memory_pool: all tracepoint events

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
memory_pool: hide warnings by default for memory leaks

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
tests: revert the DNS address

Works 100% of the time:
http://jenkins.biosal.anl.boisvert.info:8080/

Works sometimes (there is some DNS propagation issue):
http://jenkins-biosal.mcs.anl.gov:8080/

These 2 addresses point to the same thing.

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
core: use error code 2 on Blue Gene/Q

Suggested-by: Ray Loy <rloy@alcf.anl.gov>
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
scripts: add script to analyze memory tracepoints

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
cray: add script to build on Cray XC30

Link: https://github.com/GeneAssembly/biosal/issues/822
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
genomics: increase pool chunk size for aggregators

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
memory:  add BGQ initialization routine for memory system

The ticket #824 shows that 4 GiB is lost to fragmentation.

Hopefully, this patch will solve the issue.

Link: https://github.com/GeneAssembly/biosal/issues/824
Suggested-by: Hal Finkel <hfinkel@anl.gov>
Link: https://github.com/GeneAssembly/biosal/issues/827
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
Merge branch 'master' of github.com:sebhtml/biosal into energy
thorium: add a queue for messages when request count is too high

Any message sent through transport needs a couple of calls to MPI_Test
before the send operation is completed. Sometimes, the number of MPI
requests is very high, which causes some clutter to accumulate in the
MPI request queue and therefore increases the node latency.

This patch limits the amount of MPI requests at any given time.

Link: https://github.com/GeneAssembly/biosal/issues/826
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: add compilation option for clutter avoidance

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
examples: remove trailing spaces

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
blue gene: don'T register signal handlers

Instead of registering signal handlers, let the operating system
generate a core dump instead.

Suggested-by: Hal Finkel <hfinkel@anl.gov>
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
memory: call mallopt with default glibc values on Blue Gene/Q

Link: https://github.com/GeneAssembly/biosal/issues/819
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
genomics: change the minimum coverage to 1

With 2:

[boisvert@bigmem biosal]$ grep '>' output-c2/unitigs.fasta|awk '{print $2}'|sed 's/length=//g'|sort -r -n|head
23427
23427
23427
23427
21321
21321
21321
21321
21321
21321

With 1:

[boisvert@bigmem biosal]$ grep '>' output/unitigs.fasta|awk '{print $2}'|sed 's/length=//g'|sort -r -n|head
32675
32675
32675
32675
32675
27847
27847
27847
27847
27847

This should yield better contiguity in metagenome assemblies.

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
blue gene: don't use jemalloc

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
core: fix coding style (missing space after comma)

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

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
engine: add thorium_actor_log() function

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
Signed-off-by: George K. Thiruvathukal <gkt@cs.luc.edu>
genomics: use the new logging API in unitig_manager

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