Marcin, my understanding is that in this case, patched v1.10.1rc1 is working just fine. am I right ?
I prepared two patches one to remove the warning when binding on one core if only one core is available, an other one to add a warning if the user asks a binding policy that makes no sense with the required mapping policy I will finalize them tomorrow hopefully Cheers, Gilles On Tuesday, October 6, 2015, marcin.krotkiewski < marcin.krotkiew...@gmail.com> wrote: > Hi, Gilles > > you mentionned you had one failure with 1.10.1rc1 and -bind-to core > could you please send the full details (script, allocation and output) > in your slurm script, you can do > srun -N $SLURM_NNODES -n $SLURM_NNODES --cpu_bind=none -l grep > Cpus_allowed_list /proc/self/status > before invoking mpirun > > It was an interactive job allocated with > > salloc --account=staff --ntasks=32 --mem-per-cpu=2G --time=120:0:0 > > The slurm environment is the following > > SLURM_JOBID=12714491 > SLURM_JOB_CPUS_PER_NODE='4,2,5(x2),4,7,5' > SLURM_JOB_ID=12714491 > SLURM_JOB_NODELIST='c1-[2,4,8,13,16,23,26]' > SLURM_JOB_NUM_NODES=7 > SLURM_JOB_PARTITION=normal > SLURM_MEM_PER_CPU=2048 > SLURM_NNODES=7 > SLURM_NODELIST='c1-[2,4,8,13,16,23,26]' > SLURM_NODE_ALIASES='(null)' > SLURM_NPROCS=32 > SLURM_NTASKS=32 > SLURM_SUBMIT_DIR=/cluster/home/marcink > SLURM_SUBMIT_HOST=login-0-1.local > SLURM_TASKS_PER_NODE='4,2,5(x2),4,7,5' > > The output of the command you asked for is > > 0: c1-2.local Cpus_allowed_list: 1-4,17-20 > 1: c1-4.local Cpus_allowed_list: 1,15,17,31 > 2: c1-8.local Cpus_allowed_list: 0,5,9,13-14,16,21,25,29-30 > 3: c1-13.local Cpus_allowed_list: 3-7,19-23 > 4: c1-16.local Cpus_allowed_list: 12-15,28-31 > 5: c1-23.local Cpus_allowed_list: 2-4,8,13-15,18-20,24,29-31 > 6: c1-26.local Cpus_allowed_list: 1,6,11,13,15,17,22,27,29,31 > > Running with command > > mpirun --mca rmaps_base_verbose 10 --hetero-nodes --bind-to core > --report-bindings --map-by socket -np 32 ./affinity > > I have attached two output files: one for the original 1.10.1rc1, one for > the patched version. > > When I said 'failed in one case' I was not precise. I got an error on node > c1-8, which was the first one to have different number of MPI processes on > the two sockets. It would also fail on some later nodes, just that because > of the error we never got there. > > Let me know if you need more. > > Marcin > > > > > > > > Cheers, > > Gilles > > On 10/4/2015 11:55 PM, marcin.krotkiewski wrote: > > Hi, all, > > I played a bit more and it seems that the problem results from > > trg_obj = opal_hwloc_base_find_min_bound_target_under_obj() > > called in rmaps_base_binding.c / bind_downwards being wrong. I do not know > the reason, but I think I know when the problem happens (at least on > 1.10.1rc1). It seems that by default openmpi maps by socket. The error > happens when for a given compute node there is a different number of cores > used on each socket. Consider previously studied case (the debug outputs I > sent in last post). c1-8, which was source of error, has 5 mpi processes > assigned, and the cpuset is the following: > > 0, 5, 9, 13, 14, 16, 21, 25, 29, 30 > > Cores 0,5 are on socket 0, cores 9, 13, 14 are on socket 1. Binding > progresses correctly up to and including core 13 (see end of file > out.1.10.1rc2, before the error). That is 2 cores on socket 0, and 2 cores > on socket 1. Error is thrown when core 14 should be bound - extra core on > socket 1 with no corresponding core on socket 0. At that point the returned > trg_obj points to the first core on the node (os_index 0, socket 0). > > I have submitted a few other jobs and I always had an error in such > situation. Moreover, if I now use --map-by core instead of socket, the > error is gone, and I get my expected binding: > > rank 0 @ compute-1-2.local 1, 17, > rank 1 @ compute-1-2.local 2, 18, > rank 2 @ compute-1-2.local 3, 19, > rank 3 @ compute-1-2.local 4, 20, > rank 4 @ compute-1-4.local 1, 17, > rank 5 @ compute-1-4.local 15, 31, > rank 6 @ compute-1-8.local 0, 16, > rank 7 @ compute-1-8.local 5, 21, > rank 8 @ compute-1-8.local 9, 25, > rank 9 @ compute-1-8.local 13, 29, > rank 10 @ compute-1-8.local 14, 30, > rank 11 @ compute-1-13.local 3, 19, > rank 12 @ compute-1-13.local 4, 20, > rank 13 @ compute-1-13.local 5, 21, > rank 14 @ compute-1-13.local 6, 22, > rank 15 @ compute-1-13.local 7, 23, > rank 16 @ compute-1-16.local 12, 28, > rank 17 @ compute-1-16.local 13, 29, > rank 18 @ compute-1-16.local 14, 30, > rank 19 @ compute-1-16.local 15, 31, > rank 20 @ compute-1-23.local 2, 18, > rank 29 @ compute-1-26.local 11, 27, > rank 21 @ compute-1-23.local 3, 19, > rank 30 @ compute-1-26.local 13, 29, > rank 22 @ compute-1-23.local 4, 20, > rank 31 @ compute-1-26.local 15, 31, > rank 23 @ compute-1-23.local 8, 24, > rank 27 @ compute-1-26.local 1, 17, > rank 24 @ compute-1-23.local 13, 29, > rank 28 @ compute-1-26.local 6, 22, > rank 25 @ compute-1-23.local 14, 30, > rank 26 @ compute-1-23.local 15, 31, > > Using --map-by core seems to fix the issue on 1.8.8, 1.10.0 and 1.10.1rc1. > However, there is still a difference in behavior between 1.10.1rc1 and > earlier versions. In the SLURM job described in last post, 1.10.1rc1 fails > to bind only in 1 case, while the earlier versions fail in 21 out of 32 > cases. You mentioned there was a bug in hwloc. Not sure if it can explain > the difference in behavior. > > Hope this helps to nail this down. > > Marcin > > > > > On 10/04/2015 09:55 AM, Gilles Gouaillardet wrote: > > Ralph, > > I suspect ompi tries to bind to threads outside the cpuset. > this could be pretty similar to a previous issue when ompi tried to bind > to cores outside the cpuset. > /* when a core has more than one thread, would ompi assume all the threads > are available if the core is available ? */ > I will investigate this from tomorrow > > Cheers, > > Gilles > > On Sunday, October 4, 2015, Ralph Castain < > <javascript:_e(%7B%7D,'cvml','r...@open-mpi.org');>r...@open-mpi.org > <javascript:_e(%7B%7D,'cvml','r...@open-mpi.org');>> wrote: > >> Thanks - please go ahead and release that allocation as I’m not going to >> get to this immediately. I’ve got several hot irons in the fire right now, >> and I’m not sure when I’ll get a chance to track this down. >> >> Gilles or anyone else who might have time - feel free to take a gander >> and see if something pops out at you. >> >> Ralph >> >> >> On Oct 3, 2015, at 11:05 AM, marcin.krotkiewski < >> marcin.krotkiew...@gmail.com> wrote: >> >> >> Done. I have compiled 1.10.0 and 1.10.rc1 with --enable-debug and executed >> >> mpirun --mca rmaps_base_verbose 10 --hetero-nodes --report-bindings >> --bind-to core -np 32 ./affinity >> >> In case of 1.10.rc1 I have also added :overload-allowed - output in a >> separate file. This option did not make much difference for 1.10.0, so I >> did not attach it here. >> >> First thing I noted for 1.10.0 are lines like >> >> [login-0-1.local:03399] [[37945,0],0] GOT 1 CPUS >> [login-0-1.local:03399] [[37945,0],0] PROC [[37945,1],27] BITMAP >> [login-0-1.local:03399] [[37945,0],0] PROC [[37945,1],27] ON c1-26 IS NOT >> BOUND >> >> with an empty BITMAP. >> >> The SLURM environment is >> >> set | grep SLURM >> SLURM_JOBID=12714491 >> SLURM_JOB_CPUS_PER_NODE='4,2,5(x2),4,7,5' >> SLURM_JOB_ID=12714491 >> SLURM_JOB_NODELIST='c1-[2,4,8,13,16,23,26]' >> SLURM_JOB_NUM_NODES=7 >> SLURM_JOB_PARTITION=normal >> SLURM_MEM_PER_CPU=2048 >> SLURM_NNODES=7 >> SLURM_NODELIST='c1-[2,4,8,13,16,23,26]' >> SLURM_NODE_ALIASES='(null)' >> SLURM_NPROCS=32 >> SLURM_NTASKS=32 >> SLURM_SUBMIT_DIR=/cluster/home/marcink >> SLURM_SUBMIT_HOST=login-0-1.local >> SLURM_TASKS_PER_NODE='4,2,5(x2),4,7,5' >> >> I have submitted an interactive job on screen for 120 hours now to work >> with one example, and not change it for every post :) >> >> If you need anything else, let me know. I could introduce some >> patch/printfs and recompile, if you need it. >> >> Marcin >> >> >> >> On 10/03/2015 07:17 PM, Ralph Castain wrote: >> >> Rats - just realized I have no way to test this as none of the machines I >> can access are setup for cgroup-based multi-tenant. Is this a debug version >> of OMPI? If not, can you rebuild OMPI with —enable-debug? >> >> Then please run it with —mca rmaps_base_verbose 10 and pass along the >> output. >> >> Thanks >> Ralph >> >> >> On Oct 3, 2015, at 10:09 AM, Ralph Castain <r...@open-mpi.org >> <javascript:_e(%7B%7D,'cvml','r...@open-mpi.org');>> wrote: >> >> What version of slurm is this? I might try to debug it here. I’m not sure >> where the problem lies just yet. >> >> >> On Oct 3, 2015, at 8:59 AM, marcin.krotkiewski < >> <javascript:_e(%7B%7D,'cvml','marcin.krotkiew...@gmail.com');> >> marcin.krotkiew...@gmail.com >> <javascript:_e(%7B%7D,'cvml','marcin.krotkiew...@gmail.com');>> wrote: >> >> Here is the output of lstopo. In short, (0,16) are core 0, (1,17) - core >> 1 etc. >> >> Machine (64GB) >> NUMANode L#0 (P#0 32GB) >> Socket L#0 + L3 L#0 (20MB) >> L2 L#0 (256KB) + L1d L#0 (32KB) + L1i L#0 (32KB) + Core L#0 >> PU L#0 (P#0) >> PU L#1 (P#16) >> L2 L#1 (256KB) + L1d L#1 (32KB) + L1i L#1 (32KB) + Core L#1 >> PU L#2 (P#1) >> PU L#3 (P#17) >> L2 L#2 (256KB) + L1d L#2 (32KB) + L1i L#2 (32KB) + Core L#2 >> PU L#4 (P#2) >> PU L#5 (P#18) >> L2 L#3 (256KB) + L1d L#3 (32KB) + L1i L#3 (32KB) + Core L#3 >> PU L#6 (P#3) >> PU L#7 (P#19) >> L2 L#4 (256KB) + L1d L#4 (32KB) + L1i L#4 (32KB) + Core L#4 >> PU L#8 (P#4) >> PU L#9 (P#20) >> L2 L#5 (256KB) + L1d L#5 (32KB) + L1i L#5 (32KB) + Core L#5 >> PU L#10 (P#5) >> PU L#11 (P#21) >> L2 L#6 (256KB) + L1d L#6 (32KB) + L1i L#6 (32KB) + Core L#6 >> PU L#12 (P#6) >> PU L#13 (P#22) >> L2 L#7 (256KB) + L1d L#7 (32KB) + L1i L#7 (32KB) + Core L#7 >> PU L#14 (P#7) >> PU L#15 (P#23) >> HostBridge L#0 >> PCIBridge >> PCI 8086:1521 >> Net L#0 "eth0" >> PCI 8086:1521 >> Net L#1 "eth1" >> PCIBridge >> PCI 15b3:1003 >> Net L#2 "ib0" >> OpenFabrics L#3 "mlx4_0" >> PCIBridge >> PCI 102b:0532 >> PCI 8086:1d02 >> Block L#4 "sda" >> NUMANode L#1 (P#1 32GB) + Socket L#1 + L3 L#1 (20MB) >> L2 L#8 (256KB) + L1d L#8 (32KB) + L1i L#8 (32KB) + Core L#8 >> PU L#16 (P#8) >> PU L#17 (P#24) >> L2 L#9 (256KB) + L1d L#9 (32KB) + L1i L#9 (32KB) + Core L#9 >> PU L#18 (P#9) >> PU L#19 (P#25) >> L2 L#10 (256KB) + L1d L#10 (32KB) + L1i L#10 (32KB) + Core L#10 >> PU L#20 (P#10) >> PU L#21 (P#26) >> L2 L#11 (256KB) + L1d L#11 (32KB) + L1i L#11 (32KB) + Core L#11 >> PU L#22 (P#11) >> PU L#23 (P#27) >> L2 L#12 (256KB) + L1d L#12 (32KB) + L1i L#12 (32KB) + Core L#12 >> PU L#24 (P#12) >> PU L#25 (P#28) >> L2 L#13 (256KB) + L1d L#13 (32KB) + L1i L#13 (32KB) + Core L#13 >> PU L#26 (P#13) >> PU L#27 (P#29) >> L2 L#14 (256KB) + L1d L#14 (32KB) + L1i L#14 (32KB) + Core L#14 >> PU L#28 (P#14) >> PU L#29 (P#30) >> L2 L#15 (256KB) + L1d L#15 (32KB) + L1i L#15 (32KB) + Core L#15 >> PU L#30 (P#15) >> PU L#31 (P#31) >> >> >> >> On 10/03/2015 05:46 PM, Ralph Castain wrote: >> >> Maybe I’m just misreading your HT map - that slurm nodelist syntax is a >> new one to me, but they tend to change things around. Could you run lstopo >> on one of those compute nodes and send the output? >> >> I’m just suspicious because I’m not seeing a clear pairing of HT numbers >> in your output, but HT numbering is BIOS-specific and I may just not be >> understanding your particular pattern. Our error message is clearly >> indicating that we are seeing individual HTs (and not complete cores) >> assigned, and I don’t know the source of that confusion. >> >> >> On Oct 3, 2015, at 8:28 AM, marcin.krotkiewski < >> <javascript:_e(%7B%7D,'cvml','marcin.krotkiew...@gmail.com');> >> marcin.krotkiew...@gmail.com >> <javascript:_e(%7B%7D,'cvml','marcin.krotkiew...@gmail.com');>> wrote: >> >> >> On 10/03/2015 04:38 PM, Ralph Castain wrote: >> >> If mpirun isn’t trying to do any binding, then you will of course get the >> right mapping as we’ll just inherit whatever we received. >> >> Yes. I meant that whatever you received (what SLURM gives) is a correct >> cpu map and assigns _whole_ CPUs, not a single HT to MPI processes. In the >> case mentioned earlier openmpi should start 6 tasks on c1-30. If HT would >> be treated as separate and independent cores, sched_getaffinity of an MPI >> process started on c1-30 would return a map with 6 entries only. In my case >> it returns a map with 12 entries - 2 for each core. So one process is in >> fact allocated both HTs, not only one. Is what I'm saying correct? >> >> Looking at your output, it’s pretty clear that you are getting >> independent HTs assigned and not full cores. >> >> How do you mean? Is the above understanding wrong? I would expect that on >> c1-30 with --bind-to core openmpi should bind to logical cores 0 and 16 >> (rank 0), 1 and 17 (rank 2) and so on. All those logical cores are >> available in sched_getaffinity map, and there is twice as many logical >> cores as there are MPI processes started on the node. >> >> My guess is that something in slurm has changed such that it detects that >> HT has been enabled, and then begins treating the HTs as completely >> independent cpus. >> >> Try changing “-bind-to core” to “-bind-to hwthread -use-hwthread-cpus” >> and see if that works >> >> I have and the binding is wrong. For example, I got this output >> >> rank 0 @ compute-1-30.local 0, >> rank 1 @ compute-1-30.local 16, >> >> Which means that two ranks have been bound to the same physical core >> (logical cores 0 and 16 are two HTs of the same core). If I use --bind-to >> core, I get the following correct binding >> >> rank 0 @ compute-1-30.local 0, 16, >> >> The problem is many other ranks get bad binding with 'rank XXX is not >> bound (or bound to all available processors)' warning. >> >> But I think I was not entirely correct saying that 1.10.1rc1 did not fix >> things. It still might have improved something, but not everything. >> Consider this job: >> >> SLURM_JOB_CPUS_PER_NODE='5,4,6,5(x2),7,5,9,5,7,6' >> SLURM_JOB_NODELIST='c8-[31,34],c9-[30-32,35-36],c10-[31-34]' >> >> If I run 32 tasks as follows (with 1.10.1rc1) >> >> mpirun --hetero-nodes --report-bindings --bind-to core -np 32 ./affinity >> >> I get the following error: >> >> -------------------------------------------------------------------------- >> A request was made to bind to that would result in binding more >> processes than cpus on a resource: >> >> Bind to: CORE >> Node: c9-31 >> #processes: 2 >> #cpus: 1 >> >> You can override this protection by adding the "overload-allowed" >> option to your binding directive. >> -------------------------------------------------------------------------- >> >> >> If I now use --bind-to core:overload-allowed, then openmpi starts and >> _most_ of the threads are bound correctly (i.e., map contains two logical >> cores in ALL cases), except this case that required the overload flag: >> >> rank 15 @ compute-9-31.local 1, 17, >> rank 16 @ compute-9-31.local 11, 27, >> rank 17 @ compute-9-31.local 2, 18, >> rank 18 @ compute-9-31.local 12, 28, >> rank 19 @ compute-9-31.local 1, 17, >> >> Note pair 1,17 is used twice. The original SLURM delivered map (no >> binding) on this node is >> >> rank 15 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, 29, >> rank 16 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, 29, >> rank 17 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, 29, >> rank 18 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, 29, >> rank 19 @ compute-9-31.local 1, 2, 11, 12, 13, 17, 18, 27, 28, 29, >> >> Why does openmpi use cores (1,17) twice instead of using core (13,29)? >> Clearly, the original SLURM-delivered map has 5 CPUs included, enough for 5 >> MPI processes. >> >> Cheers, >> >> Marcin >> >> >> >> On Oct 3, 2015, at 7:12 AM, marcin.krotkiewski < >> <javascript:_e(%7B%7D,'cvml','marcin.krotkiew...@gmail.com');> >> marcin.krotkiew...@gmail.com >> <javascript:_e(%7B%7D,'cvml','marcin.krotkiew...@gmail.com');>> wrote: >> >> >> On 10/03/2015 01:06 PM, Ralph Castain wrote: >> >> Thanks Marcin. Looking at this, I’m guessing that Slurm may be treating >> HTs as “cores” - i.e., as independent cpus. Any chance that is true? >> >> Not to the best of my knowledge, and at least not intentionally. SLURM >> starts as many processes as there are physical cores, not threads. To >> verify this, consider this test case: >> >> > > _______________________________________________ > users mailing listus...@open-mpi.org > <javascript:_e(%7B%7D,'cvml','us...@open-mpi.org');> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/10/27790.php > > > > > _______________________________________________ > users mailing listus...@open-mpi.org > <javascript:_e(%7B%7D,'cvml','us...@open-mpi.org');> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/10/27791.php > > > > > _______________________________________________ > users mailing listus...@open-mpi.org > <javascript:_e(%7B%7D,'cvml','us...@open-mpi.org');> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/10/27792.php > > >
