fix issue in failed test

Link: http://biosal.s3.amazonaws.com/quality-assurance-department/2014-08-07-17:24:46.log
Link: https://github.com/GeneAssembly/biosal/issues/531
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
don't duplicate timer outputs

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
add timer for vertices

Link: https://github.com/GeneAssembly/biosal/issues/529
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
add a timer for actor computation in spate

Link: https://github.com/GeneAssembly/biosal/issues/532
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
add timer for arcs

Link: https://github.com/GeneAssembly/biosal/issues/530
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>