[gridengine users] Resource Reservation logging

Txema Heredia txema.llistes at gmail.com
Mon Oct 7 13:59:36 UTC 2013


El 07/10/13 14:58, Reuti escribió:
> Hi,
>
> Am 07.10.2013 um 13:15 schrieb Txema Heredia:
>
>> The problem is that, right now, the mandatory usage of h_rt is not an option. So we need to work considering that all jobs will last to infinity and beyond.
>>
>> Right now, the scheduler configuration is:
>> max_reservation 50
>> default_duration 24:00:00
>>
>> During the weekend, most of the parallel ( and -R y) jobs started running, but now there is something fishy in my queues:
>>
>> The first 3 jobs in my waiting queue belong to user1. All 3 jobs request -pe mpich_round 12, -R y and -l h_vmem=4G (h_vmem is set to consumable = YES, not JOB).
> Which amount of memory did you specify in the exechost definition, i.e. what's in the machine physically?
>
> -- Reuti

26 nodes have 96GB of ram. One node has 48GB.

Currently nodes range from 4 to 10 free slots and from 26 to 82.1 free GB

The first jobs in my waiting queue (after the 3 reserving ones) require 
measly 0.9G, 3G and 12G, all with slots=1 and -R n. None of them is 
scheduled. But if I manually increase their priority so they are put 
BEFORE the 3 -R y jobs, they are immediately scheduled.

>
>
>> This user has already one job like these running. User1 has a RQS that limits him to use only 12 slots in the whole cluster. Thus the 3 waiting jobs will not be able to run until the first one finishes.
>>
>> This is the current schedule log:
>>
>> # grep "::::\|RESERVING" schedule | tail -200 | grep "::::\|Q:all" | tail -37 | sort
>> ::::::::
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-0-1.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-0-6.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-0-8.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-0-9.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-1-11.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-1-6.local:slots:1.000000
>> 2734185:1:RESERVING:1381142325:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-0-1.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-0-6.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-0-8.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-0-9.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-1-11.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-1-6.local:slots:1.000000
>> 2734186:1:RESERVING:1381228785:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-0-1.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-0-6.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-0-8.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-0-9.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-1-11.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-1-6.local:slots:1.000000
>> 2734187:1:RESERVING:1381315245:86460:Q:all.q at compute-1-7.local:slots:1.000000
>>
>>
>> Right now, the cluster is using 190 slots of 320 total. The schedule log says that the 3 waiting jobs form user1 are the only jobs making any kind of reservation. These jobs are reserving a total of 36 cores. These 3 jobs are effectively blocking 36 already-free slots because the RQS doesn't allow user1 to make usage of more than 12 slots at once. This is not "nice" but I understand that the scheduler has its limitations and cannot predict the future.
>>
>> Taking into account the jobs running + the slots & memory locked by the reserving jobs, there is a grand total of 226 slots locked. Thus leaving 94 free slots.
>>
>> Here comes the problem: Even though there are 94 free slots and lots of spare memory, NONE of the 4300 waiting jobs is running. There are nodes with 6 free slots and 59 GB of free RAM but none of the waiting jobs is scheduled. New jobs only star running when one of the 190 slots occupied by running jobs is freed. None of these other waiting jobs is requesting -R y, -pe nor h_rt.
>>
>>
>> Additionaly, this is creating some odd behaviour. It seems that, on each scheduler run, it is trying to start jobs in those "blocked slots", but it fails with no apparent reason. Some of the jobs are even trying to start twice, but almost none (generally none at all) gets to run:
>>
>> # tail -2000 schedule | grep -A 1000 "::::::" | grep "Q:all" | grep STARTING | sort
>> 2734121:1:STARTING:1381144160:86460:Q:all.q at compute-0-11.local:slots:1.000000
>> 2734122:1:STARTING:1381144160:86460:Q:all.q at compute-0-8.local:slots:1.000000
>> 2734123:1:STARTING:1381144160:86460:Q:all.q at compute-0-0.local:slots:1.000000
>> 2734124:1:STARTING:1381144160:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2734125:1:STARTING:1381144160:86460:Q:all.q at compute-0-11.local:slots:1.000000
>> 2734126:1:STARTING:1381144160:86460:Q:all.q at compute-1-13.local:slots:1.000000
>> 2734127:1:STARTING:1381144160:86460:Q:all.q at compute-1-1.local:slots:1.000000
>> 2734128:1:STARTING:1381144160:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2734129:1:STARTING:1381144160:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2734130:1:STARTING:1381144160:86460:Q:all.q at compute-1-12.local:slots:1.000000
>> 2734131:1:STARTING:1381144160:86460:Q:all.q at compute-1-4.local:slots:1.000000
>> 2734132:1:STARTING:1381144160:86460:Q:all.q at compute-1-1.local:slots:1.000000
>> 2734133:1:STARTING:1381144160:86460:Q:all.q at compute-0-0.local:slots:1.000000
>> 2734134:1:STARTING:1381144160:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2734135:1:STARTING:1381144160:86460:Q:all.q at compute-1-11.local:slots:1.000000
>> 2734136:1:STARTING:1381144160:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2734137:1:STARTING:1381144160:86460:Q:all.q at compute-0-11.local:slots:1.000000
>> 2734138:1:STARTING:1381144160:86460:Q:all.q at compute-1-12.local:slots:1.000000
>> 2734139:1:STARTING:1381144160:86460:Q:all.q at compute-1-13.local:slots:1.000000
>> 2734140:1:STARTING:1381144160:86460:Q:all.q at compute-1-1.local:slots:1.000000
>> 2734141:1:STARTING:1381144160:86460:Q:all.q at compute-1-9.local:slots:1.000000
>> 2734142:1:STARTING:1381144160:86460:Q:all.q at compute-0-3.local:slots:1.000000
>> 2734143:1:STARTING:1381144160:86460:Q:all.q at compute-0-6.local:slots:1.000000
>> 2734144:1:STARTING:1381144160:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2734145:1:STARTING:1381144160:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2734146:1:STARTING:1381144160:86460:Q:all.q at compute-1-3.local:slots:1.000000
>> 2734147:1:STARTING:1381144160:86460:Q:all.q at compute-1-11.local:slots:1.000000
>> 2734148:1:STARTING:1381144160:86460:Q:all.q at compute-0-4.local:slots:1.000000
>> 2734149:1:STARTING:1381144160:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2734150:1:STARTING:1381144160:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2734151:1:STARTING:1381144160:86460:Q:all.q at compute-1-8.local:slots:1.000000
>> 2734152:1:STARTING:1381144160:86460:Q:all.q at compute-1-2.local:slots:1.000000
>> 2734153:1:STARTING:1381144160:86460:Q:all.q at compute-0-10.local:slots:1.000000
>> 2734154:1:STARTING:1381144160:86460:Q:all.q at compute-0-6.local:slots:1.000000
>> 2734155:1:STARTING:1381144160:86460:Q:all.q at compute-1-11.local:slots:1.000000
>> 2734156:1:STARTING:1381144160:86460:Q:all.q at compute-0-4.local:slots:1.000000
>> 2734157:1:STARTING:1381144160:86460:Q:all.q at compute-0-1.local:slots:1.000000
>> 2734158:1:STARTING:1381144160:86460:Q:all.q at compute-1-8.local:slots:1.000000
>> 2734159:1:STARTING:1381144160:86460:Q:all.q at compute-1-2.local:slots:1.000000
>> 2734160:1:STARTING:1381144160:86460:Q:all.q at compute-0-10.local:slots:1.000000
>> 2734161:1:STARTING:1381144160:86460:Q:all.q at compute-1-6.local:slots:1.000000
>> 2735158:1:STARTING:1381144160:86460:Q:all.q at compute-0-5.local:slots:1.000000
>> 2735159:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2735160:1:STARTING:1381144160:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2735161:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2735162:1:STARTING:1381144160:86460:Q:all.q at compute-0-0.local:slots:1.000000
>> 2735163:1:STARTING:1381144160:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2735164:1:STARTING:1381144160:86460:Q:all.q at compute-0-11.local:slots:1.000000
>> 2735165:1:STARTING:1381144160:86460:Q:all.q at compute-0-0.local:slots:1.000000
>> 2735166:1:STARTING:1381144160:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2735167:1:STARTING:1381144160:86460:Q:all.q at compute-1-8.local:slots:1.000000
>> 2735168:1:STARTING:1381144160:86460:Q:all.q at compute-1-12.local:slots:1.000000
>> 2735169:1:STARTING:1381144160:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2735170:1:STARTING:1381144160:86460:Q:all.q at compute-0-0.local:slots:1.000000
>> 2735171:1:STARTING:1381144160:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2735172:1:STARTING:1381144160:86460:Q:all.q at compute-1-8.local:slots:1.000000
>> 2735173:1:STARTING:1381144160:86460:Q:all.q at compute-1-12.local:slots:1.000000
>> 2735174:1:STARTING:1381144160:86460:Q:all.q at compute-1-9.local:slots:1.000000
>> 2735175:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2735176:1:STARTING:1381144160:86460:Q:all.q at compute-1-8.local:slots:1.000000
>> 2735177:1:STARTING:1381144160:86460:Q:all.q at compute-0-10.local:slots:1.000000
>> 2735178:1:STARTING:1381144160:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2735179:1:STARTING:1381144160:86460:Q:all.q at compute-0-0.local:slots:1.000000
>> 2735180:1:STARTING:1381144160:86460:Q:all.q at compute-1-11.local:slots:1.000000
>> 2735181:1:STARTING:1381144160:86460:Q:all.q at compute-0-11.local:slots:1.000000
>> 2735182:1:STARTING:1381144160:86460:Q:all.q at compute-1-13.local:slots:1.000000
>> 2735183:1:STARTING:1381144160:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2735184:1:STARTING:1381144160:86460:Q:all.q at compute-1-9.local:slots:1.000000
>> 2735185:1:STARTING:1381144160:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2735186:1:STARTING:1381144160:86460:Q:all.q at compute-1-3.local:slots:1.000000
>> 2735187:1:STARTING:1381144160:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2735188:1:STARTING:1381144160:86460:Q:all.q at compute-1-8.local:slots:1.000000
>> 2735189:1:STARTING:1381144160:86460:Q:all.q at compute-1-2.local:slots:1.000000
>> 2735190:1:STARTING:1381144160:86460:Q:all.q at compute-0-10.local:slots:1.000000
>> 2735191:1:STARTING:1381144160:86460:Q:all.q at compute-0-8.local:slots:1.000000
>> 2735192:1:STARTING:1381144160:86460:Q:all.q at compute-1-4.local:slots:1.000000
>> 2735193:1:STARTING:1381144160:86460:Q:all.q at compute-0-0.local:slots:1.000000
>> 2743479:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2743480:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2743481:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2743482:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2743483:1:STARTING:1381144160:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2743484:1:STARTING:1381144160:86460:Q:all.q at compute-0-11.local:slots:1.000000
>> 2743485:1:STARTING:1381144160:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2743486:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2743487:1:STARTING:1381144160:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2743488:1:STARTING:1381144160:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2743489:1:STARTING:1381144160:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2743490:1:STARTING:1381144160:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2743491:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2743492:1:STARTING:1381144160:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2743493:1:STARTING:1381144160:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2743494:1:STARTING:1381144160:86460:Q:all.q at compute-0-11.local:slots:1.000000
>> 2743495:1:STARTING:1381144160:86460:Q:all.q at compute-1-13.local:slots:1.000000
>> 2743496:1:STARTING:1381144160:86460:Q:all.q at compute-0-8.local:slots:1.000000
>> 2743497:1:STARTING:1381144160:86460:Q:all.q at compute-1-9.local:slots:1.000000
>> 2743498:1:STARTING:1381144160:86460:Q:all.q at compute-0-2.local:slots:1.000000
>> 2743499:1:STARTING:1381144160:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2743500:1:STARTING:1381144160:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2743501:1:STARTING:1381144160:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2743502:1:STARTING:1381144160:86460:Q:all.q at compute-1-2.local:slots:1.000000
>> 2743503:1:STARTING:1381144160:86460:Q:all.q at compute-1-13.local:slots:1.000000
>> 2743504:1:STARTING:1381144160:86460:Q:all.q at compute-1-0.local:slots:1.000000
>> 2743505:1:STARTING:1381144160:86460:Q:all.q at compute-1-10.local:slots:1.000000
>> 2743506:1:STARTING:1381144160:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2743507:1:STARTING:1381144160:86460:Q:all.q at compute-1-7.local:slots:1.000000
>> 2743508:1:STARTING:1381144160:86460:Q:all.q at compute-1-2.local:slots:1.000000
>> 2743509:1:STARTING:1381144160:86460:Q:all.q at compute-1-12.local:slots:1.000000
>> 2743510:1:STARTING:1381144160:86460:Q:all.q at compute-0-8.local:slots:1.000000
>> 2743511:1:STARTING:1381144160:86460:Q:all.q at compute-1-4.local:slots:1.000000
>> 2743512:1:STARTING:1381144160:86460:Q:all.q at compute-1-9.local:slots:1.000000
>> 2743513:1:STARTING:1381144160:86460:Q:all.q at compute-1-5.local:slots:1.000000
>> 2743514:1:STARTING:1381144160:86460:Q:all.q at compute-0-7.local:slots:1.000000
>> 2743515:1:STARTING:1381144160:86460:Q:all.q at compute-1-8.local:slots:1.000000
>> 2743516:1:STARTING:1381144160:86460:Q:all.q at compute-1-2.local:slots:1.000000
>> 2743517:1:STARTING:1381144160:86460:Q:all.q at compute-0-10.local:slots:1.000000
>> 2743518:1:STARTING:1381144160:86460:Q:all.q at compute-0-8.local:slots:1.000000
>>
>>
>> Even though jobs appear here listed as "starting" they are not running at all. But they are issuing a "starting" message on each scheduling interval.
>>
>> Why are the reservations blocking a third of the cluster??? It shouldn't be a backfilling issue, they are blocking the usage of 3 times the slots reserved. Why the "starting" jobs cannot run?
>>
>> Txema
>>
>>
>>
>> El 07/10/13 09:28, Christian Krause escribió:
>>> Hello,
>>>
>>> We solved it the way that `h_rt` is set to FORCED in the complex list:
>>>
>>>      #name                    shortcut      type        relop requestable consumable default  urgency
>>>      #------------------------------------------------------------------------------------------------
>>>      h_rt                     h_rt          TIME        <=    FORCED      YES        0:0:0    0
>>>
>>> And have a JSV rejecting jobs that don't request it (because they would be pending indefinetely
>>> unless you have a default duration or use qalter).
>>>
>>> You could also use a JSV to enforce that only jobs with large resources (in your case more than some
>>> amount of slots) are able to request reservation, i.e.:
>>>
>>>      # pseudo JSV code
>>>           SLOT_RESERVATION_THRESHOLD=...
>>>           if slots < SLOT_RESERVATION_THRESHOLD then
>>>          "disable reservation / reject"
>>>      else
>>>          "enable reservation"
>>>      fi
>>>
>>>
>>> On Fri, Oct 04, 2013 at 04:25:29PM +0200, Txema Heredia wrote:
>>>> Hi all,
>>>>
>>>> I have a 27-node cluster. Currently there are 320 out of 320 slots
>>>> filled up. All by jobs requesting 1-slot.
>>>>
>>>> At the top of my waiting queue there are 28 different jobs
>>>> requesting 3 to 12 cores using two different parallel environments.
>>>> All these jobs are requesting -R y. They are being ignored and
>>>> overrun by the myriad of 1-slot requesting  jobs behind them in the
>>>> waiting queue.
>>>>
>>>> I have enabled the scheduler logging. During the last 4 hours, it
>>>> has logged 724 new jobs starting, in all the 27 nodes. Not a single
>>>> job on the system is requesting -l h_rt, but single-core jobs keep
>>>> being scheduled  and all the parallel jobs are starving.
>>>>
>>>> As far as I understand, the backfilling is killing my reservations,
>>>> even if no one is requesting any kind of time, but if I set the
>>>> "default_duration" to INFINITY, all the RESERVING log messages
>>>> disappear.
>>>>
>>>> Additionaly, for some odd reason, I only receive RESERVING messages
>>>> from the jobs requesting a given number of slots (-pe whatever N).
>>>> The jobs requesting a slot-range (-pe threaded 4-10) seem to reserve
>>>> nothing.
>>>>
>>>> My scheduler configuration is as follows:
>>>>
>>>> # qconf -ssconf
>>>> algorithm                         default
>>>> schedule_interval                 0:0:5
>>>> maxujobs                          0
>>>> queue_sort_method                 load
>>>> job_load_adjustments              np_load_avg=0.50
>>>> load_adjustment_decay_time        0:7:30
>>>> load_formula                      np_load_avg
>>>> schedd_job_info                   true
>>>> flush_submit_sec                  0
>>>> flush_finish_sec                  0
>>>> params                            MONITOR=1
>>>> reprioritize_interval             0:0:0
>>>> halftime                          168
>>>> usage_weight_list cpu=0.187000,mem=0.116000,io=0.697000
>>>> compensation_factor               5.000000
>>>> weight_user                       0.250000
>>>> weight_project                    0.250000
>>>> weight_department                 0.250000
>>>> weight_job                        0.250000
>>>> weight_tickets_functional         1000000000
>>>> weight_tickets_share              1000000000
>>>> share_override_tickets            TRUE
>>>> share_functional_shares           TRUE
>>>> max_functional_jobs_to_schedule   200
>>>> report_pjob_tickets               TRUE
>>>> max_pending_tasks_per_job         50
>>>> halflife_decay_list               none
>>>> policy_hierarchy                  OSF
>>>> weight_ticket                     0.010000
>>>> weight_waiting_time               0.000000
>>>> weight_deadline                   3600000.000000
>>>> weight_urgency                    0.100000
>>>> weight_priority                   1.000000
>>>> max_reservation                   50
>>>> default_duration                  24:00:00
>>>>
>>>>
>>>> I have also tested it with params PROFILE=1 and default_duration
>>>> INFINITY. But, when I set it, not a single reservation is logged in
>>>> /opt/gridengine/default/common/schedule and new jobs keep starting.
>>>>
>>>>
>>>> What am I missing? Is it possible to kill the backfilling? Are my
>>>> reservations really working?
>>>>
>>>> Thanks in advance,
>>>>
>>>> Txema
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