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> > 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 >>> <marcin.krotkiew...@gmail.com <mailto: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: >>> >>> SLURM_JOB_CPUS_PER_NODE='6,8(x2),10' >>> SLURM_JOB_NODELIST='c1-[30-31],c2-[32,34]' >>> >>> If I now execute only one mpi process WITH NO BINDING, it will go onto >>> c1-30 and should have a map with 6 CPUs (12 hw threads). I run >>> >>> mpirun --bind-to none -np 1 ./affinity >>> rank 0 @ compute-1-30.local 0, 1, 3, 4, 5, 6, 16, 17, 19, 20, 21, 22, >>> >>> I have attached the affinity.c program FYI. Clearly, sched_getaffinity in >>> my test code returns the correct map. >>> >>> Now if I try to start all 32 processes in this example (still no binding): >>> >>> rank 0 @ compute-1-30.local 0, 1, 3, 4, 5, 6, 16, 17, 19, 20, 21, 22, >>> rank 1 @ compute-1-30.local 0, 1, 3, 4, 5, 6, 16, 17, 19, 20, 21, 22, >>> rank 10 @ compute-1-31.local 2, 3, 7, 11, 12, 13, 14, 15, 18, 19, 23, 27, >>> 28, 29, 30, 31, >>> rank 11 @ compute-1-31.local 2, 3, 7, 11, 12, 13, 14, 15, 18, 19, 23, 27, >>> 28, 29, 30, 31, >>> rank 12 @ compute-1-31.local 2, 3, 7, 11, 12, 13, 14, 15, 18, 19, 23, 27, >>> 28, 29, 30, 31, >>> rank 13 @ compute-1-31.local 2, 3, 7, 11, 12, 13, 14, 15, 18, 19, 23, 27, >>> 28, 29, 30, 31, >>> rank 6 @ compute-1-31.local 2, 3, 7, 11, 12, 13, 14, 15, 18, 19, 23, 27, >>> 28, 29, 30, 31, >>> rank 2 @ compute-1-30.local 0, 1, 3, 4, 5, 6, 16, 17, 19, 20, 21, 22, >>> rank 7 @ compute-1-31.local 2, 3, 7, 11, 12, 13, 14, 15, 18, 19, 23, 27, >>> 28, 29, 30, 31, >>> rank 8 @ compute-1-31.local 2, 3, 7, 11, 12, 13, 14, 15, 18, 19, 23, 27, >>> 28, 29, 30, 31, >>> rank 3 @ compute-1-30.local 0, 1, 3, 4, 5, 6, 16, 17, 19, 20, 21, 22, >>> rank 14 @ compute-2-32.local 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, >>> 27, 28, 29, 30, >>> rank 4 @ compute-1-30.local 0, 1, 3, 4, 5, 6, 16, 17, 19, 20, 21, 22, >>> rank 15 @ compute-2-32.local 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, >>> 27, 28, 29, 30, >>> rank 9 @ compute-1-31.local 2, 3, 7, 11, 12, 13, 14, 15, 18, 19, 23, 27, >>> 28, 29, 30, 31, >>> rank 5 @ compute-1-30.local 0, 1, 3, 4, 5, 6, 16, 17, 19, 20, 21, 22, >>> rank 16 @ compute-2-32.local 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, >>> 27, 28, 29, 30, >>> rank 17 @ compute-2-32.local 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, >>> 27, 28, 29, 30, >>> rank 29 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 30 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 18 @ compute-2-32.local 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, >>> 27, 28, 29, 30, >>> rank 19 @ compute-2-32.local 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, >>> 27, 28, 29, 30, >>> rank 31 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 20 @ compute-2-32.local 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, >>> 27, 28, 29, 30, >>> rank 22 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 21 @ compute-2-32.local 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, >>> 27, 28, 29, 30, >>> rank 23 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 24 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 25 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 26 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 27 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> rank 28 @ compute-2-34.local 0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, >>> 19, 20, 21, 22, 23, 30, 31, >>> >>> >>> Still looks ok to me. If I now turn the binding on, openmpi fails: >>> >>> >>> -------------------------------------------------------------------------- >>> A request was made to bind to that would result in binding more >>> processes than cpus on a resource: >>> >>> Bind to: CORE >>> Node: c1-31 >>> #processes: 2 >>> #cpus: 1 >>> >>> You can override this protection by adding the "overload-allowed" >>> option to your binding directive. >>> -------------------------------------------------------------------------- >>> >>> The above tests were done with 1.10.1rc1, so it does not fix the problem. >>> >>> Marcin >>> >>> >>>> I’m wondering because bind-to core will attempt to bind your proc to both >>>> HTs on the core. For some reason, we thought that 8.24 were HTs on the >>>> same core, which is why we tried to bind to that pair of HTs. We got an >>>> error because HT #24 was not allocated to us on node c6, but HT #8 was. >>>> >>>> >>>>> On Oct 3, 2015, at 2:43 AM, marcin.krotkiewski >>>>> <marcin.krotkiew...@gmail.com <mailto:marcin.krotkiew...@gmail.com>> >>>>> wrote: >>>>> >>>>> Hi, Ralph, >>>>> >>>>> I submit my slurm job as follows >>>>> >>>>> salloc --ntasks=64 --mem-per-cpu=2G --time=1:0:0 >>>>> >>>>> Effectively, the allocated CPU cores are spread amount many cluster >>>>> nodes. SLURM uses cgroups to limit the CPU cores available for mpi >>>>> processes running on a given cluster node. Compute nodes are 2-socket, >>>>> 8-core E5-2670 systems with HyperThreading on >>>>> >>>>> node 0 cpus: 0 1 2 3 4 5 6 7 16 17 18 19 20 21 22 23 >>>>> node 1 cpus: 8 9 10 11 12 13 14 15 24 25 26 27 28 29 30 31 >>>>> node distances: >>>>> node 0 1 >>>>> 0: 10 21 >>>>> 1: 21 10 >>>>> >>>>> I run MPI program with command >>>>> >>>>> mpirun --report-bindings --bind-to core -np 64 ./affinity >>>>> >>>>> The program simply runs sched_getaffinity for each process and prints out >>>>> the result. >>>>> >>>>> ----------- >>>>> TEST RUN 1 >>>>> ----------- >>>>> For this particular job the problem is more severe: openmpi fails to run >>>>> at all with error >>>>> >>>>> -------------------------------------------------------------------------- >>>>> Open MPI tried to bind a new process, but something went wrong. The >>>>> process was killed without launching the target application. Your job >>>>> will now abort. >>>>> >>>>> Local host: c6-6 >>>>> Application name: ./affinity >>>>> Error message: hwloc_set_cpubind returned "Error" for bitmap "8,24" >>>>> Location: odls_default_module.c:551 >>>>> -------------------------------------------------------------------------- >>>>> >>>>> This is SLURM environment variables: >>>>> >>>>> SLURM_JOBID=12712225 >>>>> SLURM_JOB_CPUS_PER_NODE='3(x2),2,1(x3),2(x2),1,3(x3),5,1,4,1,3,2,3,7,1,5,6,1' >>>>> SLURM_JOB_ID=12712225 >>>>> SLURM_JOB_NODELIST='c6-[3,6-8,12,14,17,22-23],c8-[4,7,9,17,20,28],c15-[5,10,18,20,22-24,28],c16-11' >>>>> SLURM_JOB_NUM_NODES=24 >>>>> SLURM_JOB_PARTITION=normal >>>>> SLURM_MEM_PER_CPU=2048 >>>>> SLURM_NNODES=24 >>>>> SLURM_NODELIST='c6-[3,6-8,12,14,17,22-23],c8-[4,7,9,17,20,28],c15-[5,10,18,20,22-24,28],c16-11' >>>>> SLURM_NODE_ALIASES='(null)' >>>>> SLURM_NPROCS=64 >>>>> SLURM_NTASKS=64 >>>>> SLURM_SUBMIT_DIR=/cluster/home/marcink >>>>> SLURM_SUBMIT_HOST=login-0-2.local >>>>> SLURM_TASKS_PER_NODE='3(x2),2,1(x3),2(x2),1,3(x3),5,1,4,1,3,2,3,7,1,5,6,1' >>>>> >>>>> There is also a lot of warnings like >>>>> >>>>> [compute-6-6.local:20158] MCW rank 4 is not bound (or bound to all >>>>> available processors) >>>>> >>>>> >>>>> ----------- >>>>> TEST RUN 2 >>>>> ----------- >>>>> >>>>> In another allocation I got a different error >>>>> >>>>> -------------------------------------------------------------------------- >>>>> A request was made to bind to that would result in binding more >>>>> processes than cpus on a resource: >>>>> >>>>> Bind to: CORE >>>>> Node: c6-19 >>>>> #processes: 2 >>>>> #cpus: 1 >>>>> >>>>> You can override this protection by adding the "overload-allowed" >>>>> option to your binding directive. >>>>> -------------------------------------------------------------------------- >>>>> >>>>> and the allocation was the following >>>>> >>>>> SLURM_JOBID=12712250 >>>>> SLURM_JOB_CPUS_PER_NODE='3(x2),2,1,15,1,3,16,2,1,3(x2),2,5,4' >>>>> SLURM_JOB_ID=12712250 >>>>> SLURM_JOB_NODELIST='c6-[3,6-8,12,14,17,19,22-23],c8-[4,7,9,17,28]' >>>>> SLURM_JOB_NUM_NODES=15 >>>>> SLURM_JOB_PARTITION=normal >>>>> SLURM_MEM_PER_CPU=2048 >>>>> SLURM_NNODES=15 >>>>> SLURM_NODELIST='c6-[3,6-8,12,14,17,19,22-23],c8-[4,7,9,17,28]' >>>>> SLURM_NODE_ALIASES='(null)' >>>>> SLURM_NPROCS=64 >>>>> SLURM_NTASKS=64 >>>>> SLURM_SUBMIT_DIR=/cluster/home/marcink >>>>> SLURM_SUBMIT_HOST=login-0-2.local >>>>> SLURM_TASKS_PER_NODE='3(x2),2,1,15,1,3,16,2,1,3(x2),2,5,4' >>>>> >>>>> >>>>> If in this case I run on only 32 cores >>>>> >>>>> mpirun --report-bindings --bind-to core -np 32 ./affinity >>>>> >>>>> the process starts, but I get the original binding problem: >>>>> >>>>> [compute-6-8.local:31414] MCW rank 8 is not bound (or bound to all >>>>> available processors) >>>>> >>>>> Running with --hetero-nodes yields exactly the same results >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Hope the above is useful. The problem with binding under SLURM with CPU >>>>> cores spread over nodes seems to be very reproducible. It is actually >>>>> very often that OpenMPI dies with some error like above. These tests were >>>>> run with openmpi-1.8.8 and 1.10.0, both giving same results. >>>>> >>>>> One more suggestion. The warning message (MCW rank 8 is not bound...) is >>>>> ONLY displayed when I use --report-bindings. It is never shown if I leave >>>>> out this option, and although the binding is wrong the user is not >>>>> notified. I think it would be better to show this warning in all cases >>>>> binding fails. >>>>> >>>>> Let me know if you need more information. I can help to debug this - it >>>>> is a rather crucial issue. >>>>> >>>>> Thanks! >>>>> >>>>> Marcin >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 10/02/2015 11:49 PM, Ralph Castain wrote: >>>>>> Can you please send me the allocation request you made (so I can see >>>>>> what you specified on the cmd line), and the mpirun cmd line? >>>>>> >>>>>> Thanks >>>>>> Ralph >>>>>> >>>>>>> On Oct 2, 2015, at 8:25 AM, Marcin Krotkiewski < >>>>>>> <mailto:marcin.krotkiew...@gmail.com>marcin.krotkiew...@gmail.com >>>>>>> <mailto:marcin.krotkiew...@gmail.com>> wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I fail to make OpenMPI bind to cores correctly when running from within >>>>>>> SLURM-allocated CPU resources spread over a range of compute nodes in >>>>>>> an otherwise homogeneous cluster. I have found this thread >>>>>>> >>>>>>> http://www.open-mpi.org/community/lists/users/2014/06/24682.php >>>>>>> <http://www.open-mpi.org/community/lists/users/2014/06/24682.php> >>>>>>> >>>>>>> and did try to use what Ralph suggested there (--hetero-nodes), but it >>>>>>> does not work (v. 1.10.0). When running with --report-bindings I get >>>>>>> messages like >>>>>>> >>>>>>> [compute-9-11.local:27571] MCW rank 10 is not bound (or bound to all >>>>>>> available processors) >>>>>>> >>>>>>> for all ranks outside of my first physical compute node. Moreover, >>>>>>> everything works as expected if I ask SLURM to assign entire compute >>>>>>> nodes. So it does look like Ralph's diagnose presented in that thread >>>>>>> is correct, just the --hetero-nodes switch does not work for me. >>>>>>> >>>>>>> I have written a short code that uses sched_getaffinity to print the >>>>>>> effective bindings: all MPI ranks except of those on the first node are >>>>>>> bound to all CPU cores allocated by SLURM. >>>>>>> >>>>>>> Do I have to do something except of --hetero-nodes, or is this a >>>>>>> problem that needs further investigation? >>>>>>> >>>>>>> Thanks a lot! >>>>>>> >>>>>>> Marcin >>>>>>> >>>>>>> _______________________________________________ >>>>>>> users mailing list >>>>>>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>>>>>> Link to this post: >>>>>>> http://www.open-mpi.org/community/lists/users/2015/10/27770.php >>>>>>> <http://www.open-mpi.org/community/lists/users/2015/10/27770.php> >>>>>> _______________________________________________ >>>>>> users mailing list >>>>>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>>>>> Link to this post: >>>>>> http://www.open-mpi.org/community/lists/users/2015/10/27774.php >>>>>> <http://www.open-mpi.org/community/lists/users/2015/10/27774.php> >>>>> _______________________________________________ >>>>> users mailing list >>>>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>>>> Link to this post: >>>>> http://www.open-mpi.org/community/lists/users/2015/10/27776.php >>>>> <http://www.open-mpi.org/community/lists/users/2015/10/27776.php> >>>> _______________________________________________ >>>> users mailing list >>>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>>> Subscription: >>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users>http://www.open-mpi.org/mailman/listinfo.cgi/users >>>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>>> Link to this post: >>>> <http://www.open-mpi.org/community/lists/users/2015/10/27778.php>http://www.open-mpi.org/community/lists/users/2015/10/27778.php >>>> <http://www.open-mpi.org/community/lists/users/2015/10/27778.php> >>> >>> <affinity.c>_______________________________________________ >>> users mailing list >>> us...@open-mpi.org <mailto:us...@open-mpi.org> >>> Subscription: >>> <http://www.open-mpi.org/mailman/listinfo.cgi/users>http://www.open-mpi.org/mailman/listinfo.cgi/users >>> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >>> Link to this post: >>> <http://www.open-mpi.org/community/lists/users/2015/10/27781.php>http://www.open-mpi.org/community/lists/users/2015/10/27781.php >>> <http://www.open-mpi.org/community/lists/users/2015/10/27781.php> >> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org <mailto:us...@open-mpi.org> >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> <http://www.open-mpi.org/mailman/listinfo.cgi/users> >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2015/10/27782.php >> <http://www.open-mpi.org/community/lists/users/2015/10/27782.php> > _______________________________________________ > users mailing list > us...@open-mpi.org <mailto:us...@open-mpi.org> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > <http://www.open-mpi.org/mailman/listinfo.cgi/users> > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/10/27783.php > <http://www.open-mpi.org/community/lists/users/2015/10/27783.php>
