tests: automate job submission on Beagle

Link: https://github.com/GeneAssembly/biosal/issues/770
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
test: add commit number in Cray automated jobs

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
tests: fix build name in Cray automated test

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
tests: don't use colon symbol in job name

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
cray: add all modules in the build system

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
transport: revert bug added in 6a53cbe

This patch reverts the commit 6a53cbe
("thorium: prepare message in transport").

The transport does not know about actors, it only send messages
(count, buffer, source node, destination node). In theory, the
preparation of received messages should work inside the
transport subsystem. But it does not.

On Beagle (Cray XE6), this error is generated:

Assertion failed in file
/notbackedup/tmp/ulib/mpt/nightly/6.0/081313/mpich2/src/mpi/datatype/get_count.c
at line 34: size >= 0 && status->count >= 0

This patch restores the old code path (which works fine).

Link: https://github.com/GeneAssembly/biosal/issues/774
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
blue gene: add script that automate jobs on Cetus

Testing the product on the IBM Blue Gene/Q platform implies the
following steps:

- connect to the platform
- change directory
- pull code for updates
- build product
- write submission program for job
- submit job

The script included in this patch does most of this to automate the
process (avoid errors and don't waste human time).

Link: https://github.com/GeneAssembly/biosal/issues/771
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
documentation: update quality assurance process

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
documentation: update compiler version for Cray

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
documentation: add compiler version for Blue Gene/Q

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
tests: fix test tool for Blue Gene/Q

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
scripts: remove trailing spaces in cray build script

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: add message block

Link: https://github.com/GeneAssembly/biosal/issues/772
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: use message blocks in the worker-node route

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: add multiplexing in the worker-to-node route

thorium_message_multiplexer: original_message_count 13938274 real_message_count 1091403 (0.0783)
thorium_message_multiplexer: original_message_count 14713230 real_message_count 1182619 (0.0804)
thorium_message_multiplexer: original_message_count 14749892 real_message_count 1201124 (0.0814)
thorium_message_multiplexer: original_message_count 14825961 real_message_count 1201118 (0.0810)

time ./scripts/assembly_debugging/spate-saureus-fasta-gz-4x8.sh |tee log
real    1m32.063s

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

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: fix an iterator bug in node

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: use a dynamic approach for pulling outbound messages

time ./scripts/assembly_debugging/spate-saureus-fasta-gz-4x8.sh
1m33.415s

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
thorium: remove some bloat from the node main loop

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
scripts: add a LTTng script to trace nodes

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