don't print worker loop loads by default

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
test volatile ring

walltime: 42m29.711s
dataset: meta1
commit: 0cbcac70aa27d854266e8b68f4ab69817f569ec3 (no volatile and no atomic ring)
configuration: 4 x 7

walltime: 49m31.588s
dataset: meta1
commit: 0cbcac70aa27d854266e8b68f4ab69817f569ec3 (+ volatile and no atomic ring)
configuration: 4 x 7

walltime: 44m20s
dataset: meta1
commit: b6293d1aad7080488380fe763d7a270a89a64fe5 (atomic ring)
configuration: 4 x 7

Link: http://sc.tamu.edu/help/power/powerlearn/html/parallel-smpnw/sld017.htm
Link: https://github.com/GeneAssembly/biosal/issues/312
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
use a power of 2 in the ring

Before: 0m28.518s
After: 0m28.183s

Link: http://psy-lob-saw.blogspot.com/2013/03/single-producerconsumer-lock-free-queue.html
Link: https://github.com/GeneAssembly/biosal/issues/313
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
use a mask instead of module in ring

Before: 0m28.183s
After: 0m28.882s

Link: https://github.com/nitsanw/examples/blob/master/src/java/uk/co/real_logic/queues/P1C1QueueOriginal2.java
Link: http://psy-lob-saw.blogspot.com/2013/03/single-producerconsumer-lock-free-queue.html
Link: https://github.com/GeneAssembly/biosal/issues/314
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
use cache head and tail

Link: http://stackoverflow.com/questions/14707803/line-size-of-l1-and-l2-caches
Link: http://psy-lob-saw.blogspot.com/2013/03/single-producerconsumer-lock-free-queue.html
Link: https://github.com/GeneAssembly/biosal/issues/315
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
BSAL_INPUT_OPEN must only take 1 file name, no file index

Link: https://github.com/GeneAssembly/biosal/issues/289
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
add functions to update ring caches

Link: https://github.com/GeneAssembly/biosal/issues/317
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
fix bug in ring example

Link: https://github.com/GeneAssembly/biosal/issues/318
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
use one persistent storage pool per consumer in aggregator

medium2 4x7
Before: 0m28.340s
After: 0m22.640s

Link: https://github.com/GeneAssembly/biosal/issues/309
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
fix a race when there are not a lot of sequences

Link: https://github.com/GeneAssembly/biosal/issues/287
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
add documentation for quality control

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>