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, tmish...@jcity.maeda.co.jp 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, tmish...@jcity.maeda.co.jp 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@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, tmish...@jcity.maeda.co.jp 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@manage ~]$ qsub -I -l nodes=1:ppn=32 >>>>> qsub: waiting for job 8352.manage.cluster to start >>>>> qsub: job 8352.manage.cluster ready >>>>> >>>>> [mishima@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@node03 ~]$ cd ~/Desktop/openmpi-1.7/demos/ >>>>> [mishima@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@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 >>>>> us...@open-mpi.org >>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>>> >>>> _______________________________________________ >>>> users mailing list >>>> us...@open-mpi.org>> > http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
