Yes, I'm able to reproduce it on a single node as well. Actually, even on just a single CPU (and -np 1) - won't let me launch unless both threads of that core are in the cgroup.
-----Original Message----- From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Gilles Gouaillardet Sent: Friday, 29 January 2016 1:33 PM To: Open MPI Users <us...@open-mpi.org> Subject: Re: [OMPI users] Any changes to rmaps in 1.10.2? I was able to reproduce the issue on one node with a cpuset manually set. fwiw, i cannot reproduce the issue using taskset instead of cpuset (!) Cheers, Gilles On 1/29/2016 11:08 AM, Ben Menadue wrote: > 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 > > _______________________________________________ > 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/2016/01/28402.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/2016/01/28404.php
