No worries about PBS itself - better to allow you to just run this way. Easy to add a switch for this purpose.
For now, just add --oversubscribe to the command line On Jan 31, 2014, at 3:32 PM, Paul Hargrove <phhargr...@lbl.gov> wrote: > Ralph, > > The mods may have been done by the staff at PSC rather than by SGI. > Note the "_psc" suffix: > $ which pbsnodes > /usr/local/packages/torque/2.3.13_psc/bin/pbsnodes > > Their sources appear to be available in the f/s too. > Using "tar -d" to compare that to the pristine torque-2.3.13 tarball show the > following files were modified: > torque-2.3.13/src/resmom/job_func.c > torque-2.3.13/src/resmom/mom_main.c > torque-2.3.13/src/resmom/requests.c > torque-2.3.13/src/resmom/linux/mom_mach.h > torque-2.3.13/src/resmom/linux/mom_mach.c > torque-2.3.13/src/resmom/linux/cpuset.c > torque-2.3.13/src/resmom/start_exec.c > torque-2.3.13/src/scheduler.tcl/pbs_sched.c > torque-2.3.13/src/cmds/qalter.c > torque-2.3.13/src/cmds/qsub.c > torque-2.3.13/src/cmds/qstat.c > torque-2.3.13/src/server/resc_def_all.c > torque-2.3.13/src/server/req_quejob.c > torque-2.3.13/torque.spec > > I'll provide what assistance I can in testing. > That includes providing (off-list) the actual diffs of PSC's torque against > the tarball, if desired. > > In the meantime, since -npernode didn't work, what is the right way to say: > "I have 1 slot but I want to overcommit and run 16 mpi ranks". > > -Paul > > > On Fri, Jan 31, 2014 at 3:20 PM, Ralph Castain <r...@open-mpi.org> wrote: > > On Jan 31, 2014, at 3:13 PM, Paul Hargrove <phhargr...@lbl.gov> wrote: > >> Ralph, >> >> As I said this is NOT a cluster - it is a 4k-core shared memory machine. > > I understood - that wasn't the nature of my question > >> TORQUE is allocating cpus (time-shared mode, IIRC), not nodes. >> So, there is always exactly one line in $PBS_NODESFILE. > > Interesting - because that isn't the standard way Torque behaves. It is > supposed to put one line/slot in the nodefile, each line containing the name > of the node. Clearly, SGI has reconfigured Torque to do something different. > >> >> The system runs as 2 partitions of 2k-cores each. >> So, the contents odf$PBS_NODESFILE has exactly 2 possible values, each 1 >> line. >> >> The values of PBS_PPN and PBS_NCPUS both reflect the size of the allocation. >> >> At a minimum, shouldn't Open MPI be multiplying the lines in $PBS_NODESFILE >> by the value of $PBS_PPN? > > No, as above, that isn't the way Torque generally behaves. It would appear > that we need a "switch" here to handle SGI's modifications. Should be doable > - just haven't had anyone using an SGI machine before :-) > >> >> Additionally, when I try "mpirun -npernode 16 ./ring_c" I am still told >> there are not enough slots. >> Shouldn't that be working with 1 line is $PBS_NODESFILE? >> >> -Paul >> >> >> >> >> On Fri, Jan 31, 2014 at 2:47 PM, Ralph Castain <r...@open-mpi.org> wrote: >> We read the nodes from the PBS_NODEFILE, Paul - can you pass that along? >> >> On Jan 31, 2014, at 2:33 PM, Paul Hargrove <phhargr...@lbl.gov> wrote: >> >>> I am trying to test the trunk on an SGI UV (to validate Nathan's port of >>> btl:vader to SGI's variant of xpmem). >>> >>> At configure time, PBS's TM support was correctly located. >>> >>> My PBS batch script includes >>> #PBS -l ncpus=16 >>> because that is what this installation requires (not nodes, mppnodes, or >>> anything like that). >>> One is allocating cpus on a large shared-memory machine, not a set of nodes >>> in a cluster. >>> >>> However, this appears to be causing mpirun to think I have just 1 slot: >>> >>> + mpirun -np 2 ./ring_c >>> -------------------------------------------------------------------------- >>> There are not enough slots available in the system to satisfy the 2 slots >>> that were requested by the application: >>> ./ring_c >>> >>> Either request fewer slots for your application, or make more slots >>> available >>> for use. >>> -------------------------------------------------------------------------- >>> >>> In case they contain useful info, here are the PBS env vars in the job: >>> >>> PBS_HT_NCPUS=32 >>> PBS_VERSION=TORQUE-2.3.13 >>> PBS_JOBNAME=qs >>> PBS_ENVIRONMENT=PBS_BATCH >>> PBS_HOME=/var/spool/torque >>> PBS_O_WORKDIR=/usr/users/6/hargrove/SCRATCH/OMPI/openmpi-trunk-linux-x86_64-uv-trunk/BLD/examples >>> PBS_PPN=16 >>> PBS_TASKNUM=1 >>> PBS_O_HOME=/usr/users/6/hargrove >>> PBS_MOMPORT=15003 >>> PBS_O_QUEUE=debug >>> PBS_O_LOGNAME=hargrove >>> PBS_O_LANG=en_US.UTF-8 >>> PBS_JOBCOOKIE=9EEF5DF75FA705A241FEF66EDFE01C5B >>> PBS_NODENUM=0 >>> PBS_O_SHELL=/usr/psc/shells/bash >>> PBS_SERVER=tg-login1.blacklight.psc.teragrid.org >>> PBS_JOBID=314827.tg-login1.blacklight.psc.teragrid.org >>> PBS_NCPUS=16 >>> PBS_O_HOST=tg-login1.blacklight.psc.teragrid.org >>> PBS_VNODENUM=0 >>> PBS_QUEUE=debug_r1 >>> PBS_O_MAIL=/var/mail/hargrove >>> PBS_NODEFILE=/var/spool/torque/aux//314827.tg-login1.blacklight.psc.teragrid.org >>> PBS_O_PATH=[...removed...] >>> >>> If any additional info is needed to help make mpirun "just work", please >>> let me know. >>> >>> However, at this point I am mostly interested in any work-arounds that will >>> let me run something other than a singleton on this system. >>> >>> -Paul >>> >>> -- >>> Paul H. Hargrove phhargr...@lbl.gov >>> Future Technologies Group >>> Computer and Data Sciences Department Tel: +1-510-495-2352 >>> Lawrence Berkeley National Laboratory Fax: +1-510-486-6900 >>> _______________________________________________ >>> devel mailing list >>> de...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/devel >> >> >> _______________________________________________ >> devel mailing list >> de...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/devel >> >> >> >> -- >> Paul H. Hargrove phhargr...@lbl.gov >> Future Technologies Group >> Computer and Data Sciences Department Tel: +1-510-495-2352 >> Lawrence Berkeley National Laboratory Fax: +1-510-486-6900 >> _______________________________________________ >> devel mailing list >> de...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/devel > > > _______________________________________________ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel > > > > -- > Paul H. Hargrove phhargr...@lbl.gov > Future Technologies Group > Computer and Data Sciences Department Tel: +1-510-495-2352 > Lawrence Berkeley National Laboratory Fax: +1-510-486-6900 > _______________________________________________ > devel mailing list > de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/devel
