Also correct the value of NICE_OFFSET used within the perl API.

Bug 3098.

Bug 3051.

Otherwise updates would be rejected for running jobs even if there
would be no impact. Most common when the job_submit plugin is overriding
QOS/GRES values on everything; without this change an update to "comment"
or other fields would fail with ESLURM_JOB_NOT_PENDING.

Bug 3117.

Never ever run NHC, even on an edge case that NHC_NO would still launch NHC
after.

Bug 3105.

Switch to list_for_each, and check if access list actually changed
after each update before updating last_prat_update. This prevents
the backfill scheduler from resetting mid-cycle unnecessarily.

Bug 3123.

Switch to list_for_each, and check if access list actually changed
after each update before updating last_prat_update. This prevents
the backfill scheduler from resetting mid-cycle unnecessarily.

Bug 3123.

Buffer was being allocated based upon the size of the wrong structure.
  The buffer would have been larger than required, so this bug
  should not have caused any failures.
bug 3127

Add protocol version to slurmd startup communications for slurmstepd to
    permit changes in the protocol.

Added memory limits to the job and step. Without these, only one
  step may be able to run at a time and break the test

Add "flag" field to launch_tasks_request_msg. Remove the following fields
    (moved into flags): multi_prog, task_flags, user_managed_io, pty,
    buffered_stdio, and labelio. More flags to be added later.

*** CID 149289:  Null pointer dereferences  (REVERSE_INULL)
/slurm/src/slurmctld/step_mgr.c: 1993 in _step_dealloc_lps()
1987     	xassert(job_resrcs_ptr->cpus);
1988     	xassert(job_resrcs_ptr->cpus_used);
1989
1990     	if (step_ptr->step_layout == NULL)	/* batch step */
1991     		return;
1992
>>>     CID 149289:  Null pointer dereferences  (REVERSE_INULL)
>>>     Null-checking "job_resrcs_ptr" suggests that it may be null, but it has already been dereferenced on all paths leading to the check.
1993     	if (job_resrcs_ptr == NULL)
1994     		return;
1995     	i_first = bit_ffs(job_resrcs_ptr->node_bitmap);
1996     	i_last  = bit_fls(job_resrcs_ptr->node_bitmap);
1997     	if (i_first == -1)	/* empty bitmap */
1998     		return;

** CID 149288:  Resource leaks  (RESOURCE_LEAK)
/slurm/src/api/reconfigure.c: 171 in _send_message_controller()

________________________________________________________________________________________________________
*** CID 149288:  Resource leaks  (RESOURCE_LEAK)
/slurm/src/api/reconfigure.c: 171 in _send_message_controller()
165     	}
166     	resp_msg = xmalloc(sizeof(slurm_msg_t));
167     	slurm_msg_t_init(resp_msg);
168
169     	if ((rc = slurm_receive_msg(fd, resp_msg, 0)) != 0) {
170     		slurm_shutdown_msg_conn(fd);
>>>     CID 149288:  Resource leaks  (RESOURCE_LEAK)
>>>     Variable "resp_msg" going out of scope leaks the storage it points to.
171     		return SLURMCTLD_COMMUNICATIONS_RECEIVE_ERROR;
172     	}
173
174     	if (slurm_shutdown_msg_conn(fd) != SLURM_SUCCESS)
175     		rc = SLURMCTLD_COMMUNICATIONS_SHUTDOWN_ERROR;
176     	else if (resp_msg->msg_type != RESPONSE_SLURM_RC)

** CID 149287:  Integer handling issues  (NEGATIVE_RETURNS)
/slurm/src/slurmdbd/backup.c: 65 in run_dbd_backup()

________________________________________________________________________________________________________
*** CID 149287:  Integer handling issues  (NEGATIVE_RETURNS)
/slurm/src/slurmdbd/backup.c: 65 in run_dbd_backup()
59     	primary_resumed = false;
60
61     	memset(&slurmdbd_conn, 0, sizeof(slurm_persist_conn_t));
62     	slurmdbd_conn.rem_host = slurmdbd_conf->dbd_addr;
63     	slurmdbd_conn.rem_port = slurmdbd_conf->dbd_port;
64     	slurmdbd_conn.cluster_name = "backup_slurmdbd";
>>>     CID 149287:  Integer handling issues  (NEGATIVE_RETURNS)
>>>     Assigning: "slurmdbd_conn.fd" = a negative value.
65     	slurmdbd_conn.fd = -1;
66     	slurmdbd_conn.shutdown = &shutdown_time;
67
68     	slurm_persist_conn_open_without_init(&slurmdbd_conn);
69
70     	/* repeatedly ping Primary */

** CID 149286:  Integer handling issues  (INCOMPATIBLE_CAST)

________________________________________________________________________________________________________
*** CID 149286:  Integer handling issues  (INCOMPATIBLE_CAST)
/slurm/src/common/slurmdbd_defs.c: 3096 in slurmdbd_unpack_init_msg()
3090
3091     	*msg = msg_ptr;
3092
3093     	/* We don't use rollback going forward and version was packed after it
3094     	 * unfortunately */
3095     	if (rpc_version < SLURM_17_02_PROTOCOL_VERSION)
>>>     CID 149286:  Integer handling issues  (INCOMPATIBLE_CAST)
>>>     Pointer "&tmp32" points to an object whose effective type is "unsigned int" (32 bits, unsigned) but is dereferenced as a narrower "unsigned short" (16 bits, unsigned).  This may lead to unexpected results depending on machine endianness.
3096     		safe_unpack16((uint16_t *)&tmp32, buffer);
3097     	safe_unpack16(&msg_ptr->version, buffer);
3098     	safe_unpackstr_xmalloc(&msg_ptr->cluster_name, &tmp32, buffer);
3099
3100     	/* We find out the version of the caller right here so use
3101     	   that as the rpc_version. */

** CID 149285:  Null pointer dereferences  (FORWARD_NULL)
/slurm/src/common/slurm_persist_conn.c: 588 in slurm_persist_conn_open()

________________________________________________________________________________________________________
*** CID 149285:  Null pointer dereferences  (FORWARD_NULL)
/slurm/src/common/slurm_persist_conn.c: 588 in slurm_persist_conn_open()
582     				error("%s: Failed to unpack persistent connection init resp message from %s:%d",
583     				      __func__,
584     				      persist_conn->rem_host,
585     				      persist_conn->rem_port);
586     			_close_fd(&persist_conn->fd);
587     		} else
>>>     CID 149285:  Null pointer dereferences  (FORWARD_NULL)
>>>     Dereferencing null pointer "resp".
588     			persist_conn->version = resp->ret_info;
589     	}
590
591     end_it:
592
593     	slurm_persist_free_rc_msg(resp);

** CID 149284:  Error handling issues  (CHECKED_RETURN)
/slurm/src/common/slurmdbd_defs.c: 1665 in _send_fini_msg()

________________________________________________________________________________________________________
*** CID 149284:  Error handling issues  (CHECKED_RETURN)
/slurm/src/common/slurmdbd_defs.c: 1665 in _send_fini_msg()
1659     	buffer = init_buf(1024);
1660     	pack16((uint16_t) DBD_FINI, buffer);
1661     	req.commit  = 0;
1662     	req.close_conn   = 1;
1663     	slurmdbd_pack_fini_msg(&req, SLURM_PROTOCOL_VERSION, buffer);
1664
>>>     CID 149284:  Error handling issues  (CHECKED_RETURN)
>>>     Calling "slurm_persist_send_msg" without checking return value (as is done elsewhere 5 out of 6 times).
1665     	slurm_persist_send_msg(slurmdbd_conn, buffer);
1666     	free_buf(buffer);
1667
1668     	return SLURM_SUCCESS;
1669     }
1670

Leave macros defined for now to avoid bit reuse.

Leave the select/bluegene directory alone, as it will be removed
entirely once BG/Q support is removed, and the cleanup isn't worth
the risk as that is code is rarely changed.

Remove from build system, and delete L/P specific files.
Run autogen.sh as well.

Add in missing brackets. Caught by GCC 6.1 -Wall.

Add "sbatch_wait_nodes" to SchedulerParameters to control default sbatch
    behaviour with respect to waiting for all allocated nodes to be ready for
    use. Job can override the configuration option using the --wait-all-nodes=#
    option.
bug 3120

Prior logic would treat execute line like this:
$ sbatch --wait-all-nodes -N3 tmp
with "-N3" as being the argument to the "--wait-all-nodes" option.
See bug 3120

Add salloc/sbatch/srun option --use-min-nodes to prefer smaller node counts
    when a range of node counts is specified (e.g. "-N 2-4").
bug 2996

Switch a few SLURM mentions for Slurm as well.