George, If i understand correctly, you are running mpirun on dancer, which has 2 sockets, 4 cores per socket and 2 hwthreads per core, and orted are running on arc[00-08], though the tasks only run on arc00, which has 2 sockets, 10 cores per socket and 2 hwthreads per core
to me, it looks like OpenMPI assumes all nodes are similar to dancer, which is incorrect. Can you try again with the --hetero-nodes option ? (iirc, that should not be needed because nodes should have different "hwloc signatures", and OpenMPI is supposed to handle that automatically and correctly) That could be a side effect of your MCA params, can you try to remove them and mpirun --host arc00 --bind-to core -np 2 --report bindings grep Cpus_alliwed_list /proc/self/status And one more test plus the --hetero-nodes option ? Bottom line, you might have to set yet an other MCA param equivalent to the --hetero-nodes option. Cheers, Gilles r...@open-mpi.org wrote: >Interesting - well, it looks like ORTE is working correctly. The map is what >you would expect, and so is planned binding. > > >What this tells us is that we are indeed binding (so far as ORTE is concerned) >to the correct places. Rank 0 is being bound to 0,8, and that is what the OS >reports. Rank 1 is bound to 4,12, and rank 2 is bound to 1,9. All of this >matches what the OS reported. > > >So it looks like it is report-bindings that is messed up for some reason. > > > >On Sep 3, 2016, at 7:14 AM, George Bosilca <bosi...@icl.utk.edu> wrote: > > >$mpirun -np 3 --tag-output --bind-to core --report-bindings >--display-devel-map --mca rmaps_base_verbose 10 true > > >[dancer.icl.utk.edu:17451] [[41198,0],0]: Final mapper priorities >[dancer.icl.utk.edu:17451] Mapper: ppr Priority: 90 >[dancer.icl.utk.edu:17451] Mapper: seq Priority: 60 >[dancer.icl.utk.edu:17451] Mapper: resilient Priority: 40 >[dancer.icl.utk.edu:17451] Mapper: mindist Priority: 20 >[dancer.icl.utk.edu:17451] Mapper: round_robin Priority: 10 >[dancer.icl.utk.edu:17451] Mapper: staged Priority: 5 >[dancer.icl.utk.edu:17451] Mapper: rank_file Priority: 0 >[dancer.icl.utk.edu:17451] mca:rmaps: mapping job [41198,1] >[dancer.icl.utk.edu:17451] mca:rmaps: setting mapping policies for job >[41198,1] >[dancer.icl.utk.edu:17451] mca:rmaps[153] mapping not set by user - using >bysocket >[dancer.icl.utk.edu:17451] mca:rmaps:ppr: job [41198,1] not using ppr mapper >PPR NULL policy PPR NOTSET >[dancer.icl.utk.edu:17451] mca:rmaps:seq: job [41198,1] not using seq mapper >[dancer.icl.utk.edu:17451] mca:rmaps:resilient: cannot perform initial map of >job [41198,1] - no fault groups >[dancer.icl.utk.edu:17451] mca:rmaps:mindist: job [41198,1] not using mindist >mapper >[dancer.icl.utk.edu:17451] mca:rmaps:rr: mapping job [41198,1] >[dancer.icl.utk.edu:17451] AVAILABLE NODES FOR MAPPING: >[dancer.icl.utk.edu:17451] node: arc00 daemon: NULL >[dancer.icl.utk.edu:17451] node: arc01 daemon: NULL >[dancer.icl.utk.edu:17451] node: arc02 daemon: NULL >[dancer.icl.utk.edu:17451] node: arc03 daemon: NULL >[dancer.icl.utk.edu:17451] node: arc04 daemon: NULL >[dancer.icl.utk.edu:17451] node: arc05 daemon: NULL >[dancer.icl.utk.edu:17451] node: arc06 daemon: NULL >[dancer.icl.utk.edu:17451] node: arc07 daemon: NULL >[dancer.icl.utk.edu:17451] node: arc08 daemon: NULL >[dancer.icl.utk.edu:17451] mca:rmaps:rr: mapping no-span by Package for job >[41198,1] slots 180 num_procs 3 >[dancer.icl.utk.edu:17451] mca:rmaps:rr: found 2 Package objects on node arc00 >[dancer.icl.utk.edu:17451] mca:rmaps:rr: calculated nprocs 20 >[dancer.icl.utk.edu:17451] mca:rmaps:rr: assigning nprocs 20 >[dancer.icl.utk.edu:17451] mca:rmaps:base: computing vpids by slot for job >[41198,1] >[dancer.icl.utk.edu:17451] mca:rmaps:base: assigning rank 0 to node arc00 >[dancer.icl.utk.edu:17451] mca:rmaps:base: assigning rank 1 to node arc00 >[dancer.icl.utk.edu:17451] mca:rmaps:base: assigning rank 2 to node arc00 >[dancer.icl.utk.edu:17451] mca:rmaps: compute bindings for job [41198,1] with >policy CORE[4008] >[dancer.icl.utk.edu:17451] [[41198,0],0] reset_usage: node arc00 has 3 procs >on it >[dancer.icl.utk.edu:17451] [[41198,0],0] reset_usage: ignoring proc >[[41198,1],0] >[dancer.icl.utk.edu:17451] [[41198,0],0] reset_usage: ignoring proc >[[41198,1],1] >[dancer.icl.utk.edu:17451] [[41198,0],0] reset_usage: ignoring proc >[[41198,1],2] >[dancer.icl.utk.edu:17451] [[41198,0],0] bind_depth: 5 map_depth 1 >[dancer.icl.utk.edu:17451] mca:rmaps: bind downward for job [41198,1] with >bindings CORE >[dancer.icl.utk.edu:17451] [[41198,0],0] GOT 1 CPUS >[dancer.icl.utk.edu:17451] [[41198,0],0] PROC [[41198,1],0] BITMAP 0,8 >[dancer.icl.utk.edu:17451] [[41198,0],0] BOUND PROC [[41198,1],0][arc00] TO >socket 0[core 0[hwt 0-1]]: [BB/../../..][../../../.. >] >[dancer.icl.utk.edu:17451] [[41198,0],0] GOT 1 CPUS >[dancer.icl.utk.edu:17451] [[41198,0],0] PROC [[41198,1],1] BITMAP 4,12 >[dancer.icl.utk.edu:17451] [[41198,0],0] BOUND PROC [[41198,1],1][arc00] TO >socket 1[core 4[hwt 0-1]]: [../../../..][BB/../../.. >] >[dancer.icl.utk.edu:17451] [[41198,0],0] GOT 1 CPUS >[dancer.icl.utk.edu:17451] [[41198,0],0] PROC [[41198,1],2] BITMAP 1,9 >[dancer.icl.utk.edu:17451] [[41198,0],0] BOUND PROC [[41198,1],2][arc00] TO >socket 0[core 1[hwt 0-1]]: [../BB/../..][../../../.. >] >[1,0]<stderr>:[arc00:07612] MCW rank 0 bound to socket 0[core 0[hwt 0]], >socket 0[core 8[hwt 0]]: [B./../../../../../../../B./.. >][../../../../../../../../../..] >[1,1]<stderr>:[arc00:07612] MCW rank 1 bound to socket 0[core 4[hwt 0]], >socket 1[core 12[hwt 0]]: [../../../../B./../../../../. >.][../../B./../../../../../../..] >[1,2]<stderr>:[arc00:07612] MCW rank 2 bound to socket 0[core 1[hwt 0]], >socket 0[core 9[hwt 0]]: [../B./../../../../../../../B. >][../../../../../../../../../..] > > >On Sat, Sep 3, 2016 at 9:44 AM, r...@open-mpi.org <r...@open-mpi.org> wrote: > >Okay, can you add --display-devel-map --mca rmaps_base_verbose 10 to your cmd >line? > > >It sounds like there is something about that topo that is bothering the mapper > > >On Sep 2, 2016, at 9:31 PM, George Bosilca <bosi...@icl.utk.edu> wrote: > > >Thanks Gilles, that's a very useful trick. The bindings reported by ORTE are >in sync with the one reported by the OS. > > >$ mpirun -np 2 --tag-output --bind-to core --report-bindings grep >Cpus_allowed_list /proc/self/status > >[1,0]<stderr>:[arc00:90813] MCW rank 0 bound to socket 0[core 0[hwt 0]], >socket 0[core 4[hwt 0]]: >[B./../../../B./../../../../..][../../../../../../../../../..] > >[1,1]<stderr>:[arc00:90813] MCW rank 1 bound to socket 1[core 10[hwt 0]], >socket 1[core 14[hwt 0]]: >[../../../../../../../../../..][B./../../../B./../../../../..] > >[1,0]<stdout>:Cpus_allowed_list: 0,8 > >[1,1]<stdout>:Cpus_allowed_list: 1,9 > > >George. > > > > >On Sat, Sep 3, 2016 at 12:27 AM, Gilles Gouaillardet ><gilles.gouaillar...@gmail.com> wrote: > >George, > >I cannot help much with this i am afraid > >My best bet would be to rebuild OpenMPI with --enable-debug and an external >recent hwloc (iirc hwloc v2 cannot be used in Open MPI yet) > >You might also want to try >mpirun --tag-output --bind-to xxx --report-bindings grep Cpus_allowed_list >/proc/self/status > >So you can confirm both openmpi and /proc/self/status report the same thing > >Hope this helps a bit ... > >Gilles > > > >George Bosilca <bosi...@icl.utk.edu> wrote: > >While investigating the ongoing issue with OMPI messaging layer, I run into >some troubles with process binding. I read the documentation, but I still find >this puzzling. > > >Disclaimer: all experiments were done with current master (9c496f7) compiled >in optimized mode. The hardware: a single node 20 core Xeon E5-2650 v3 >(hwloc-ls is at the end of this email). > > >First and foremost, trying to bind to NUMA nodes was a sure way to get a >segfault: > > >$ mpirun -np 2 --mca btl vader,self --bind-to numa --report-bindings true > >-------------------------------------------------------------------------- > >No objects of the specified type were found on at least one node: > > > Type: NUMANode > > Node: arc00 > > >The map cannot be done as specified. > >-------------------------------------------------------------------------- > >[dancer:32162] *** Process received signal *** > >[dancer:32162] Signal: Segmentation fault (11) > >[dancer:32162] Signal code: Address not mapped (1) > >[dancer:32162] Failing at address: 0x3c > >[dancer:32162] [ 0] /lib64/libpthread.so.0[0x3126a0f7e0] > >[dancer:32162] [ 1] >/home/bosilca/opt/trunk/fast/lib/libopen-rte.so.0(+0x560e0)[0x7f9075bc60e0] > >[dancer:32162] [ 2] >/home/bosilca/opt/trunk/fast/lib/libopen-rte.so.0(orte_grpcomm_API_xcast+0x84)[0x7f9075bc6f54] > >[dancer:32162] [ 3] >/home/bosilca/opt/trunk/fast/lib/libopen-rte.so.0(orte_plm_base_orted_exit+0x1a8)[0x7f9075bd9308] > >[dancer:32162] [ 4] >/home/bosilca/opt/trunk/fast/lib/openmpi/mca_plm_rsh.so(+0x384e)[0x7f907361284e] > >[dancer:32162] [ 5] >/home/bosilca/opt/trunk/fast/lib/libopen-rte.so.0(orte_state_base_check_all_complete+0x324)[0x7f9075bedca4] > >[dancer:32162] [ 6] >/home/bosilca/opt/trunk/fast/lib/libopen-pal.so.0(opal_libevent2022_event_base_loop+0x53c)[0x7f90758eafec] > >[dancer:32162] [ 7] mpirun[0x401251] > >[dancer:32162] [ 8] mpirun[0x400e24] > >[dancer:32162] [ 9] /lib64/libc.so.6(__libc_start_main+0xfd)[0x312621ed1d] > >[dancer:32162] [10] mpirun[0x400d49] > >[dancer:32162] *** End of error message *** > >Segmentation fault > > >As you can see on the hwloc output below, there are 2 NUMA nodes on the node >and HWLOC correctly identifies them, making OMPI error message confusing. >Anyway, we should not segfault but report a more meaning error message. > > >Binding to slot (I got this from the man page for 2.0) is apparently not >supported anymore. Reminder: We should update the manpage accordingly. > > >Trying to bind to core looks better, the application at least starts. >Unfortunately the reported bindings (or at least my understanding of these >bindings) are troubling. Assuming that the way we report the bindings is >correct, why are my processes assigned to 2 cores far apart each ? > > >$ mpirun -np 2 --mca btl vader,self --bind-to core --report-bindings true > >[arc00:39350] MCW rank 0 bound to socket 0[core 0[hwt 0]], socket 0[core 8[hwt >0]]: [B./../../../../../../../B./..][../../../../../../../../../..] > >[arc00:39350] MCW rank 1 bound to socket 0[core 1[hwt 0]], socket 0[core 9[hwt >0]]: [../B./../../../../../../../B.][../../../../../../../../../..] > > >Maybe because I only used the binding option. Adding the mapping to the mix >(--map-by option) seem hopeless, the binding remains unchanged for 2 processes. > > >$ mpirun -np 2 --mca btl vader,self --bind-to core --report-bindings true > >[arc00:40401] MCW rank 0 bound to socket 0[core 0[hwt 0]], socket 0[core 8[hwt >0]]: [B./../../../../../../../B./..][../../../../../../../../../..] > >[arc00:40401] MCW rank 1 bound to socket 0[core 1[hwt 0]], socket 0[core 9[hwt >0]]: [../B./../../../../../../../B.][../../../../../../../../../..] > > >At this point I really wondered what is going on. To clarify I tried to launch >3 processes on the node. Bummer ! the reported binding shows that one of my >processes got assigned to cores on different sockets. > > >$ mpirun -np 3 --mca btl vader,self --bind-to core --report-bindings true > >[arc00:40311] MCW rank 0 bound to socket 0[core 0[hwt 0]], socket 0[core 8[hwt >0]]: [B./../../../../../../../B./..][../../../../../../../../../..] > >[arc00:40311] MCW rank 2 bound to socket 0[core 1[hwt 0]], socket 0[core 9[hwt >0]]: [../B./../../../../../../../B.][../../../../../../../../../..] > >[arc00:40311] MCW rank 1 bound to socket 0[core 4[hwt 0]], socket 1[core >12[hwt 0]]: [../../../../B./../../../../..][../../B./../../../../../../..] > > >Why is rank 1 on core 4 and rank 2 on core 1 ? Maybe specifying the mapping >will help. Will I get a more sensible binding (as suggested by our online >documentation and the man pages) ? > > >$ mpirun -np 3 --mca btl vader,self --bind-to core --map-by core >--report-bindings true > >[arc00:40254] MCW rank 0 bound to socket 0[core 0[hwt 0]], socket 0[core 8[hwt >0]]: [B./../../../../../../../B./..][../../../../../../../../../..] > >[arc00:40254] MCW rank 1 bound to socket 0[core 1[hwt 0]], socket 0[core 9[hwt >0]]: [../B./../../../../../../../B.][../../../../../../../../../..] > >[arc00:40254] MCW rank 2 bound to socket 0[core 2[hwt 0]], socket 1[core >10[hwt 0]]: [../../B./../../../../../../..][B./../../../../../../../../..] > > >There is a difference. The logical rank of processes is now respected but one >of my processes is still bound to 2 cores on different sockets, but these >cores are different from the case when the mapping was not specified. > > >Trying to bind on sockets I got an even more confusing outcome. So I went the >hard way, what can go wrong if I manually define the binding via a rankfile ? >Fail ! My processes continue to report an unsettling bindings (there is some >relationship with my rank file but most of the issues I reported above still >remain). > > >$ more rankfile > >rank 0=arc00 slot=0 > >rank 1=arc00 slot=2 > >$ mpirun -np 2 --mca btl vader,self -rf rankfile --report-bindings true > >[arc00:40718] MCW rank 0 bound to socket 0[core 0[hwt 0]], socket 0[core 8[hwt >0]]: [B./../../../../../../../B./..][../../../../../../../../../..] > >[arc00:40718] MCW rank 1 bound to socket 0[core 2[hwt 0]], socket 1[core >10[hwt 0]]: [../../B./../../../../../../..][B./../../../../../../../../..] > > >At this point I got pretty much completely confused with how OMPI binding >works. I'm counting on a good samaritan to explain how this works. > > >Thanks, > > George. > > >PS: rankfile feature of using relative hostnames (+n?) seems to be busted as >the example from the man page leads to the following complaint > > >-------------------------------------------------------------------------- > >A relative host was specified, but no prior allocation has been made. > >Thus, there is no way to determine the proper host to be used. > > >hostfile entry: +n0 > > >Please see the orte_hosts man page for further information. > >-------------------------------------------------------------------------- > > > >$ hwloc-ls > >Machine (63GB) > > NUMANode L#0 (P#0 31GB) > > Socket L#0 + L3 L#0 (25MB) > > L2 L#0 (256KB) + L1d L#0 (32KB) + L1i L#0 (32KB) + Core L#0 > > PU L#0 (P#0) > > PU L#1 (P#20) > > L2 L#1 (256KB) + L1d L#1 (32KB) + L1i L#1 (32KB) + Core L#1 > > PU L#2 (P#1) > > PU L#3 (P#21) > > L2 L#2 (256KB) + L1d L#2 (32KB) + L1i L#2 (32KB) + Core L#2 > > PU L#4 (P#2) > > PU L#5 (P#22) > > L2 L#3 (256KB) + L1d L#3 (32KB) + L1i L#3 (32KB) + Core L#3 > > PU L#6 (P#3) > > PU L#7 (P#23) > > L2 L#4 (256KB) + L1d L#4 (32KB) + L1i L#4 (32KB) + Core L#4 > > PU L#8 (P#4) > > PU L#9 (P#24) > > L2 L#5 (256KB) + L1d L#5 (32KB) + L1i L#5 (32KB) + Core L#5 > > PU L#10 (P#5) > > PU L#11 (P#25) > > L2 L#6 (256KB) + L1d L#6 (32KB) + L1i L#6 (32KB) + Core L#6 > > PU L#12 (P#6) > > PU L#13 (P#26) > > L2 L#7 (256KB) + L1d L#7 (32KB) + L1i L#7 (32KB) + Core L#7 > > PU L#14 (P#7) > > PU L#15 (P#27) > > L2 L#8 (256KB) + L1d L#8 (32KB) + L1i L#8 (32KB) + Core L#8 > > PU L#16 (P#8) > > PU L#17 (P#28) > > L2 L#9 (256KB) + L1d L#9 (32KB) + L1i L#9 (32KB) + Core L#9 > > PU L#18 (P#9) > > PU L#19 (P#29) > > NUMANode L#1 (P#1 31GB) > > Socket L#1 + L3 L#1 (25MB) > > L2 L#10 (256KB) + L1d L#10 (32KB) + L1i L#10 (32KB) + Core L#10 > > PU L#20 (P#10) > > PU L#21 (P#30) > > L2 L#11 (256KB) + L1d L#11 (32KB) + L1i L#11 (32KB) + Core L#11 > > PU L#22 (P#11) > > PU L#23 (P#31) > > L2 L#12 (256KB) + L1d L#12 (32KB) + L1i L#12 (32KB) + Core L#12 > > PU L#24 (P#12) > > PU L#25 (P#32) > > L2 L#13 (256KB) + L1d L#13 (32KB) + L1i L#13 (32KB) + Core L#13 > > PU L#26 (P#13) > > PU L#27 (P#33) > > L2 L#14 (256KB) + L1d L#14 (32KB) + L1i L#14 (32KB) + Core L#14 > > PU L#28 (P#14) > > PU L#29 (P#34) > > L2 L#15 (256KB) + L1d L#15 (32KB) + L1i L#15 (32KB) + Core L#15 > > PU L#30 (P#15) > > PU L#31 (P#35) > > L2 L#16 (256KB) + L1d L#16 (32KB) + L1i L#16 (32KB) + Core L#16 > > PU L#32 (P#16) > > PU L#33 (P#36) > > L2 L#17 (256KB) + L1d L#17 (32KB) + L1i L#17 (32KB) + Core L#17 > > PU L#34 (P#17) > > PU L#35 (P#37) > > L2 L#18 (256KB) + L1d L#18 (32KB) + L1i L#18 (32KB) + Core L#18 > > PU L#36 (P#18) > > PU L#37 (P#38) > > L2 L#19 (256KB) + L1d L#19 (32KB) + L1i L#19 (32KB) + Core L#19 > > PU L#38 (P#19) > > PU L#39 (P#39) > > > >_______________________________________________ >devel mailing list >devel@lists.open-mpi.org >https://rfd.newmexicoconsortium.org/mailman/listinfo/devel > > >_______________________________________________ >devel mailing list >devel@lists.open-mpi.org >https://rfd.newmexicoconsortium.org/mailman/listinfo/devel > > > >_______________________________________________ >devel mailing list >devel@lists.open-mpi.org >https://rfd.newmexicoconsortium.org/mailman/listinfo/devel > > >_______________________________________________ >devel mailing list >devel@lists.open-mpi.org >https://rfd.newmexicoconsortium.org/mailman/listinfo/devel > >
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