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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

slide4
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

slide5

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
slide7
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

slide9

Non-egligible FP

Instruction profile:

Higher L/S

slide10
CPI

Low CPI

8P means QP001 with HT enabled

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
slide17
Thanks

Any questions?

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