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Option Details and Options Pro ContraSorted descending TBB?
RazerS-Piktogram-Parallel-by-Reads-sm.png c) Distance between pairs is restricted   waiting times, regulation for more than two pairs get complex  
RazerS-Piktogram-Parallel-by-Reads-sm.png b) pairs operate in the same window little regulation, simple find() waiting times  
RazerS-Piktogram-Parallel-Hybrid-sm.png One filter over all reads, verification parallelized   spin locks for verifier necessary, probably bad use of capacity in repeats  
RazerS-Piktogram-Parallel-by-Genome-sm.png     prob. not cache local as it needs to switch between genomes  
Pipeline
Parallelize by Reads
Parallelize by Genome
RazerS-Piktogram-Parallel-by-Reads-sm.png a) pairs operate independent from each other no regulation necessary one might run away (cache)  
RazerS-Piktogram-Parallel-by-Genome-sm.png Filter and verifiere copy per genome   needs a lot of memory  
RazerS-Piktogram-Parallel-Hybrid-sm.png a) windows simple find() filters are not parallel (problem with high number of cores)  
RazerS-Piktogram-Parallel-Hybrid-sm.png b) tokens   complex find() TBB
RazerS-Piktogram-Parallel-Hybrid-sm.png c) distance between filter and verifier   complex find()  
       
RazerS-Piktogram-Parallel-by-Reads-sm.png coupled filter-verifier-pairs no spin lock for verifier    
RazerS-Piktogram-Parallel-by-Reads-sm.png each pair over a subset of the reads filter is parallel    
RazerS-Piktogram-Parallel-by-Reads-sm.png distance between filter and verifier fixed ?      
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Topic revision: r3 - 14 Feb 2010, mriese
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