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ThesisMCRazerWeeklyReports
09 Aug 2023 - 17:03
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Week 1 (25.1.)
Week 2 (1.2.)
Week 3 (8.2.)
Week 4 (15.2.)
Week 5 (22.2.)
Week 6 (1.3.)
Week 7 (8.3.)
Week 8 (15.3.)
Week 9 (22.3.)
Week 1 (25.1.)
Q-gram index with open hashing
Week 2 (1.2.)
Adapt mapRead functions to parallelism
Overview over parallelization options
Speed test between normal qgram index and open addressing version
Week 3 (8.2.)
Slides for the talk at the Charité
Parallel version compiles without -fopenmp
hunt for segmentation fault
Week 4 (15.2.)
Presentation at the Charité
Herr Kleffe erwartet sich:
Einen schnellen read mapper
Reduktion der Indexgröße, bzw. weniger Speicherverbrauch
Exam preparation
Week 5 (22.2.)
Window version compiles and runs with openmp
Output for speed analysis (how many base pairs per sec., how many verifications per sec., for each thread and block)
Week 6 (1.3.)
R script to analyse the 'speed output'
Documentation for findWindow functions
Window has the same speed as the normal version.
Week 7 (8.3.)
reduce the size of the critical region
analyse higher q's
Week 8 (15.3.)
script that splits up the reads and runs them with the serial version
On small sample (100,000 reads) the parallel version is faster than the parallelizing script
comparing different window sizes and granularity of the blocks
Week 9 (22.3.)
speed comparison for different number of cores
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