Pbb a parallel bioinformatics benchmark suite for shared memory multiprocessors
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PBB: A Parallel Bioinformatics Benchmark Suite for Shared Memory Multiprocessors. CHEN Wenguang HPC Inst., CS Dept., Tsinghua University. Outlines. Motivation Benchmark selection & construction Benchmark characteristics Performance results Conclusions, Q&A. Motivation.

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Pbb a parallel bioinformatics benchmark suite for shared memory multiprocessors

PBB: A Parallel Bioinformatics Benchmark Suite for Shared Memory Multiprocessors

CHEN Wenguang

HPC Inst., CS Dept., Tsinghua University


Outlines
Outlines

  • Motivation

  • Benchmark selection & construction

  • Benchmark characteristics

  • Performance results

  • Conclusions, Q&A


Motivation
Motivation

  • Widely use of bioinformatics applications

  • The trend of multi-core

    => There should be a parallel bioinfo. benchmark

  • SPEC CPU2000 may not match the characteristics of bioinformatics workloads well

  • Existing bioinformatics benchmark are not satisfactory

    => We need a new one


Existing Bioinformatics Benchmarks:

BioBench:

  • does not cover some important domains

  • no parallel program

    BioPerf:

  • includes only one parallel benchmark

    BioParallel:

    our previous work, includes 5 parallel application


PBB benchmark suite:

Being more complete

7 applications covering 7 of the most important domains of bioinfo.

Keeping pace with the changing world

all the applications are parallelized


Benchmark selection construction
Benchmark Selection & Construction

  • Identify the most important application domains

  • Choose representative applications for each domain

    most popular, most advanced

  • Benchmark optimization & parallelization


The 7 applications:

  • Pairwise sequence alignment: BLAST-P

  • Global alignment: PLSA

  • Multiple sequences alignment: MUSCLE

  • Protein 3D structure prediction: Rosetta

  • Phylogenetic tree reconstruction: SEMPHY

  • Gene regulatory network learning: ModuleNet

  • Pattern study of Single Nucleotide Polymorphisms: SNP


Benchmark characteristics
Benchmark Characteristics

Systems Used:

Workload analysis is performed on QP001


Non-egligible FP

Instruction profile:

Higher L/S


CPI

Low CPI

8P means QP001 with HT enabled


Fsb bandwidth utilization
FSB bandwidth utilization

Low utilization


Performance results
Performance Results

Benchmark scores:

: time used to run application i on the reference system

: time used to run application i on the tested system

Rosetta is excluded for it produces random results



Parallel speedup
Parallel speedup

Tested on Unisys-ES700 with 16 Xeon



Conclusions
Conclusions

Workload characteristics:

  • High percentage of load/store instructions

  • Non-negligible floating point instructions, but still significantly lower than SPECCPU 2000FP

  • Low CPI

  • Low memory bandwidth demand


Thanks

Any questions?


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