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