[slurm-users] Strange error, submission denied

Marcus Wagner wagner at itc.rwth-aachen.de
Thu Feb 14 08:22:36 UTC 2019


Hi Andreas,



On 2/14/19 8:56 AM, Henkel, Andreas wrote:
> Hi Marcus,
>
> More ideas:
> CPUs doesn’t always count as core but may take the meaning of one thread, hence makes different
> Maybe the behavior of CR_ONE_TASK  is still not solid nor properly documente and ntasks and ntasks-per-node are honored different internally. If so solely using ntasks can mean using alle threads for Slurm even if the binding may be correct according to binding.
> Obviously in your results Slurm handles the options differently.
>
> Have you tried configuring the node with cpus=96? What output do you get from slurmd -C?
Not yet, as this is not the desired behaviour. We want to schedule by 
cores. But I will try that. slurmd -C output is the following:

NodeName=ncm0708 slurmd: Considering each NUMA node as a socket
CPUs=96 Boards=1 SocketsPerBoard=4 CoresPerSocket=12 ThreadsPerCore=2 
RealMemory=191905
UpTime=6-21:30:02

> Is this a new architecture like skylake? In case of subnuma-Layouts Slurm can not handle it without hwloc2.
Yes, we have Skylake and as you can see in the above output, we have 
subnuma-clustering enabled. Still, we only use hwloc coming with CentOS 
7: hwloc-1.11.8-4.el7.x86_64
Where did you get the information, that hwloc2 is needed?
> Have you tried to use srun -v(vv) instead of sbatch? Maybe you can get a glimpse of what Slurm actually does with your options.
The only strange thing I can observe is the following:
srun: threads        : 60

What threads is srun talking about there?
Nonetheless, here the full output:

$> srun --ntasks=48 --ntasks-per-node=48 -vvv hostname
srun: defined options for program `srun'
srun: --------------- ---------------------
srun: user           : `mw445520'
srun: uid            : 40574
srun: gid            : 40574
srun: cwd            : /rwthfs/rz/cluster/home/mw445520/tests/slurm/cgroup
srun: ntasks         : 48 (set)
srun: nodes          : 1 (default)
srun: jobid          : 4294967294 (default)
srun: partition      : default
srun: profile        : `NotSet'
srun: job name       : `hostname'
srun: reservation    : `(null)'
srun: burst_buffer   : `(null)'
srun: wckey          : `(null)'
srun: cpu_freq_min   : 4294967294
srun: cpu_freq_max   : 4294967294
srun: cpu_freq_gov   : 4294967294
srun: switches       : -1
srun: wait-for-switches : -1
srun: distribution   : unknown
srun: cpu-bind       : default (0)
srun: mem-bind       : default (0)
srun: verbose        : 3
srun: slurmd_debug   : 0
srun: immediate      : false
srun: label output   : false
srun: unbuffered IO  : false
srun: overcommit     : false
srun: threads        : 60
srun: checkpoint_dir : /w0/slurm/checkpoint
srun: wait           : 0
srun: nice           : -2
srun: account        : (null)
srun: comment        : (null)
srun: dependency     : (null)
srun: exclusive      : false
srun: bcast          : false
srun: qos            : (null)
srun: constraints    :
srun: reboot         : yes
srun: preserve_env   : false
srun: network        : (null)
srun: propagate      : NONE
srun: prolog         : (null)
srun: epilog         : (null)
srun: mail_type      : NONE
srun: mail_user      : (null)
srun: task_prolog    : (null)
srun: task_epilog    : (null)
srun: multi_prog     : no
srun: sockets-per-node  : -2
srun: cores-per-socket  : -2
srun: threads-per-core  : -2
srun: ntasks-per-node   : 48
srun: ntasks-per-socket : -2
srun: ntasks-per-core   : -2
srun: plane_size        : 4294967294
srun: core-spec         : NA
srun: power             :
srun: cpus-per-gpu      : 0
srun: gpus              : (null)
srun: gpu-bind          : (null)
srun: gpu-freq          : (null)
srun: gpus-per-node     : (null)
srun: gpus-per-socket   : (null)
srun: gpus-per-task     : (null)
srun: mem-per-gpu       : 0
srun: remote command    : `hostname'
srun: debug:  propagating SLURM_PRIO_PROCESS=0
srun: debug:  propagating UMASK=0007
srun: debug2: srun PMI messages to port=34521
srun: debug:  Entering slurm_allocation_msg_thr_create()
srun: debug:  port from net_stream_listen is 35465
srun: debug:  Entering _msg_thr_internal
srun: debug:  Munge authentication plugin loaded
srun: error: CPU count per node can not be satisfied
srun: error: Unable to allocate resources: Requested node configuration 
is not available



Best
Marcus


>
> Best,
> Andreas
>
>
>> Am 14.02.2019 um 08:34 schrieb Marcus Wagner <wagner at itc.rwth-aachen.de>:
>>
>> Hi Chris,
>>
>>
>> this are 96 thread nodes with 48 cores. You are right, that if we set it to 24, the job will get scheduled. But then, only half of the node is used. On the other side, if I only use --ntasks=48, slurm schedules all tasks onto the same node. The hyperthread of each core is included in the cgroup and the task_affinity plugin also correctly binds the hyperthread together with the core (small ugly testscript from us, the last two numbers are the core and its hyperthread):
>>
>> ncm0728.hpc.itc.rwth-aachen.de <0> OMP_STACKSIZE: <#> unlimited+p2 +pemap 0,48
>> ncm0728.hpc.itc.rwth-aachen.de <10> OMP_STACKSIZE: <#> unlimited+p2 +pemap 26,74
>> ncm0728.hpc.itc.rwth-aachen.de <11> OMP_STACKSIZE: <#> unlimited+p2 +pemap 29,77
>> ncm0728.hpc.itc.rwth-aachen.de <12> OMP_STACKSIZE: <#> unlimited+p2 +pemap 6,54
>> ncm0728.hpc.itc.rwth-aachen.de <13> OMP_STACKSIZE: <#> unlimited+p2 +pemap 9,57
>> ncm0728.hpc.itc.rwth-aachen.de <14> OMP_STACKSIZE: <#> unlimited+p2 +pemap 30,78
>> ncm0728.hpc.itc.rwth-aachen.de <15> OMP_STACKSIZE: <#> unlimited+p2 +pemap 33,81
>> ncm0728.hpc.itc.rwth-aachen.de <16> OMP_STACKSIZE: <#> unlimited+p2 +pemap 7,55
>> ncm0728.hpc.itc.rwth-aachen.de <17> OMP_STACKSIZE: <#> unlimited+p2 +pemap 10,58
>> ncm0728.hpc.itc.rwth-aachen.de <18> OMP_STACKSIZE: <#> unlimited+p2 +pemap 31,79
>> ncm0728.hpc.itc.rwth-aachen.de <19> OMP_STACKSIZE: <#> unlimited+p2 +pemap 34,82
>> ncm0728.hpc.itc.rwth-aachen.de <1> OMP_STACKSIZE: <#> unlimited+p2 +pemap 3,51
>> ncm0728.hpc.itc.rwth-aachen.de <20> OMP_STACKSIZE: <#> unlimited+p2 +pemap 8,56
>> ncm0728.hpc.itc.rwth-aachen.de <21> OMP_STACKSIZE: <#> unlimited+p2 +pemap 11,59
>> ncm0728.hpc.itc.rwth-aachen.de <22> OMP_STACKSIZE: <#> unlimited+p2 +pemap 32,80
>> ncm0728.hpc.itc.rwth-aachen.de <23> OMP_STACKSIZE: <#> unlimited+p2 +pemap 35,83
>> ncm0728.hpc.itc.rwth-aachen.de <24> OMP_STACKSIZE: <#> unlimited+p2 +pemap 12,60
>> ncm0728.hpc.itc.rwth-aachen.de <25> OMP_STACKSIZE: <#> unlimited+p2 +pemap 15,63
>> ncm0728.hpc.itc.rwth-aachen.de <26> OMP_STACKSIZE: <#> unlimited+p2 +pemap 36,84
>> ncm0728.hpc.itc.rwth-aachen.de <27> OMP_STACKSIZE: <#> unlimited+p2 +pemap 39,87
>> ncm0728.hpc.itc.rwth-aachen.de <28> OMP_STACKSIZE: <#> unlimited+p2 +pemap 13,61
>> ncm0728.hpc.itc.rwth-aachen.de <29> OMP_STACKSIZE: <#> unlimited+p2 +pemap 16,64
>> ncm0728.hpc.itc.rwth-aachen.de <2> OMP_STACKSIZE: <#> unlimited+p2 +pemap 24,72
>> ncm0728.hpc.itc.rwth-aachen.de <30> OMP_STACKSIZE: <#> unlimited+p2 +pemap 37,85
>> ncm0728.hpc.itc.rwth-aachen.de <31> OMP_STACKSIZE: <#> unlimited+p2 +pemap 40,88
>> ncm0728.hpc.itc.rwth-aachen.de <32> OMP_STACKSIZE: <#> unlimited+p2 +pemap 14,62
>> ncm0728.hpc.itc.rwth-aachen.de <33> OMP_STACKSIZE: <#> unlimited+p2 +pemap 17,65
>> ncm0728.hpc.itc.rwth-aachen.de <34> OMP_STACKSIZE: <#> unlimited+p2 +pemap 38,86
>> ncm0728.hpc.itc.rwth-aachen.de <35> OMP_STACKSIZE: <#> unlimited+p2 +pemap 41,89
>> ncm0728.hpc.itc.rwth-aachen.de <36> OMP_STACKSIZE: <#> unlimited+p2 +pemap 18,66
>> ncm0728.hpc.itc.rwth-aachen.de <37> OMP_STACKSIZE: <#> unlimited+p2 +pemap 21,69
>> ncm0728.hpc.itc.rwth-aachen.de <38> OMP_STACKSIZE: <#> unlimited+p2 +pemap 42,90
>> ncm0728.hpc.itc.rwth-aachen.de <39> OMP_STACKSIZE: <#> unlimited+p2 +pemap 45,93
>> ncm0728.hpc.itc.rwth-aachen.de <3> OMP_STACKSIZE: <#> unlimited+p2 +pemap 27,75
>> ncm0728.hpc.itc.rwth-aachen.de <40> OMP_STACKSIZE: <#> unlimited+p2 +pemap 19,67
>> ncm0728.hpc.itc.rwth-aachen.de <41> OMP_STACKSIZE: <#> unlimited+p2 +pemap 22,70
>> ncm0728.hpc.itc.rwth-aachen.de <42> OMP_STACKSIZE: <#> unlimited+p2 +pemap 43,91
>> ncm0728.hpc.itc.rwth-aachen.de <43> OMP_STACKSIZE: <#> unlimited+p2 +pemap 46,94
>> ncm0728.hpc.itc.rwth-aachen.de <44> OMP_STACKSIZE: <#> unlimited+p2 +pemap 20,68
>> ncm0728.hpc.itc.rwth-aachen.de <45> OMP_STACKSIZE: <#> unlimited+p2 +pemap 23,71
>> ncm0728.hpc.itc.rwth-aachen.de <46> OMP_STACKSIZE: <#> unlimited+p2 +pemap 44,92
>> ncm0728.hpc.itc.rwth-aachen.de <47> OMP_STACKSIZE: <#> unlimited+p2 +pemap 47,95
>> ncm0728.hpc.itc.rwth-aachen.de <4> OMP_STACKSIZE: <#> unlimited+p2 +pemap 1,49
>> ncm0728.hpc.itc.rwth-aachen.de <5> OMP_STACKSIZE: <#> unlimited+p2 +pemap 4,52
>> ncm0728.hpc.itc.rwth-aachen.de <6> OMP_STACKSIZE: <#> unlimited+p2 +pemap 25,73
>> ncm0728.hpc.itc.rwth-aachen.de <7> OMP_STACKSIZE: <#> unlimited+p2 +pemap 28,76
>> ncm0728.hpc.itc.rwth-aachen.de <8> OMP_STACKSIZE: <#> unlimited+p2 +pemap 2,50
>> ncm0728.hpc.itc.rwth-aachen.de <9> OMP_STACKSIZE: <#> unlimited+p2 +pemap 5,53
>>
>>
>> --ntasks=48:
>>
>>     NodeList=ncm0728
>>     BatchHost=ncm0728
>>     NumNodes=1 NumCPUs=48 NumTasks=48 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
>>     TRES=cpu=48,mem=182400M,node=1,billing=48
>>
>>
>> --ntasks=48
>> --ntasks-per-node=24:
>>
>>     NodeList=ncm[0438-0439]
>>     BatchHost=ncm0438
>>     NumNodes=2 NumCPUs=48 NumTasks=48 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
>>     TRES=cpu=48,mem=182400M,node=2,billing=48
>>
>>
>> --ntasks=48
>> --ntasks-per-node=48:
>>
>> sbatch: error: CPU count per node can not be satisfied
>> sbatch: error: Batch job submission failed: Requested node configuration is not available
>>
>>
>> Isn't the first essentially the same as the last, with the difference, that I want to force slurm to put all tasks onto one node?
>>
>>
>>
>> Best
>> Marcus
>>
>>
>>> On 2/14/19 7:15 AM, Chris Samuel wrote:
>>>> On Wednesday, 13 February 2019 4:48:05 AM PST Marcus Wagner wrote:
>>>>
>>>> #SBATCH --ntasks-per-node=48
>>> I wouldn't mind betting is that if you set that to 24 it will work, and each
>>> thread will be assigned a single core with the 2 thread units on it.
>>>
>>> All the best,
>>> Chris
>> -- 
>> Marcus Wagner, Dipl.-Inf.
>>
>> IT Center
>> Abteilung: Systeme und Betrieb
>> RWTH Aachen University
>> Seffenter Weg 23
>> 52074 Aachen
>> Tel: +49 241 80-24383
>> Fax: +49 241 80-624383
>> wagner at itc.rwth-aachen.de
>> www.itc.rwth-aachen.de
>>
>>

-- 
Marcus Wagner, Dipl.-Inf.

IT Center
Abteilung: Systeme und Betrieb
RWTH Aachen University
Seffenter Weg 23
52074 Aachen
Tel: +49 241 80-24383
Fax: +49 241 80-624383
wagner at itc.rwth-aachen.de
www.itc.rwth-aachen.de




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