Thank you, Ralph.
Then, this problem should depend on our environment. But, at least, inversion problem is not the cause because node05 has normal hier order. I can not connect to our cluster now. Tuesday, going back to my office, I'll send you further report. Before that, please let me know your configuration. I will follow your configuation as much as possible. Our configuraion is very simple, only -with-tm -with-ibverbs -disable-ipv6. (on CentOS 5.8) The 1.7 series is a llite bit unstable on our cluster yet. Similar freezing(hang up) was observed with 1.7.3. At that time, lama worked well but putting "-rank-by something" caused same freezing (curiously, rank-by works with 1.7.4rc1). I checked where it stopped using gdb, then I found that it stopped to wait for event in a function of libevent(I can not recall the name). Is this related to your "connection issue in the OOB subsystem"? Or libevent version conflict? I guess these two problems are related each other. They stopped at very early stage before reaching mapping function because no message appeared before freezing, which is my random guess. Could you give me any hint or comment? Regards, Tetsuya Mishima > It seems to be working fine for me: > > [rhc@bend001 tcp]$ mpirun -np 2 -host bend001 -report-bindings -mca rmaps_lama_bind 1c -mca rmaps lama hostname > bend001 > [bend001:17005] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: [../BB/../../../..][../../../../../..] > [bend001:17005] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: [BB/../../../../..][../../../../../..] > bend001 > [rhc@bend001 tcp]$ > > (I also checked the internals using "-mca rmaps_base_verbose 10") so it could be your hier inversion causing problems again. Or it could be that you are hitting a connection issue we are seeing in > some scenarios in the OOB subsystem - though if you are able to run using a non-lama mapper, that would seem unlikely. > > > On Dec 20, 2013, at 8:09 PM, tmish...@jcity.maeda.co.jp wrote: > > > > Hi Ralph, > > Thank you very much. I tried many things such as: > > mpirun -np 2 -host node05 -report-bindings -mca rmaps lama -mca > rmaps_lama_bind 1c myprog > > But every try failed. At least they were accepted by openmpi-1.7.3 as far > as I remember. > Anyway, please check it when you have a time, because using lama comes from > my curiosity. > > Regards, > Tetsuya Mishima > > > I'll try to take a look at it - my expectation is that lama might get > stuck because you didn't tell it a pattern to map, and I doubt that code > path has seen much testing. > > > On Dec 20, 2013, at 5:52 PM, tmish...@jcity.maeda.co.jp wrote: > > > > Hi Ralph, I'm glad to hear that, thanks. > > By the way, yesterday I tried to check how lama in 1.7.4rc treat numa > node. > > Then, even wiht this simple command line, it freezed without any > massage: > > mpirun -np 2 -host node05 -mca rmaps lama myprog > > Could you check what happened? > > Is it better to open new thread or continue this thread? > > Regards, > Tetsuya Mishima > > > I'll make it work so that NUMA can be either above or below socket > > On Dec 20, 2013, at 2:57 AM, tmish...@jcity.maeda.co.jp wrote: > > > > Hi Brice, > > Thank you for your comment. I understand what you mean. > > My opinion was made just considering easy way to adjust the code for > inversion of hierarchy in object tree. > > Tetsuya Mishima > > > I don't think there's any such difference. > Also, all these NUMA architectures are reported the same by hwloc, > and > therefore used the same in Open MPI. > > And yes, L3 and NUMA are topologically-identical on AMD Magny-Cours > (and > most recent AMD and Intel platforms). > > Brice > > > > Le 20/12/2013 11:33, tmish...@jcity.maeda.co.jp a écrit : > > Hi Ralph, > > The numa-node in AMD Mangy-Cours/Interlagos is so called cc(cache > coherent)NUMA, > which seems to be a little bit different from the traditional numa > defined > in openmpi. > > I notice that ccNUMA object is almost same as L3cache object. > So "-bind-to l3cache" or "-map-by l3cache" is valid for what I want > to > do. > Therefore, "do not touch it" is one of the solution, I think ... > > Anyway, mixing up these two types of numa is the problem. > > Regards, > Tetsuya Mishima > > 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, 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 > _______________________________________________ > users mailing list > us...@open-mpi.org > 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