thorium: add perf documentation

Changes from yesterday (with perf) lowered the running time
from 3min15s to 2m16.985s.

Link: https://github.com/GeneAssembly/biosal/issues/720
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: use lockless workers and lockless actors

Link: https://github.com/GeneAssembly/biosal/issues/720
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
core: change code path when using one hash group

Link: https://github.com/GeneAssembly/biosal/issues/720
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
Fixed coding style with 2 tabs and comments.

Signed-off-by: Huy Bui <huybui@anl.gov>
thorium: add compute-to-communication ratio in actor profiles

Link: https://github.com/GeneAssembly/biosal/issues/720
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
Merge remote branch 'huy/master' into energy
management: add script to sync to mirror

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
genomics: increase visitor count in graph visiting code paths

Link: https://github.com/GeneAssembly/biosal/issues/726
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
management: switch back to energy

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

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
optimize some hash table operations

Link: https://github.com/GeneAssembly/biosal/issues/725
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
core: disable memory fences in ring (it works on x86)

Link: https://github.com/GeneAssembly/biosal/issues/725
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: disable wait code path since we don't use it

time ./scripts/assembly_debugging/spate-saureus-fasta-gz-4x8.sh &> log
real    2m8.855s

Link: https://github.com/GeneAssembly/biosal/issues/725
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
cray: add fancy linking option

Link: https://github.com/GeneAssembly/biosal/issues/722
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
core: use memory fences in ring structure

Otherwise, changes are not visible and the code does nothing at all !

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
build: add a script to build native executable (not x86-64) with gcc

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
core: use flags with '&' instead (BITMAP_GET_BIT, BITMAP_SET_BIT, BITMAP_DEFINE_BIT)

Link: https://github.com/GeneAssembly/biosal/issues/727
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
core: use bitmap macros in hash table

Link: https://github.com/GeneAssembly/biosal/issues/727
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>