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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 00:44:47


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