I noticed that the CpuFreqDef config option was only partially implemented. The value was parsed, but the never used. So I took the liberty of re-purposing it to mean sort of the opposite, namely the frequency governor to use when running a job step in case the job doesn't explicitly provide any --cpu-freq option.

I also changed the default of the CpuFreqGovernors option to be "ondemand,performance", since ondemand isn't available with the intel_pstate driver.

Otherwise the patch should be relatively straightforward and only changes a few minor things here and there.

Add TopologyParam option of "TopoOptional" to optimize network topology
    only for jobs requesting it.
bug 2567

Timeout stalled transfers and cleanup related data structures. Default
to wait five minutes since last update. Hook onto registration/ping message
type to trigger cleanup in a minimally invasive manner.

While here restructure certain functions to use list_* functions
rather than iterate on the structures.

Otherwise --mail-type=ALL will send an unexpected stage_out message back
to the user.

Bug 2541.

Siphash is a state of the art keyed hash function that is performance competitive with the usual non-cryptographic hash functions. It's used as the default hash function backing hash tables in e.g. Perl, Python, Rust, and so on. Here we initially use it for the gid cache hash table, and in the common xhash implementation.

For commits:
f980c588
510abf23

Bug 1783

select/cray - Initiate step node health check at start of step termination
    rather than after application completely ends so that NHC can capture
    information about hung (non-killable) processes.
bug 2192

Make default compression vary based on library availability.

power/cray - Fix bug introduced in 15.08.10 preventin operation in many
    cases.
bug 2628

burst_buffer/cray - Fix for script creating or deleting persistent buffer
    would fail "paths" operation and hold the job.
bug 2624

and it doesn't meet basic requirements.

that wasn't set up correctly.

power/cray - Fix bug introduced in 15.08.10 preventin operation in many
    cases.
bug 2628

Bug 2431

burst_buffer/cray - Fix for script creating or deleting persistent buffer
    would fail "paths" operation and hold the job.
bug 2624

and it doesn't meet basic requirements.

Bug 2622.

burst_buffer/cray - Decrement job's prolog_running counter if pre_run fails.
bug 2621

If a job is no longer in configuring state, then clear the prolog_running
  counter on slurmctld restart or reconfigure.
bug 2621

When determining when a pending job will be able to start, rather
  than testing after removing each running job and trying to schedule
  the pending jobs, remove multiple jobs that all end about the
  same time before testing. This reduces the number of calls to
  the job placement logic, which is time consuming.

Fix for job "--contiguous" option that could cause job allocation/launch
    failure or slurmctld crash.
bug 2573

constraints mattered in a job.

    Details include:
    A job doesn't request memory but the system is running
    with CR_*MEMORY with no default memory limit and the job requests nodes
    with features of different sizes.  Previously the order of constraints
    mattered where the smaller memory node would need to be requested first
    or the job would fail.

    Bug 2608

This reverts commit f559a55c.

constraints mattered in a job.

Details include:
A job doesn't request memory but the system is running
with CR_*MEMORY with no default memory limit and the job requests nodes
with features of different sizes.  Previously the order of constraints
mattered where the smaller memory node would need to be requested first
or the job would fail.

Bug 2608

Previous logic would get an account and/or QOS time limit and use
  that value to overwrite the incoming RPC's NO_VAL value, which
  would change a job's time limit when changing an unrelated
  field (e.g. priority, QOS, etc.).
bug 2610

bug 2609

Fix backfill scheduler race condition that could cause invalid pointer in
    select/cons_res plugin. Bug introduced in 15.08.9, commit:
    efd9d35e

The scenario is as follows
1. Backfill scheduler is running, then releases locks
2. Main scheduling loop starts a job "A"
3. Backfill scheduler resumes, finds job "A" in its queue and
   resets it's partition pointer.
4. Job "A" completes and tries to remove resource allocation record
   from select/cons_res data structure, but fails to find it because
   it is looking in the table for the wrong partition.
5. Job "A" record gets purged from slurmctld
6. Select/cons_res plugin attempts to operate on resource allocation
   data structure, finds pointer into the now purged data structure
   of job "A" and aborts or gets SEGV
Bug 2603

canceled while launching.