Gilles,Yes, it seemed that all was fine with binding in the patched 1.10.1rc1 - thank you. Eagerly waiting for the other patches, let me know and I will test them later this week.
Marcin On 10/06/2015 12:09 PM, Gilles Gouaillardet wrote:
Marcin,my understanding is that in this case, patched v1.10.1rc1 is working just fine.am I right ? I prepared two patchesone 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 policyI will finalize them tomorrow hopefully Cheers, GillesOn Tuesday, October 6, 2015, marcin.krotkiewski <marcin.krotkiew...@gmail.com <mailto:marcin.krotkiew...@gmail.com>> wrote:Hi, Gillesyou 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 mpirunIt 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. MarcinCheers, 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 <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. RalphOn 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 RalphOn 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 <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 <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 worksI 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, MarcinOn Oct 3, 2015, at 7:12 AM, marcin.krotkiewski <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 list us...@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 list us...@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 list us...@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_______________________________________________ users mailing list 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/2015/10/27814.php
