A simple utility that evaluates parallel performance in tribble

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Tests low-level multi-threading performance of tribble Creates a thread pool that reads the input VCF file in parallel with N threads from 1 to maxThreads (in powers of 2) and emits the wall time needed to process the entire file.  Assumes the VCF file has a chromosome named 1 that has at least 250 Mb.

The output is a nice table showing performance of Tribble

  THREAD: 1-250000001 read 2288096 objects
TIME: 1 thread runtime 12.58
  THREAD: 125000001-250000001 read 1098468 objects
  THREAD: 1-125000001 read 1189628 objects
TIME: 2 thread runtime 8.66
  THREAD: 124000001-186000001 read 406935 objects
  THREAD: 62000001-124000001 read 569656 objects
  THREAD: 1-62000001 read 619972 objects
  THREAD: 186000001-248000001 read 678173 objects
TIME: 4 thread runtime 8.57
  THREAD: 124000001-155000001 read 101636 objects
  THREAD: 93000001-124000001 read 271390 objects
  THREAD: 62000001-93000001 read 298266 objects
  THREAD: 155000001-186000001 read 305299 objects
  THREAD: 31000001-62000001 read 297745 objects
  THREAD: 1-31000001 read 322227 objects
  THREAD: 217000001-248000001 read 334136 objects
  THREAD: 186000001-217000001 read 344037 objects
TIME: 8 thread runtime 9.68

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This commit is contained in:

Mark DePristo 2011-08-15 21:42:23 -04:00

parent ed2df49743

commit c3c11b2462

Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL

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