[slurm-users] Strange error, submission denied
Marcus Wagner
wagner at itc.rwth-aachen.de
Thu Feb 14 11:54:09 UTC 2019
Hi Andreas,
as slurmd -C shows, it detects 4 numa-nodes taking these as sockets.
This was also the way, we configured slurm.
numactl -H clearly shows the four domains and which belongs to which socket:
node distances:
node 0 1 2 3
0: 10 11 21 21
1: 11 10 21 21
2: 21 21 10 11
3: 21 21 11 10
This is fairly the same with hwloc:
$> hwloc-distances
Relative latency matrix between 4 NUMANodes (depth 3) by logical indexes
(below Machine L#0):
index 0 1 2 3
0 1.000 1.100 2.100 2.100
1 1.100 1.000 2.100 2.100
2 2.100 2.100 1.000 1.100
3 2.100 2.100 1.100 1.000
We use the task/affinity plugin together with task/cgroup, but in the
cgroup.conf set affinity to off, such that the task affinity plugin is
doing the magic.
We also see slurm configured that way to do a round robin over the
numanodes by default (12 tasks on 48 core machine):
ncm0071.hpc.itc.rwth-aachen.de <0> OMP_STACKSIZE: <#> unlimited+p2
+pemap 0,48
ncm0071.hpc.itc.rwth-aachen.de <1> OMP_STACKSIZE: <#> unlimited+p2
+pemap 3,51
ncm0071.hpc.itc.rwth-aachen.de <2> OMP_STACKSIZE: <#> unlimited+p2
+pemap 24,72
ncm0071.hpc.itc.rwth-aachen.de <3> OMP_STACKSIZE: <#> unlimited+p2
+pemap 27,75
ncm0071.hpc.itc.rwth-aachen.de <4> OMP_STACKSIZE: <#> unlimited+p2
+pemap 1,49
ncm0071.hpc.itc.rwth-aachen.de <5> OMP_STACKSIZE: <#> unlimited+p2
+pemap 4,52
ncm0071.hpc.itc.rwth-aachen.de <6> OMP_STACKSIZE: <#> unlimited+p2
+pemap 25,73
ncm0071.hpc.itc.rwth-aachen.de <7> OMP_STACKSIZE: <#> unlimited+p2
+pemap 28,76
ncm0071.hpc.itc.rwth-aachen.de <8> OMP_STACKSIZE: <#> unlimited+p2
+pemap 2,50
ncm0071.hpc.itc.rwth-aachen.de <9> OMP_STACKSIZE: <#> unlimited+p2
+pemap 5,53
ncm0071.hpc.itc.rwth-aachen.de <10> OMP_STACKSIZE: <#> unlimited+p2
+pemap 26,74
ncm0071.hpc.itc.rwth-aachen.de <11> OMP_STACKSIZE: <#> unlimited+p2
+pemap 29,77
using #SBATCH -m block:block results in all tasks on one numanode:
ncm0071.hpc.itc.rwth-aachen.de <0> OMP_STACKSIZE: <#> unlimited+p2
+pemap 0,48
ncm0071.hpc.itc.rwth-aachen.de <1> OMP_STACKSIZE: <#> unlimited+p2
+pemap 1,49
ncm0071.hpc.itc.rwth-aachen.de <2> OMP_STACKSIZE: <#> unlimited+p2
+pemap 2,50
ncm0071.hpc.itc.rwth-aachen.de <3> OMP_STACKSIZE: <#> unlimited+p2
+pemap 6,54
ncm0071.hpc.itc.rwth-aachen.de <4> OMP_STACKSIZE: <#> unlimited+p2
+pemap 7,55
ncm0071.hpc.itc.rwth-aachen.de <5> OMP_STACKSIZE: <#> unlimited+p2
+pemap 8,56
ncm0071.hpc.itc.rwth-aachen.de <6> OMP_STACKSIZE: <#> unlimited+p2
+pemap 12,60
ncm0071.hpc.itc.rwth-aachen.de <7> OMP_STACKSIZE: <#> unlimited+p2
+pemap 13,61
ncm0071.hpc.itc.rwth-aachen.de <8> OMP_STACKSIZE: <#> unlimited+p2
+pemap 14,62
ncm0071.hpc.itc.rwth-aachen.de <9> OMP_STACKSIZE: <#> unlimited+p2
+pemap 18,66
ncm0071.hpc.itc.rwth-aachen.de <10> OMP_STACKSIZE: <#> unlimited+p2
+pemap 19,67
ncm0071.hpc.itc.rwth-aachen.de <11> OMP_STACKSIZE: <#> unlimited+p2
+pemap 20,68
isn't it that, what would be needed, or do I miss something? What would
be "better" with hwloc2?
Besides my original problem, we are fairly happy with slurm so far, but
that one gives me grey hair :/
Best
Marcus
On 2/14/19 11:27 AM, Henkel, Andreas wrote:
> Hi Marcus,
>
> We have skylake too and it didn’t work for us. We used cgroups only and process binding went completely havoc with subnuma enabled.
> While searching for solutions I found that hwloc does support subnuma only with version > 2 (when looking for skylake in hwloc you will get hits in version 2 branches only). At least hwloc 2.x made Numa-blocks children objects whereas hwloc 1.x has Numablocks as parents only. I think that was the reason why there was a special branch in hwloc for handling subNuma-layouts of Xeon Phi.
> But I’ll be happy if you proof me wrong.
>
> Best,
> Andreas
>
>> Am 14.02.2019 um 09:32 schrieb Marcus Wagner <wagner at itc.rwth-aachen.de>:
>>
>> 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
>>
>>
--
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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