Extra data point if I do: [brockp@nyx5508 34241]$ mpirun --report-bindings --bind-to core hostname -------------------------------------------------------------------------- A request was made to bind to that would result in binding more processes than cpus on a resource:
Bind to: CORE Node: nyx5513 #processes: 2 #cpus: 1 You can override this protection by adding the "overload-allowed" option to your binding directive. -------------------------------------------------------------------------- [brockp@nyx5508 34241]$ mpirun -H nyx5513 uptime 13:01:37 up 31 days, 23:06, 0 users, load average: 10.13, 10.90, 12.38 13:01:37 up 31 days, 23:06, 0 users, load average: 10.13, 10.90, 12.38 [brockp@nyx5508 34241]$ mpirun -H nyx5513 --bind-to core hwloc-bind --get 0x00000010 0x00001000 [brockp@nyx5508 34241]$ cat $PBS_NODEFILE | grep nyx5513 nyx5513 nyx5513 Interesting, if I force bind to core, MPI barfs saying there is only 1 cpu available, PBS says it gave it two, and if I force (this is all inside an interactive job) just on that node hwloc-bind --get I get what I expect, Is there a way to get a map of what MPI thinks it has on each host? Brock Palen www.umich.edu/~brockp CAEN Advanced Computing XSEDE Campus Champion bro...@umich.edu (734)936-1985 On Jun 20, 2014, at 12:38 PM, Brock Palen <bro...@umich.edu> wrote: > I was able to produce it in my test. > > orted affinity set by cpuset: > [root@nyx5874 ~]# hwloc-bind --get --pid 103645 > 0x0000c002 > > This mask (1, 14,15) which is across sockets, matches the cpu set setup by > the batch system. > [root@nyx5874 ~]# cat /dev/cpuset/torque/12719806.nyx.engin.umich.edu/cpus > 1,14-15 > > The ranks though were then all set to the same core: > > [root@nyx5874 ~]# hwloc-bind --get --pid 103871 > 0x00008000 > [root@nyx5874 ~]# hwloc-bind --get --pid 103872 > 0x00008000 > [root@nyx5874 ~]# hwloc-bind --get --pid 103873 > 0x00008000 > > Which is core 15: > > report-bindings gave me: > You can see how a few nodes were bound to all the same core, the last one in > each case. I only gave you the results for the hose nyx5874. > > [nyx5526.engin.umich.edu:23726] MCW rank 0 is not bound (or bound to all > available processors) > [nyx5878.engin.umich.edu:103925] MCW rank 8 is not bound (or bound to all > available processors) > [nyx5533.engin.umich.edu:123988] MCW rank 1 is not bound (or bound to all > available processors) > [nyx5879.engin.umich.edu:102808] MCW rank 9 is not bound (or bound to all > available processors) > [nyx5874.engin.umich.edu:103645] MCW rank 41 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5874.engin.umich.edu:103645] MCW rank 42 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5874.engin.umich.edu:103645] MCW rank 43 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5888.engin.umich.edu:117400] MCW rank 11 is not bound (or bound to all > available processors) > [nyx5786.engin.umich.edu:30004] MCW rank 19 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5786.engin.umich.edu:30004] MCW rank 18 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5594.engin.umich.edu:33884] MCW rank 24 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5594.engin.umich.edu:33884] MCW rank 25 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5594.engin.umich.edu:33884] MCW rank 26 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5798.engin.umich.edu:53026] MCW rank 59 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5798.engin.umich.edu:53026] MCW rank 60 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5798.engin.umich.edu:53026] MCW rank 56 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5798.engin.umich.edu:53026] MCW rank 57 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5798.engin.umich.edu:53026] MCW rank 58 bound to socket 1[core 15[hwt > 0]]: [./././././././.][./././././././B] > [nyx5545.engin.umich.edu:88170] MCW rank 2 is not bound (or bound to all > available processors) > [nyx5613.engin.umich.edu:25229] MCW rank 31 is not bound (or bound to all > available processors) > [nyx5880.engin.umich.edu:01406] MCW rank 10 is not bound (or bound to all > available processors) > [nyx5770.engin.umich.edu:86538] MCW rank 6 is not bound (or bound to all > available processors) > [nyx5613.engin.umich.edu:25228] MCW rank 30 is not bound (or bound to all > available processors) > [nyx5577.engin.umich.edu:65949] MCW rank 4 is not bound (or bound to all > available processors) > [nyx5607.engin.umich.edu:30379] MCW rank 14 is not bound (or bound to all > available processors) > [nyx5544.engin.umich.edu:72960] MCW rank 47 is not bound (or bound to all > available processors) > [nyx5544.engin.umich.edu:72959] MCW rank 46 is not bound (or bound to all > available processors) > [nyx5848.engin.umich.edu:04332] MCW rank 33 is not bound (or bound to all > available processors) > [nyx5848.engin.umich.edu:04333] MCW rank 34 is not bound (or bound to all > available processors) > [nyx5544.engin.umich.edu:72958] MCW rank 45 is not bound (or bound to all > available processors) > [nyx5858.engin.umich.edu:12165] MCW rank 35 is not bound (or bound to all > available processors) > [nyx5607.engin.umich.edu:30380] MCW rank 15 is not bound (or bound to all > available processors) > [nyx5544.engin.umich.edu:72957] MCW rank 44 is not bound (or bound to all > available processors) > [nyx5858.engin.umich.edu:12167] MCW rank 37 is not bound (or bound to all > available processors) > [nyx5870.engin.umich.edu:33811] MCW rank 7 is not bound (or bound to all > available processors) > [nyx5582.engin.umich.edu:81994] MCW rank 5 is not bound (or bound to all > available processors) > [nyx5848.engin.umich.edu:04331] MCW rank 32 is not bound (or bound to all > available processors) > [nyx5557.engin.umich.edu:46654] MCW rank 50 is not bound (or bound to all > available processors) > [nyx5858.engin.umich.edu:12166] MCW rank 36 is not bound (or bound to all > available processors) > [nyx5799.engin.umich.edu:67802] MCW rank 22 is not bound (or bound to all > available processors) > [nyx5799.engin.umich.edu:67803] MCW rank 23 is not bound (or bound to all > available processors) > [nyx5556.engin.umich.edu:50889] MCW rank 3 is not bound (or bound to all > available processors) > [nyx5625.engin.umich.edu:95931] MCW rank 53 is not bound (or bound to all > available processors) > [nyx5625.engin.umich.edu:95930] MCW rank 52 is not bound (or bound to all > available processors) > [nyx5557.engin.umich.edu:46655] MCW rank 51 is not bound (or bound to all > available processors) > [nyx5625.engin.umich.edu:95932] MCW rank 54 is not bound (or bound to all > available processors) > [nyx5625.engin.umich.edu:95933] MCW rank 55 is not bound (or bound to all > available processors) > [nyx5866.engin.umich.edu:16306] MCW rank 40 is not bound (or bound to all > available processors) > [nyx5861.engin.umich.edu:22761] MCW rank 61 is not bound (or bound to all > available processors) > [nyx5861.engin.umich.edu:22762] MCW rank 62 is not bound (or bound to all > available processors) > [nyx5861.engin.umich.edu:22763] MCW rank 63 is not bound (or bound to all > available processors) > [nyx5557.engin.umich.edu:46652] MCW rank 48 is not bound (or bound to all > available processors) > [nyx5557.engin.umich.edu:46653] MCW rank 49 is not bound (or bound to all > available processors) > [nyx5866.engin.umich.edu:16304] MCW rank 38 is not bound (or bound to all > available processors) > [nyx5788.engin.umich.edu:02465] MCW rank 20 is not bound (or bound to all > available processors) > [nyx5597.engin.umich.edu:68071] MCW rank 27 is not bound (or bound to all > available processors) > [nyx5775.engin.umich.edu:27952] MCW rank 17 is not bound (or bound to all > available processors) > [nyx5866.engin.umich.edu:16305] MCW rank 39 is not bound (or bound to all > available processors) > [nyx5788.engin.umich.edu:02466] MCW rank 21 is not bound (or bound to all > available processors) > [nyx5775.engin.umich.edu:27951] MCW rank 16 is not bound (or bound to all > available processors) > [nyx5597.engin.umich.edu:68073] MCW rank 29 is not bound (or bound to all > available processors) > [nyx5597.engin.umich.edu:68072] MCW rank 28 is not bound (or bound to all > available processors) > [nyx5552.engin.umich.edu:30481] MCW rank 12 is not bound (or bound to all > available processors) > [nyx5552.engin.umich.edu:30482] MCW rank 13 is not bound (or bound to all > available processors) > > > Brock Palen > www.umich.edu/~brockp > CAEN Advanced Computing > XSEDE Campus Champion > bro...@umich.edu > (734)936-1985 > > > > On Jun 20, 2014, at 12:20 PM, Brock Palen <bro...@umich.edu> wrote: > >> Got it, >> >> I have the input from the user and am testing it out. >> >> It probably has less todo with torque and more cpuset's, >> >> I'm working on producing it myself also. >> >> Brock Palen >> www.umich.edu/~brockp >> CAEN Advanced Computing >> XSEDE Campus Champion >> bro...@umich.edu >> (734)936-1985 >> >> >> >> On Jun 20, 2014, at 12:18 PM, Ralph Castain <r...@open-mpi.org> wrote: >> >>> Thanks - I'm just trying to reproduce one problem case so I can look at it. >>> Given that I don't have access to a Torque machine, I need to "fake" it. >>> >>> >>> On Jun 20, 2014, at 9:15 AM, Brock Palen <bro...@umich.edu> wrote: >>> >>>> In this case they are a single socket, but as you can see they could be >>>> ether/or depending on the job. >>>> >>>> Brock Palen >>>> www.umich.edu/~brockp >>>> CAEN Advanced Computing >>>> XSEDE Campus Champion >>>> bro...@umich.edu >>>> (734)936-1985 >>>> >>>> >>>> >>>> On Jun 19, 2014, at 2:44 PM, Ralph Castain <r...@open-mpi.org> wrote: >>>> >>>>> Sorry, I should have been clearer - I was asking if cores 8-11 are all on >>>>> one socket, or span multiple sockets >>>>> >>>>> >>>>> On Jun 19, 2014, at 11:36 AM, Brock Palen <bro...@umich.edu> wrote: >>>>> >>>>>> Ralph, >>>>>> >>>>>> It was a large job spread across. Our system allows users to ask for >>>>>> 'procs' which are laid out in any format. >>>>>> >>>>>> The list: >>>>>> >>>>>>> [nyx5406:2][nyx5427:2][nyx5506:2][nyx5311:3] >>>>>>> [nyx5329:4][nyx5398:4][nyx5396:11][nyx5397:11] >>>>>>> [nyx5409:11][nyx5411:11][nyx5412:3] >>>>>> >>>>>> Shows that nyx5406 had 2 cores, nyx5427 also 2, nyx5411 had 11. >>>>>> >>>>>> They could be spread across any number of sockets configuration. We >>>>>> start very lax "user requests X procs" and then the user can request >>>>>> more strict requirements from there. We support mostly serial users, >>>>>> and users can colocate on nodes. >>>>>> >>>>>> That is good to know, I think we would want to turn our default to 'bind >>>>>> to core' except for our few users who use hybrid mode. >>>>>> >>>>>> Our CPU set tells you what cores the job is assigned. So in the problem >>>>>> case provided, the cpuset/cgroup shows only cores 8-11 are available to >>>>>> this job on this node. >>>>>> >>>>>> Brock Palen >>>>>> www.umich.edu/~brockp >>>>>> CAEN Advanced Computing >>>>>> XSEDE Campus Champion >>>>>> bro...@umich.edu >>>>>> (734)936-1985 >>>>>> >>>>>> >>>>>> >>>>>> On Jun 18, 2014, at 11:10 PM, Ralph Castain <r...@open-mpi.org> wrote: >>>>>> >>>>>>> The default binding option depends on the number of procs - it is >>>>>>> bind-to core for np=2, and bind-to socket for np > 2. You never said, >>>>>>> but should I assume you ran 4 ranks? If so, then we should be trying to >>>>>>> bind-to socket. >>>>>>> >>>>>>> I'm not sure what your cpuset is telling us - are you binding us to a >>>>>>> socket? Are some cpus in one socket, and some in another? >>>>>>> >>>>>>> It could be that the cpuset + bind-to socket is resulting in some odd >>>>>>> behavior, but I'd need a little more info to narrow it down. >>>>>>> >>>>>>> >>>>>>> On Jun 18, 2014, at 7:48 PM, Brock Palen <bro...@umich.edu> wrote: >>>>>>> >>>>>>>> I have started using 1.8.1 for some codes (meep in this case) and it >>>>>>>> sometimes works fine, but in a few cases I am seeing ranks being given >>>>>>>> overlapping CPU assignments, not always though. >>>>>>>> >>>>>>>> Example job, default binding options (so by-core right?): >>>>>>>> >>>>>>>> Assigned nodes, the one in question is nyx5398, we use torque CPU >>>>>>>> sets, and use TM to spawn. >>>>>>>> >>>>>>>> [nyx5406:2][nyx5427:2][nyx5506:2][nyx5311:3] >>>>>>>> [nyx5329:4][nyx5398:4][nyx5396:11][nyx5397:11] >>>>>>>> [nyx5409:11][nyx5411:11][nyx5412:3] >>>>>>>> >>>>>>>> [root@nyx5398 ~]# hwloc-bind --get --pid 16065 >>>>>>>> 0x00000200 >>>>>>>> [root@nyx5398 ~]# hwloc-bind --get --pid 16066 >>>>>>>> 0x00000800 >>>>>>>> [root@nyx5398 ~]# hwloc-bind --get --pid 16067 >>>>>>>> 0x00000200 >>>>>>>> [root@nyx5398 ~]# hwloc-bind --get --pid 16068 >>>>>>>> 0x00000800 >>>>>>>> >>>>>>>> [root@nyx5398 ~]# cat >>>>>>>> /dev/cpuset/torque/12703230.nyx.engin.umich.edu/cpus >>>>>>>> 8-11 >>>>>>>> >>>>>>>> So torque claims the CPU set setup for the job has 4 cores, but as you >>>>>>>> can see the ranks were giving identical binding. >>>>>>>> >>>>>>>> I checked the pids they were part of the correct CPU set, I also >>>>>>>> checked, orted: >>>>>>>> >>>>>>>> [root@nyx5398 ~]# hwloc-bind --get --pid 16064 >>>>>>>> 0x00000f00 >>>>>>>> [root@nyx5398 ~]# hwloc-calc --intersect PU 16064 >>>>>>>> ignored unrecognized argument 16064 >>>>>>>> >>>>>>>> [root@nyx5398 ~]# hwloc-calc --intersect PU 0x00000f00 >>>>>>>> 8,9,10,11 >>>>>>>> >>>>>>>> Which is exactly what I would expect. >>>>>>>> >>>>>>>> So ummm, i'm lost why this might happen? What else should I check? >>>>>>>> Like I said not all jobs show this behavior. >>>>>>>> >>>>>>>> Brock Palen >>>>>>>> www.umich.edu/~brockp >>>>>>>> CAEN Advanced Computing >>>>>>>> XSEDE Campus Champion >>>>>>>> bro...@umich.edu >>>>>>>> (734)936-1985 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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/2014/06/24672.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/2014/06/24673.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/2014/06/24675.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/2014/06/24676.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/2014/06/24677.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/2014/06/24678.php >> >
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