I think I begin to grok at least part of the problem. If you are assigning different cpus on each node, then you'll need to tell us that by setting --hetero-nodes otherwise we won't have any way to report that back to mpirun for its binding calculation.
Otherwise, we expect that the cpuset of the first node we launch a daemon onto (or where mpirun is executing, if we are only launching local to mpirun) accurately represents the cpuset on every node in the allocation. We still might well have a bug in our binding computation - but the above will definitely impact what you said the user did. On Jun 20, 2014, at 10:06 AM, Brock Palen <bro...@umich.edu> wrote: > 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 >>> >> > > _______________________________________________ > 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/2014/06/24681.php
