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BScParallelBamIOScheduleProject

Implementation of parallel de-/compression of BAM files

Project Schedule

Tasks

1) Extract the compression and decompression into a BgzfCompressor and a BgzfDecompressor class

2) Create Initial (Sequential) =Stream<ParallelBgzf>

3) Parallelize Stream<ParallelBgzf> in a Fork/Join Fashion

4) Write Parallel BGZF/BAM-Handling Tools

4a) Optional: Write Parallel BAM Sorter

4b) Optional: Asynchronous Parallelism

Schedule

Week Planned Activities Status
1 Read up on parallelization theory and algorithmic strategies, setup build system, start with Task 1 completed
2 Finish Task 1 and Task 2, create a concept for Task 3 completed
3 Task 3 completed
4 Finish Task 3, Task 4 completed
5 optional Task  
6 optional Task  
7 performance analysis and comparison to other solutions in progress
8-10 writing process  

Work Log

Week 1 Activities

  • Research Parallel Software Engineering (concepts and usage scenarios)
  • setup seqan environment
  • create ParallelBgzf Stream from Bgzf Stream
  • isolate decompression from ParallelBgzf Stream into Decompressor

Week 2 Activities

Mo (Nov 4, 2013)

  • Consultation Manuel
  • cleanup Decompressor
  • introduce exceptions for IO-error handling

Di (Nov 5, 2013)

  • isolate Compressor

Mi (Nov 6, 2013)

  • test isolated Compressor

Do (Nov 7, 2013)

  • test Compressor with integration to streamFlush

Fr (Nov 8, 2013)

  • test/debug Compressor with integration to streamFlush and streamWrite

Week 3 Activities

Week 3 TODO's

  • extend compressor so that it splits long inputs into blocks
  • finish testing Stream with compressor/decompressor
  • refactor Stream so that the sequential compression/decompression can be parallelized in a join/fork fashion using new classes BgzfCompressionThread and BgzfDecompressionThread

Mo (Nov 11, 2013)

  • Consultation Manuel
  • extend compressor so that it splits long inputs into blocks
  • continue testing Stream

Di (Nov 11, 2013)

  • continue testing Stream

Week 4 Activities

Week 4 TODO's

  • debug decompressor
  • extend tests for decompression
  • create parallel decompressor
  • create apps that use parallel compressor/decompressor

Fr (Dec 12, 2013)

  • Debug Decompressor/Compressor
  • Extend Tests

Mo (Dec 22, 2013)

  • debug decompressor

Di (Dec 22, 2013)

  • debug decompressor
  • refactor parallel compressor
  • implement parallel decompressor

Mi (Dec 22, 2013)

  • add tests to parallel decompressor
  • create BGZF App
  • create BAM<->SAM tools

Do (Dec 22, 2013)

  • found more problems in decompressor streamReadBlock Bookkeeping
  • more decompressor debugging

Mo (Jan 6, 2014) - Fr (Jan 10)

  • more streamReadBlock Bookkeeping

Mo (Jan 13, 2014) - Fr (Jan 17, 2014)

  • more streamReadBlock Bookkeeping

Mo (Jan 20, 2014) - Fr (Jan 24, 2014)

  • more work on BGZF App
  • Meeting
  • completed Multithreaded Decompressor integration and all associated Tests
  • fixed multithreaded compressor book-keeping bug
  • work on sam2bam

Mo (Jan 27, 2014) - Tue (Feb 5, 2014)

  • more sam2bam, bam2sam
  • profiling
  • found and fixed performance bug
  • running analysis of multithreading on compression and decompression in bgzf app
  • thesis outline

Comments

 
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Topic revision: r8 - 05 Feb 2014, olfrik
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