with the longest sequence of 36,805 amino acids), SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on a single coprocessor and up to 228.4 GCUPS on four coprocessors (B1PRQ-5110P/5120D) sharing the same host. In addition, we also developed its sister program SWAPHI-LS for the alignment of very long sequences on Intel Xeon Phi clusters.

NOTE: please tune the number of threads used according to the configuration of your Xeon Phi device. Typically #threads = 4 * (#processors - 1), but SWAPHI works best at full capacity, i.e. #threads = 4 * #processors through our evaluations.

Downloads

• latest source code (v1.0.5)^NEW

  The source code and a binary version are available for download now! Note that the binary version is compiled using the Intel C++ compiler (v13.1.3 20130607) on a x86_64 computer with Scientific Linux release 6.3 (Carbon) operating system.

Citation

• Yongchao Liu and Bertil Schmidt: "SWAPHI: Smith-Waterman protein database search on Xeon Phi coprocessors". 25th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2014), 2014, pp. 184-185. [preprint at arXiv] [poster].

Other related papers

• Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell: "MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA". 20th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2009), 2009, 121-128
• Yongchao Liu, Douglas L. Maskell, Bertil Schmidt: "CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units". BMC Research Notes, 2009, 2:73
• Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: "CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions". BMC Research Notes, 2010, 3:93
• Yongchao Liu, Adrianto Wirawan, Bertil Schmidt: "CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions". BMC Bioinformatics, 2013, 14:117.
• Yongchao Liu, Tuan-Tu Tran, Felix Lauenroth, Bertil Schmidt: "SWAPHI-LS: Smith-Waterman algorithm on Xeon Phi coprocessors for long DNA sequences". 2014 IEEE International Conference on Cluster Computing, 2014, pp.257-265
• Yongchao Liu and Bertil Schmidt: "GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences". Concurrency and Computation: Practice and Experience, 2015, 27: 958-972
• Tuan Tu Tran, Yongchao Liu, Bertil Schmidt: "Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi". Parallel Computing, 2016, 54: 128-138

Parameters

We have integrated both the database indexing and the alignment subroutines into a single executable binary, and have given two commands, i.e. index and align, for the database indexing and Smith-Waterman alignment against the indexed database, respectively. The following list the parameters for both of the two commands:

Database indexing

• -x < int> (number of Intel Xeon Phi coprocessors [REQUIRED])
• -i < str> (input sequence file in FASTA/FASTQ format [REQUIRED])
• -o < str> (prefix of output index files, default = INPUT file name [OPTIONAL])
• -m < int> (minimum sequence length, default = 0 [OPTIONAL])
• -M < int> (maximum sequence length, default = 4294967295 [OPTIONAL])
• -n < int> (the first number of sequences in the input, default = -1 [OPTIONAL])

Alignment

Input:

• -q < str> (input query sequence file)
• -d < str> (prefix of database file index)

Model:

• -i < int> (parallelization model, default = 0)

  0: inter-task model with one vector lane computing one sequence pair
  1: intra-task model with all vector lanes computing one sequence pair

Scoring scheme:

• -m < str> (scoring matrix name, default = blosum62)

  supported matrix names: blosum45, blosum50, blosum62 and blosum80.

• -g < int> (gap open penalty, default = 10)
• -e < int> (gap extension penalty, default = 2)

Compute:

• -p < int> (sequence profile used for inter-task model, default = 0)

  0: score profile
  1: query profile

• -c < int> (maximum bytes per data fetch by a device, default = 134217728)
• -t < int> (number of threads per Xeon Phi, deafult = 240)
• -x < int> (number of Xeon Phis used, default = 4)
• -l < int> (load the database entirely onto the device, default = 1)
• -k < int> (number of top alignments reported, default = 10)

Installation and Usage

Compile

1. Modify the "INTEL_DIR" macro in the "Makefile" to point to the correct Intel C++ compiler installation directory.
2. Modify the "ZLIB_HEADER" macro in the "Makefile" to point to the correct ZLIB installation directory.
3. Type "make" command to compile the software.

Typical Usage

This software works at two steps:

1. Build the database indices using the command "swaphi index [options]".
2. Perform the Smith-Waterman sequence alignment against the indexed database using the command "swaphi align [options]".

Typical command lines:

1. command line "swaphi"

   Get the command line options

2. command line "swaphi index"

   Get the database indexing command line options

3. command line "swaphi align"

   Get the alignment against the indexed database command line options

4. command line "swaphi index -x 2 -i database.fasta -o outBaseName"

   Build indices for the database for two Intel Xeon Phi coprocessors. The common base name of all index files are "outBaseName".

5. command line "swaphi align -q query.fasta -d outBaseName -x 2"

   Perform the Smith-Waterman sequence alignment against the indexed database on two Intel Xeon Phi coprocessors.

Change Log

• June 09, 2015 (v1.0.5)
  1. By default, we have removed the dependence on ZLIB. Instead, we allow users to configure whether to support gziped input or not. This can be done by enabling the macro "COMPRESSED_INPUT" in the Makefile.
  2. There is no change in the code.
• Feb 02, 2015 (version 1.0.14)
  1. The source code has already been released!

Contact

If any questions or improvements, please feel free to contact Liu, Yongchao.