Specifically add the HWLOC_TOPOLOGY_FLAG_WHOLE_SYSTEM flag when
loading configuration from HWLOC library. Previous logic in
task/cgroup did not do this, which was different behaviour from
how slurmd gets configuration information. Here's the HWLOC
documentation:
HWLOC_TOPOLOGY_FLAG_WHOLE_SYSTEM
Detect the whole system, ignore reservations and offline settings.
Gather all resources, even if some were disabled by the administrator.
For instance, ignore Linux Cpusets and gather all processors and memory
nodes, and ignore the fact that some resources may be offline.

Without this flag, I was rarely observing a bad core count, which
resulted in the logic layout out tasks wrong and generating an error:
task/cgroup: task[0] infinite loop broken while trying to provision compute elements using cyclic

bug 2502

Just in case some job fails to terminate as expected.

gang scheduling before doing code for gang scheduling.

burst_buffer/cray: Set environment variables just before starting job rather
    than at job submission time to reflect persistent buffers created or
    modified while the job is pending.
bug 2545

buffer is found.

Bug 2576

What happened was a function was doing a double read lock which isn't
awesome to begin with, but not really horrible (if all you are doing is
read locks anyway).  The problem was after the first lock was locked a
different thread was going for a write lock and so when the second
read lock came in it created deadlocked.

Avoid possibly aborting srun that gets simultaneous SIGSTOP+SIGCONT while
    creating the job step. The result is that the signal hanlder gets a
    argument (the signal received) of zero.

Here's a log, window 1:
$ srun hostname
srun: Job step creation temporarily disabled, retrying
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 18
srun: I Got signal 0
srun: Cancelled pending job step

Window 2:
$  kill -STOP 18696 ; kill -CONT 18696
$  kill -STOP 18696 ; kill -CONT 18696
$  kill -STOP 18696 ; kill -CONT 18696
....

bug 2494

Update NEWS as well.

The uid is used as part of the hash function, must remove old reference
and recalculate if it may change, otherwise _delete_assoc_hash
will not find it again when the association is removed, causing
slurmctld to segfault.

Bug 2560.

Previous gang scheduling logic maintained information about resources
  originally allocated to the job and made scheduling decisions on
  that basis.
bug 2494

This will improve ability to diagnose problems if the srun is
killed by a signal.

Update gang scheduling table when job manually suspended or resumed. Prior
    logic could mess up job suspend/resume sequencing.
bug 2494

time.

https://bugs.schedmd.com/show_bug.cgi?id=2547

The code just wasn't fully baked before and was probably written before
a lot of the other supporting code was done i.e
assoc_mgr_set_assoc|qos_tres_cnt were done specifically for this kind of
thing.  Many of the usage structures weren't realloced either as well as
the tres_cnt local to each qos and assoc wasn't updated.  So all in all
pretty bad code - bad Danny.  This makes sure all this sets up and no
memory corruption happens.

Generate burst buffer use completion email immediately afer teardown
    completes rather than at job purge time (likely minutes later).
bug 2539

Change burst buffer use completion message from
    "SLURM Job_id=1360353 Name=tmp Staged Out, StageOut time 00:01:47" to
    "SLURM Job_id=1360353 Name=tmp StageOut/Teardown time 00:01:47"

Bug 2548. No functional change, documentation only.

Otherwise "not found" value of -1 for tres_pos would cause
out-of-bounds memory access.

Bug 2543.

resolve NoInAddrAny when doing a strstr.  Continuation of commit 775c46de.

on only one port like TopologyParam=NoInAddrAny does for everything else.

There's no /proc on *BSD, and BSD handles OOM in a completely different way.

Return [0-100:2] formatting, rather than [0,2,4,6,8,...] when using
a step function.

Was inadvertantly broken in 14.11 with commit 5ffdca92.

Bug 2535.

burst_buffer/cray plugin: Prevent a requeued job from being restarted while
    file stage-out is still in progress. Previous logic could restart the job
    and not perform a new stage-in.
bug 2584, comment #45

Fix Cray NHC spawning on job requeue. Previous logic would leave nodes
allocated to a requeued job as non-usable on job termination.

Specifically, each job has a "cleaning/cleaned" flag. Once a job
terminates, the cleaning flag is set, then after the job node health
check completes, the value gets set to cleaned. If the job is requeued,
on its second (or subsequent) termination, the select/cray plugin
is called to launch the NHC. The plugin sees the "cleaned" flag
already set, it then logs:
error: select_p_job_fini: Cleaned flag already set for job 1283858, this should never happen
and returns, never launching the NHC. Since the termination of the
job NHC triggers releasing job resources (CPUs, memory, and GRES),
those resources are never released for use by other jobs.

Bug 2384

An error in slurmconfgen_smw.py caused it to parse the nic as the nid.
On some systems those values differ, causing the generated slurm.conf file to
be incorrect.

Bug 2532.

_set_collectors() already has a run_in_daemon("slurmd") that
precludes this from being an issue.

route_p_split_hostlist was not thread-safe, and would cause
one of several segfaults depending on where in the initialization
code each thread was.

Bug 2495.

Was incorrectly displaying "(null)" even when loaded successfully.

In particular, it seems that MariaDB has changed the default for
innodb_lock_wait_timeout has been lowered which can cause issues
for the various rollup processes on systems with high job counts.

Step GRES value changed from type "int" to "int64_t" to support larger
values.

Signed-off-by: Danny Auble <da@schedmd.com>