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Subject: Re: [OMPI users] "-bind-to numa" of openmpi-1.7.4rc1 dosen't work for our magny cours based 32 core node
From: Ralph Castain (rhc_at_[hidden])
Date: 2013-12-19 00:25:15


Ick - yeah, that would be a problem. I haven't seen that type of hierarchical inversion before - is node03 a different type of chip?

Might take awhile for me to adjust the code to handle hier inversion... :-(

On Dec 18, 2013, at 9:05 PM, tmishima_at_[hidden] wrote:

>
>
> Hi Ralph,
>
> I found the reason. I attached the main part of output with 32
> core node(node03) and 8 core node(node05) at the bottom.
>
> From this information, socket of node03 includes numa-node.
> On the other hand, numa-node of node05 includes socket.
> The direction of object tree is opposite.
>
> Since "-map-by socket" may be assumed as default,
> for node05, "-bind-to numa and -map-by socket" means
> upward search. For node03, this should be downward.
>
> I guess that openmpi-1.7.4rc1 will always assume numa-node
> includes socket. Is it right? Then, upward search is assumed
> in orte_rmaps_base_compute_bindings even for node03 when I
> put "-bind-to numa and -map-by socket" option.
>
> [node03.cluster:15508] [[38286,0],0] rmaps:base:compute_usage
> [node03.cluster:15508] mca:rmaps: compute bindings for job [38286,1] with
> policy NUMA
> [node03.cluster:15508] mca:rmaps: bind upwards for job [38286,1] with
> bindings NUMA
> [node03.cluster:15508] [[38286,0],0] bind:upward target NUMANode type
> Machine
>
> That's the reason of this trouble. Therefore, adding "-map-by core" works.
> (mapping pattern seems to be strange ...)
>
> [mishima_at_node03 demos]$ mpirun -np 8 -bind-to numa -map-by core
> -report-bindings myprog
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type
> NUMANode
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type
> NUMANode
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type
> NUMANode
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type
> NUMANode
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type
> NUMANode
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type
> NUMANode
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type
> NUMANode
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type Cache
> [node03.cluster:15885] [[38679,0],0] bind:upward target NUMANode type
> NUMANode
> [node03.cluster:15885] MCW rank 2 bound to socket 0[core 0[hwt 0]], socket
> 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], so
> cket 0[core 3[hwt 0]]:
> [B/B/B/B/./././.][./././././././.][./././././././.][./././././././.]
> [node03.cluster:15885] MCW rank 3 bound to socket 0[core 0[hwt 0]], socket
> 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], so
> cket 0[core 3[hwt 0]]:
> [B/B/B/B/./././.][./././././././.][./././././././.][./././././././.]
> [node03.cluster:15885] MCW rank 4 bound to socket 0[core 4[hwt 0]], socket
> 0[core 5[hwt 0]], socket 0[core 6[hwt 0]], so
> cket 0[core 7[hwt 0]]:
> [././././B/B/B/B][./././././././.][./././././././.][./././././././.]
> [node03.cluster:15885] MCW rank 5 bound to socket 0[core 4[hwt 0]], socket
> 0[core 5[hwt 0]], socket 0[core 6[hwt 0]], so
> cket 0[core 7[hwt 0]]:
> [././././B/B/B/B][./././././././.][./././././././.][./././././././.]
> [node03.cluster:15885] MCW rank 6 bound to socket 0[core 4[hwt 0]], socket
> 0[core 5[hwt 0]], socket 0[core 6[hwt 0]], so
> cket 0[core 7[hwt 0]]:
> [././././B/B/B/B][./././././././.][./././././././.][./././././././.]
> [node03.cluster:15885] MCW rank 7 bound to socket 0[core 4[hwt 0]], socket
> 0[core 5[hwt 0]], socket 0[core 6[hwt 0]], so
> cket 0[core 7[hwt 0]]:
> [././././B/B/B/B][./././././././.][./././././././.][./././././././.]
> [node03.cluster:15885] MCW rank 0 bound to socket 0[core 0[hwt 0]], socket
> 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], so
> cket 0[core 3[hwt 0]]:
> [B/B/B/B/./././.][./././././././.][./././././././.][./././././././.]
> [node03.cluster:15885] MCW rank 1 bound to socket 0[core 0[hwt 0]], socket
> 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], so
> cket 0[core 3[hwt 0]]:
> [B/B/B/B/./././.][./././././././.][./././././././.][./././././././.]
> Hello world from process 6 of 8
> Hello world from process 5 of 8
> Hello world from process 0 of 8
> Hello world from process 7 of 8
> Hello world from process 3 of 8
> Hello world from process 4 of 8
> Hello world from process 2 of 8
> Hello world from process 1 of 8
>
> Regards,
> Tetsuya Mishima
>
> [node03.cluster:15508] Type: Machine Number of child objects: 4
> Name=NULL
> total=132358820KB
> Backend=Linux
> OSName=Linux
> OSRelease=2.6.18-308.16.1.el5
> OSVersion="#1 SMP Tue Oct 2 22:01:43 EDT 2012"
> Architecture=x86_64
> Cpuset: 0xffffffff
> Online: 0xffffffff
> Allowed: 0xffffffff
> Bind CPU proc: TRUE
> Bind CPU thread: TRUE
> Bind MEM proc: FALSE
> Bind MEM thread: TRUE
> Type: Socket Number of child objects: 2
> Name=NULL
> total=33071780KB
> CPUModel="AMD Opteron(tm) Processor 6136"
> Cpuset: 0x000000ff
> Online: 0x000000ff
> Allowed: 0x000000ff
> Type: NUMANode Number of child objects: 1
>
>
> [node05.cluster:21750] Type: Machine Number of child objects: 2
> Name=NULL
> total=33080072KB
> Backend=Linux
> OSName=Linux
> OSRelease=2.6.18-308.16.1.el5
> OSVersion="#1 SMP Tue Oct 2 22:01:43 EDT 2012"
> Architecture=x86_64
> Cpuset: 0x000000ff
> Online: 0x000000ff
> Allowed: 0x000000ff
> Bind CPU proc: TRUE
> Bind CPU thread: TRUE
> Bind MEM proc: FALSE
> Bind MEM thread: TRUE
> Type: NUMANode Number of child objects: 1
> Name=NULL
> local=16532232KB
> total=16532232KB
> Cpuset: 0x0000000f
> Online: 0x0000000f
> Allowed: 0x0000000f
> Type: Socket Number of child objects: 1
>
>
>> Hmm...try adding "-mca rmaps_base_verbose 10 -mca ess_base_verbose 5" to
> your cmd line and let's see what it thinks it found.
>>
>>
>> On Dec 18, 2013, at 6:55 PM, tmishima_at_[hidden] wrote:
>>
>>>
>>>
>>> Hi, I report one more problem with openmpi-1.7.4rc1,
>>> which is more serious.
>>>
>>> For our 32 core nodes(AMD magny cours based) which has
>>> 8 numa-nodes, "-bind-to numa" does not work. Without
>>> this option, it works. For your infomation, at the
>>> bottom of this mail, I added the lstopo information
>>> of the node.
>>>
>>> Regards,
>>> Tetsuya Mishima
>>>
>>> [mishima_at_manage ~]$ qsub -I -l nodes=1:ppn=32
>>> qsub: waiting for job 8352.manage.cluster to start
>>> qsub: job 8352.manage.cluster ready
>>>
>>> [mishima_at_node03 demos]$ mpirun -np 8 -report-bindings -bind-to numa
> myprog
>>> [node03.cluster:15316] [[37582,0],0] bind:upward target NUMANode type
>>> Machine
>>>
> --------------------------------------------------------------------------
>>> A request was made to bind to NUMA, but an appropriate target could not
>>> be found on node node03.
>>>
> --------------------------------------------------------------------------
>>> [mishima_at_node03 ~]$ cd ~/Desktop/openmpi-1.7/demos/
>>> [mishima_at_node03 demos]$ mpirun -np 8 -report-bindings myprog
>>> [node03.cluster:15282] MCW rank 2 bound to socket 1[core 8[hwt 0]]:
>>> [./././././././.][B/././././././.][./././././././.][
>>> ./././././././.]
>>> [node03.cluster:15282] MCW rank 3 bound to socket 1[core 9[hwt 0]]:
>>> [./././././././.][./B/./././././.][./././././././.][
>>> ./././././././.]
>>> [node03.cluster:15282] MCW rank 4 bound to socket 2[core 16[hwt 0]]:
>>> [./././././././.][./././././././.][B/././././././.]
>>> [./././././././.]
>>> [node03.cluster:15282] MCW rank 5 bound to socket 2[core 17[hwt 0]]:
>>> [./././././././.][./././././././.][./B/./././././.]
>>> [./././././././.]
>>> [node03.cluster:15282] MCW rank 6 bound to socket 3[core 24[hwt 0]]:
>>> [./././././././.][./././././././.][./././././././.]
>>> [B/././././././.]
>>> [node03.cluster:15282] MCW rank 7 bound to socket 3[core 25[hwt 0]]:
>>> [./././././././.][./././././././.][./././././././.]
>>> [./B/./././././.]
>>> [node03.cluster:15282] MCW rank 0 bound to socket 0[core 0[hwt 0]]:
>>> [B/././././././.][./././././././.][./././././././.][
>>> ./././././././.]
>>> [node03.cluster:15282] MCW rank 1 bound to socket 0[core 1[hwt 0]]:
>>> [./B/./././././.][./././././././.][./././././././.][
>>> ./././././././.]
>>> Hello world from process 2 of 8
>>> Hello world from process 5 of 8
>>> Hello world from process 4 of 8
>>> Hello world from process 3 of 8
>>> Hello world from process 1 of 8
>>> Hello world from process 7 of 8
>>> Hello world from process 6 of 8
>>> Hello world from process 0 of 8
>>> [mishima_at_node03 demos]$ ~/opt/hwloc/bin/lstopo-no-graphics
>>> Machine (126GB)
>>> Socket L#0 (32GB)
>>> NUMANode L#0 (P#0 16GB) + L3 L#0 (5118KB)
>>> L2 L#0 (512KB) + L1d L#0 (64KB) + L1i L#0 (64KB) + Core L#0 + PU
> L#0
>>> (P#0)
>>> L2 L#1 (512KB) + L1d L#1 (64KB) + L1i L#1 (64KB) + Core L#1 + PU
> L#1
>>> (P#1)
>>> L2 L#2 (512KB) + L1d L#2 (64KB) + L1i L#2 (64KB) + Core L#2 + PU
> L#2
>>> (P#2)
>>> L2 L#3 (512KB) + L1d L#3 (64KB) + L1i L#3 (64KB) + Core L#3 + PU
> L#3
>>> (P#3)
>>> NUMANode L#1 (P#1 16GB) + L3 L#1 (5118KB)
>>> L2 L#4 (512KB) + L1d L#4 (64KB) + L1i L#4 (64KB) + Core L#4 + PU
> L#4
>>> (P#4)
>>> L2 L#5 (512KB) + L1d L#5 (64KB) + L1i L#5 (64KB) + Core L#5 + PU
> L#5
>>> (P#5)
>>> L2 L#6 (512KB) + L1d L#6 (64KB) + L1i L#6 (64KB) + Core L#6 + PU
> L#6
>>> (P#6)
>>> L2 L#7 (512KB) + L1d L#7 (64KB) + L1i L#7 (64KB) + Core L#7 + PU
> L#7
>>> (P#7)
>>> Socket L#1 (32GB)
>>> NUMANode L#2 (P#6 16GB) + L3 L#2 (5118KB)
>>> L2 L#8 (512KB) + L1d L#8 (64KB) + L1i L#8 (64KB) + Core L#8 + PU
> L#8
>>> (P#8)
>>> L2 L#9 (512KB) + L1d L#9 (64KB) + L1i L#9 (64KB) + Core L#9 + PU
> L#9
>>> (P#9)
>>> L2 L#10 (512KB) + L1d L#10 (64KB) + L1i L#10 (64KB) + Core L#10 +
> PU
>>> L#10 (P#10)
>>> L2 L#11 (512KB) + L1d L#11 (64KB) + L1i L#11 (64KB) + Core L#11 +
> PU
>>> L#11 (P#11)
>>> NUMANode L#3 (P#7 16GB) + L3 L#3 (5118KB)
>>> L2 L#12 (512KB) + L1d L#12 (64KB) + L1i L#12 (64KB) + Core L#12 +
> PU
>>> L#12 (P#12)
>>> L2 L#13 (512KB) + L1d L#13 (64KB) + L1i L#13 (64KB) + Core L#13 +
> PU
>>> L#13 (P#13)
>>> L2 L#14 (512KB) + L1d L#14 (64KB) + L1i L#14 (64KB) + Core L#14 +
> PU
>>> L#14 (P#14)
>>> L2 L#15 (512KB) + L1d L#15 (64KB) + L1i L#15 (64KB) + Core L#15 +
> PU
>>> L#15 (P#15)
>>> Socket L#2 (32GB)
>>> NUMANode L#4 (P#4 16GB) + L3 L#4 (5118KB)
>>> L2 L#16 (512KB) + L1d L#16 (64KB) + L1i L#16 (64KB) + Core L#16 +
> PU
>>> L#16 (P#16)
>>> L2 L#17 (512KB) + L1d L#17 (64KB) + L1i L#17 (64KB) + Core L#17 +
> PU
>>> L#17 (P#17)
>>> L2 L#18 (512KB) + L1d L#18 (64KB) + L1i L#18 (64KB) + Core L#18 +
> PU
>>> L#18 (P#18)
>>> L2 L#19 (512KB) + L1d L#19 (64KB) + L1i L#19 (64KB) + Core L#19 +
> PU
>>> L#19 (P#19)
>>> NUMANode L#5 (P#5 16GB) + L3 L#5 (5118KB)
>>> L2 L#20 (512KB) + L1d L#20 (64KB) + L1i L#20 (64KB) + Core L#20 +
> PU
>>> L#20 (P#20)
>>> L2 L#21 (512KB) + L1d L#21 (64KB) + L1i L#21 (64KB) + Core L#21 +
> PU
>>> L#21 (P#21)
>>> L2 L#22 (512KB) + L1d L#22 (64KB) + L1i L#22 (64KB) + Core L#22 +
> PU
>>> L#22 (P#22)
>>> L2 L#23 (512KB) + L1d L#23 (64KB) + L1i L#23 (64KB) + Core L#23 +
> PU
>>> L#23 (P#23)
>>> Socket L#3 (32GB)
>>> NUMANode L#6 (P#2 16GB) + L3 L#6 (5118KB)
>>> L2 L#24 (512KB) + L1d L#24 (64KB) + L1i L#24 (64KB) + Core L#24 +
> PU
>>> L#24 (P#24)
>>> L2 L#25 (512KB) + L1d L#25 (64KB) + L1i L#25 (64KB) + Core L#25 +
> PU
>>> L#25 (P#25)
>>> L2 L#26 (512KB) + L1d L#26 (64KB) + L1i L#26 (64KB) + Core L#26 +
> PU
>>> L#26 (P#26)
>>> L2 L#27 (512KB) + L1d L#27 (64KB) + L1i L#27 (64KB) + Core L#27 +
> PU
>>> L#27 (P#27)
>>> NUMANode L#7 (P#3 16GB) + L3 L#7 (5118KB)
>>> L2 L#28 (512KB) + L1d L#28 (64KB) + L1i L#28 (64KB) + Core L#28 +
> PU
>>> L#28 (P#28)
>>> L2 L#29 (512KB) + L1d L#29 (64KB) + L1i L#29 (64KB) + Core L#29 +
> PU
>>> L#29 (P#29)
>>> L2 L#30 (512KB) + L1d L#30 (64KB) + L1i L#30 (64KB) + Core L#30 +
> PU
>>> L#30 (P#30)
>>> L2 L#31 (512KB) + L1d L#31 (64KB) + L1i L#31 (64KB) + Core L#31 +
> PU
>>> L#31 (P#31)
>>> HostBridge L#0
>>> PCIBridge
>>> PCI 14e4:1639
>>> Net L#0 "eth0"
>>> PCI 14e4:1639
>>> Net L#1 "eth1"
>>> PCIBridge
>>> PCI 14e4:1639
>>> Net L#2 "eth2"
>>> PCI 14e4:1639
>>> Net L#3 "eth3"
>>> PCIBridge
>>> PCIBridge
>>> PCIBridge
>>> PCI 1000:0072
>>> Block L#4 "sdb"
>>> Block L#5 "sda"
>>> PCI 1002:4390
>>> Block L#6 "sr0"
>>> PCIBridge
>>> PCI 102b:0532
>>> HostBridge L#7
>>> PCIBridge
>>> PCI 15b3:6274
>>> Net L#7 "ib0"
>>> OpenFabrics L#8 "mthca0"
>>>
>>> _______________________________________________
>>> users mailing list
>>> users_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
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