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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: tmishima_at_[hidden]
Date: 2013-12-19 03:28:45


I can wait it'll be fixed in 1.7.5 or later, because putting "-bind-to
numa"
and "-map-by numa" at the same time works as a workaround.

Thanks,
Tetsuya Mishima

> Yeah, it will impact everything that uses hwloc topology maps, I fear.
>
> One side note: you'll need to add --hetero-nodes to your cmd line. If we
don't see that, we assume that all the node topologies are identical -
which clearly isn't true here.
>
> I'll try to resolve the hier inversion over the holiday - won't be for
1.7.4, but hopefully for 1.7.5
>
> Thanks
> Ralph
>
> On Dec 18, 2013, at 9:44 PM, tmishima_at_[hidden] wrote:
>
> >
> >
> > I think it's normal for AMD opteron having 8/16 cores such as
> > magny cours or interlagos. Because it usually has 2 numa nodes
> > in a cpu(socket), numa-node can not include a socket. This type
> > of hierarchy would be natural.
> >
> > (node03 is Dell PowerEdge R815 and maybe quite common, I guess)
> >
> > By the way, I think this inversion should affect rmaps_lama mapping.
> >
> > Tetsuya Mishima
> >
> >> 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]
> >>> 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]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
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