Hi Gilles, Ralph, Okay, it definitely seems to be due to the cpuset having only one of the hyperthreads of each physical core:
[13:02:13 root@r60:4363542.r-man2] # echo 0-15 > cpuset.cpus 13:03 bjm900@r60 ~ > cat /cgroup/cpuset/pbspro/4363542.r-man2/cpuset.cpus 0-15 13:03 bjm900@r60 ~ > /apps/openmpi/1.10.2/bin/mpirun hostname -------------------------------------------------------------------------- A request for multiple cpus-per-proc was given, but a directive was also give to map to an object level that has less cpus than requested ones: #cpus-per-proc: 1 number of cpus: 0 map-by: BYCORE:NOOVERSUBSCRIBE Please specify a mapping level that has more cpus, or else let us define a default mapping that will allow multiple cpus-per-proc. -------------------------------------------------------------------------- [13:03:43 root@r60:4363542.r-man2] # echo 0-31 > cpuset.cpus 13:03 bjm900@r60 ~ > cat /cgroup/cpuset/pbspro/4363542.r-man2/cpuset.cpus 0-31 13:04 bjm900@r60 ~ > /apps/openmpi/1.10.2/bin/mpirun hostname <...hostnames...> Cheers, Ben -----Original Message----- From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Ben Menadue Sent: Friday, 29 January 2016 1:01 PM To: 'Open MPI Users' <us...@open-mpi.org> Subject: Re: [OMPI users] Any changes to rmaps in 1.10.2? Hi Gilles, > with respect to PBS, are both OpenMPI built the same way ? > e.g. configure --with-tm=/opt/pbs/default or something similar Both are built against TM explicitly using the --with-tm option. > you ran run > mpirun --mca plm_base_verbose 100 --mca ess_base_verbose 100 --mca ras_base_verbose 100 hostname > and you should see the "tm" module in the logs. Yes, it appears to use TM from what I can see. Outputs from 1.10.0 and 1.10.2 are attached from inside the same job - they look identical (apart from the pids), except at the very end where 1.10.2 errors out while 1.10.1 continues. > i noticed you run > mpirun -np 2 ... > is there any reason why you explicitly request 2 tasks ? The "-np 2" is because that's what I was using to benchmark the install (osu_bibw) and I just copied it over from when I realised it wasn't even starting. But it does the same regardless of whether I specify the number of processes or not (without it gets the number of tasks from PBS). > by any chance, is hyperthreading enabled on your compute node ? > /* if yes, that means all cores are in the cpuset, but with only one thread per core */ The nodes are 2 x 8-core sockets with hyper-threading on, and you can chose whether to use the extra hardware threads when submitting the job. If you want them, your cgroup includes both threads on each core (e.g. 0-31), otherwise only one thread (e.g. 0-15) (cores 16-32 are the thread siblings of cores 0-15). For reference, the PBS job I was using above had ncpus=32,mem=16G, which becomes select=2:ncpus=16:mpiprocs=16:mem=8589934592b under the hood with a cpuset containing cores 0-15 on each of the two nodes. Interestingly, if I use a cpuset containing both threads of each physical core (i.e. ask for hyperthreading on job submission), then it runs fine under 1.10.2. Cheers, Ben -----Original Message----- From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gilles Gouaillardet Sent: Friday, 29 January 2016 11:07 AM To: Open MPI Users <us...@open-mpi.org> Subject: Re: [OMPI users] Any changes to rmaps in 1.10.2? Ben, that is not needed if you submit with qsub -l nodes=1:ppn=2 do you observe the same behavior without -np 2 ? Cheers, Gilles On 1/28/2016 7:57 AM, Ben Menadue wrote: > Hi, > > Were there any changes to rmaps in going to 1.10.2? An > otherwise-identical setup that worked in 1.10.0 fails to launch in > 1.10.2, complaining that there's no CPUs available in a socket... > > With 1.10.0: > > $ /apps/openmpi/1.10.0/bin/mpirun -np 2 -mca rmaps_base_verbose 1000 > hostname [r47:18709] mca: base: components_register: registering rmaps > components [r47:18709] mca: base: components_register: found loaded > component resilient [r47:18709] mca: base: components_register: > component resilient register function successful [r47:18709] mca: > base: components_register: found loaded component rank_file > [r47:18709] mca: base: components_register: component rank_file > register function successful [r47:18709] mca: base: > components_register: found loaded component staged [r47:18709] mca: > base: components_register: component staged has no register or open > function [r47:18709] mca: base: components_register: found loaded > component ppr [r47:18709] mca: base: components_register: component > ppr register function successful [r47:18709] mca: base: > components_register: found loaded component seq [r47:18709] mca: base: > components_register: component seq register function successful > [r47:18709] mca: base: components_register: found loaded component > round_robin [r47:18709] mca: base: components_register: component > round_robin register function successful [r47:18709] mca: base: > components_register: found loaded component mindist [r47:18709] mca: > base: components_register: component mindist register function > successful [r47:18709] [[63529,0],0] rmaps:base set policy with core > [r47:18709] mca: base: components_open: opening rmaps components > [r47:18709] mca: base: components_open: found loaded component > resilient [r47:18709] mca: base: components_open: component resilient > open function successful [r47:18709] mca: base: components_open: found > loaded component rank_file [r47:18709] mca: base: components_open: > component rank_file open function successful [r47:18709] mca: base: > components_open: found loaded component staged [r47:18709] mca: base: > components_open: component staged open function successful [r47:18709] > mca: base: components_open: found loaded component ppr [r47:18709] > mca: base: components_open: component ppr open function successful > [r47:18709] mca: base: components_open: found loaded component seq > [r47:18709] mca: base: components_open: component seq open function > successful [r47:18709] mca: base: components_open: found loaded > component round_robin [r47:18709] mca: base: components_open: > component round_robin open function successful [r47:18709] mca: base: > components_open: found loaded component mindist [r47:18709] mca: base: > components_open: component mindist open function successful > [r47:18709] mca:rmaps:select: checking available component resilient > [r47:18709] mca:rmaps:select: Querying component [resilient] > [r47:18709] mca:rmaps:select: checking available component rank_file > [r47:18709] mca:rmaps:select: Querying component [rank_file] > [r47:18709] mca:rmaps:select: checking available component staged > [r47:18709] mca:rmaps:select: Querying component [staged] [r47:18709] > mca:rmaps:select: checking available component ppr [r47:18709] > mca:rmaps:select: Querying component [ppr] [r47:18709] > mca:rmaps:select: checking available component seq [r47:18709] > mca:rmaps:select: Querying component [seq] [r47:18709] > mca:rmaps:select: checking available component round_robin [r47:18709] > mca:rmaps:select: Querying component [round_robin] [r47:18709] > mca:rmaps:select: checking available component mindist [r47:18709] > mca:rmaps:select: Querying component [mindist] [r47:18709] > [[63529,0],0]: Final mapper priorities > [r47:18709] Mapper: ppr Priority: 90 > [r47:18709] Mapper: seq Priority: 60 > [r47:18709] Mapper: resilient Priority: 40 > [r47:18709] Mapper: mindist Priority: 20 > [r47:18709] Mapper: round_robin Priority: 10 > [r47:18709] Mapper: staged Priority: 5 > [r47:18709] Mapper: rank_file Priority: 0 > [r47:18709] mca:rmaps: mapping job [63529,1] [r47:18709] mca:rmaps: > creating new map for job [63529,1] [r47:18709] mca:rmaps: nprocs 2 > [r47:18709] mca:rmaps mapping given - using default [r47:18709] > mca:rmaps:ppr: job [63529,1] not using ppr mapper [r47:18709] > mca:rmaps:seq: job [63529,1] not using seq mapper [r47:18709] > mca:rmaps:resilient: cannot perform initial map of job [63529,1] > - no fault groups > [r47:18709] mca:rmaps:mindist: job [63529,1] not using mindist mapper > [r47:18709] mca:rmaps:rr: mapping job [63529,1] [r47:18709] AVAILABLE > NODES FOR MAPPING: > [r47:18709] node: r47 daemon: 0 > [r47:18709] node: r57 daemon: 1 > [r47:18709] node: r58 daemon: 2 > [r47:18709] node: r59 daemon: 3 > [r47:18709] mca:rmaps:rr: mapping no-span by Core for job [63529,1] > slots 64 num_procs 2 [r47:18709] mca:rmaps:rr: found 16 Core objects > on node r47 [r47:18709] mca:rmaps:rr: assigning proc to object 0 > [r47:18709] mca:rmaps:rr: assigning proc to object 1 [r47:18709] > mca:rmaps: computing ranks by core for job [63529,1] [r47:18709] > mca:rmaps:rank_by: found 16 objects on node r47 with 2 procs > [r47:18709] mca:rmaps:rank_by: assigned rank 0 [r47:18709] > mca:rmaps:rank_by: assigned rank 1 [r47:18709] mca:rmaps:rank_by: > found 16 objects on node r57 with 0 procs [r47:18709] > mca:rmaps:rank_by: found 16 objects on node r58 with 0 procs > [r47:18709] mca:rmaps:rank_by: found 16 objects on node r59 with 0 > procs [r47:18709] mca:rmaps: compute bindings for job [63529,1] with > policy CORE[4008] [r47:18709] mca:rmaps: bindings for job [63529,1] - > bind in place [r47:18709] mca:rmaps: bind in place for job [63529,1] > with bindings CORE [r47:18709] [[63529,0],0] reset_usage: node r47 has > 2 procs on it [r47:18709] [[63529,0],0] reset_usage: ignoring proc > [[63529,1],0] [r47:18709] [[63529,0],0] reset_usage: ignoring proc > [[63529,1],1] [r47:18709] BINDING PROC [[63529,1],0] TO Core NUMBER 0 > [r47:18709] [[63529,0],0] BOUND PROC [[63529,1],0] TO 0[Core:0] on > node r47 [r47:18709] BINDING PROC [[63529,1],1] TO Core NUMBER 1 > [r47:18709] [[63529,0],0] BOUND PROC [[63529,1],1] TO 1[Core:1] on > node r47 > r47 > r47 > [r47:18709] mca: base: close: component resilient closed [r47:18709] > mca: base: close: unloading component resilient [r47:18709] mca: base: > close: component rank_file closed [r47:18709] mca: base: close: > unloading component rank_file [r47:18709] mca: base: close: component > staged closed [r47:18709] mca: base: close: unloading component staged > [r47:18709] mca: base: close: component ppr closed [r47:18709] mca: > base: close: unloading component ppr [r47:18709] mca: base: close: > component seq closed [r47:18709] mca: base: close: unloading component > seq [r47:18709] mca: base: close: component round_robin closed > [r47:18709] mca: base: close: unloading component round_robin > [r47:18709] mca: base: close: component mindist closed [r47:18709] > mca: base: close: unloading component mindist > > With 1.10.2: > > $ /apps/openmpi/1.10.2/bin/mpirun -np 2 -mca rmaps_base_verbose 1000 > hostname [r47:18733] mca: base: components_register: registering rmaps > components [r47:18733] mca: base: components_register: found loaded > component resilient [r47:18733] mca: base: components_register: > component resilient register function successful [r47:18733] mca: > base: components_register: found loaded component rank_file > [r47:18733] mca: base: components_register: component rank_file > register function successful [r47:18733] mca: base: > components_register: found loaded component staged [r47:18733] mca: > base: components_register: component staged has no register or open > function [r47:18733] mca: base: components_register: found loaded > component ppr [r47:18733] mca: base: components_register: component > ppr register function successful [r47:18733] mca: base: > components_register: found loaded component seq [r47:18733] mca: base: > components_register: component seq register function successful > [r47:18733] mca: base: components_register: found loaded component > round_robin [r47:18733] mca: base: components_register: component > round_robin register function successful [r47:18733] mca: base: > components_register: found loaded component mindist [r47:18733] mca: > base: components_register: component mindist register function > successful [r47:18733] [[63505,0],0] rmaps:base set policy with core > [r47:18733] mca: base: components_open: opening rmaps components > [r47:18733] mca: base: components_open: found loaded component > resilient [r47:18733] mca: base: components_open: component resilient > open function successful [r47:18733] mca: base: components_open: found > loaded component rank_file [r47:18733] mca: base: components_open: > component rank_file open function successful [r47:18733] mca: base: > components_open: found loaded component staged [r47:18733] mca: base: > components_open: component staged open function successful [r47:18733] > mca: base: components_open: found loaded component ppr [r47:18733] > mca: base: components_open: component ppr open function successful > [r47:18733] mca: base: components_open: found loaded component seq > [r47:18733] mca: base: components_open: component seq open function > successful [r47:18733] mca: base: components_open: found loaded > component round_robin [r47:18733] mca: base: components_open: > component round_robin open function successful [r47:18733] mca: base: > components_open: found loaded component mindist [r47:18733] mca: base: > components_open: component mindist open function successful > [r47:18733] mca:rmaps:select: checking available component resilient > [r47:18733] mca:rmaps:select: Querying component [resilient] > [r47:18733] mca:rmaps:select: checking available component rank_file > [r47:18733] mca:rmaps:select: Querying component [rank_file] > [r47:18733] mca:rmaps:select: checking available component staged > [r47:18733] mca:rmaps:select: Querying component [staged] [r47:18733] > mca:rmaps:select: checking available component ppr [r47:18733] > mca:rmaps:select: Querying component [ppr] [r47:18733] > mca:rmaps:select: checking available component seq [r47:18733] > mca:rmaps:select: Querying component [seq] [r47:18733] > mca:rmaps:select: checking available component round_robin [r47:18733] > mca:rmaps:select: Querying component [round_robin] [r47:18733] > mca:rmaps:select: checking available component mindist [r47:18733] > mca:rmaps:select: Querying component [mindist] [r47:18733] > [[63505,0],0]: Final mapper priorities > [r47:18733] Mapper: ppr Priority: 90 > [r47:18733] Mapper: seq Priority: 60 > [r47:18733] Mapper: resilient Priority: 40 > [r47:18733] Mapper: mindist Priority: 20 > [r47:18733] Mapper: round_robin Priority: 10 > [r47:18733] Mapper: staged Priority: 5 > [r47:18733] Mapper: rank_file Priority: 0 > [r47:18733] mca:rmaps: mapping job [63505,1] [r47:18733] mca:rmaps: > creating new map for job [63505,1] [r47:18733] mca:rmaps: nprocs 2 > [r47:18733] mca:rmaps mapping given - using default [r47:18733] > mca:rmaps:ppr: job [63505,1] not using ppr mapper [r47:18733] > mca:rmaps:seq: job [63505,1] not using seq mapper [r47:18733] > mca:rmaps:resilient: cannot perform initial map of job [63505,1] > - no fault groups > [r47:18733] mca:rmaps:mindist: job [63505,1] not using mindist mapper > [r47:18733] mca:rmaps:rr: mapping job [63505,1] [r47:18733] AVAILABLE > NODES FOR MAPPING: > [r47:18733] node: r47 daemon: 0 > [r47:18733] node: r57 daemon: 1 > [r47:18733] node: r58 daemon: 2 > [r47:18733] node: r59 daemon: 3 > [r47:18733] mca:rmaps:rr: mapping no-span by Core for job [63505,1] > slots 64 num_procs 2 [r47:18733] mca:rmaps:rr: found 16 Core objects > on node r47 [r47:18733] mca:rmaps:rr: assigning proc to object 0 > ---------------------------------------------------------------------- > ---- A request for multiple cpus-per-proc was given, but a directive > was also give to map to an object level that has less cpus than > requested ones: > > #cpus-per-proc: 1 > number of cpus: 0 > map-by: BYCORE:NOOVERSUBSCRIBE > > Please specify a mapping level that has more cpus, or else let us > define a default mapping that will allow multiple cpus-per-proc. > ---------------------------------------------------------------------- > ---- [r47:18733] mca: base: close: component resilient closed > [r47:18733] mca: base: close: unloading component resilient > [r47:18733] mca: base: close: component rank_file closed [r47:18733] > mca: base: close: unloading component rank_file [r47:18733] mca: base: > close: component staged closed [r47:18733] mca: base: close: unloading > component staged [r47:18733] mca: base: close: component ppr closed > [r47:18733] mca: base: close: unloading component ppr [r47:18733] mca: > base: close: component seq closed [r47:18733] mca: base: close: > unloading component seq [r47:18733] mca: base: close: component > round_robin closed [r47:18733] mca: base: close: unloading component > round_robin [r47:18733] mca: base: close: component mindist closed > [r47:18733] mca: base: close: unloading component mindist > > There are both in the same PBS Pro job. And the cpuset definitely has > all cores available: > > $ cat /cgroup/cpuset/pbspro/4347646.r-man2/cpuset.cpus > 0-15 > > Is there something here I'm missing? > > Cheers, > Ben > > > _______________________________________________ > 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/2016/01/28393.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/2016/01/28400.php
