Am 03.04.2012 um 16:59 schrieb Eloi Gaudry: > Hi Reuti, > > I configured OpenMPI to support SGE tight integration and used the defined > below PE for submitting the job: > > [16:36][eg@moe:~]$ qconf -sp fill_up > pe_name fill_up > slots 80 > user_lists NONE > xuser_lists NONE > start_proc_args /bin/true > stop_proc_args /bin/true > allocation_rule $fill_up
It should fill a host completely before moving to the next one with this definition. > control_slaves TRUE > job_is_first_task FALSE > urgency_slots min > accounting_summary FALSE > > Here are the allocation info retrieved from `qstat -g t` for the related job: For me the output of `qstat -g t` shows MASTER and SLAVE entries but no variables. Is there any wrapper defined for `qstat` to reformat the output (or a ~/.sge_qstat defined)? And why is "num_proc=0" output everywhere - was it redefined (usually it's a load sensor set to the found cores in the machines and shoudn't be touched by hand making it a consumable complex). -- Reuti > --------------------------------------------------------------------------------- > smp...@barney.fft BIP 0/1/4 0.70 lx-amd64 > hc:num_proc=0 > hl:mem_free=31.215G > hl:mem_used=280.996M > hc:mem_available=1.715G > 1296 0.54786 semi_direc jj r 04/03/2012 16:43:49 1 > --------------------------------------------------------------------------------- > smp...@carl.fft BIP 0/1/4 0.69 lx-amd64 > hc:num_proc=0 > hl:mem_free=30.764G > hl:mem_used=742.805M > hc:mem_available=1.715G > 1296 0.54786 semi_direc jj r 04/03/2012 16:43:49 1 > --------------------------------------------------------------------------------- > smp...@charlie.fft BIP 0/2/8 0.57 lx-amd64 > hc:num_proc=0 > hl:mem_free=62.234G > hl:mem_used=836.797M > hc:mem_available=4.018G > 1296 0.54786 semi_direc jj r 04/03/2012 16:43:49 2 > --------------------------------------------------------------------------------- > > Sge reports whatr pls_gridengine_report does, i.e. what was reserved. > But here is the ouput of the current job (after started by openmpi): > [charlie:05294] ras:gridengine: JOB_ID: 1296 > [charlie:05294] ras:gridengine: PE_HOSTFILE: > /opt/sge/default/spool/charlie/active_jobs/1296.1/pe_hostfile > [charlie:05294] ras:gridengine: charlie.fft: PE_HOSTFILE shows slots=2 > [charlie:05294] ras:gridengine: barney.fft: PE_HOSTFILE shows slots=1 > [charlie:05294] ras:gridengine: carl.fft: PE_HOSTFILE shows slots=1 > > ====================== ALLOCATED NODES ====================== > > Data for node: Name: charlie Launch id: -1 Arch: ffc91200 State: 2 > Num boards: 1 Num sockets/board: 2 Num cores/socket: 4 > Daemon: [[54347,0],0] Daemon launched: True > Num slots: 2 Slots in use: 0 > Num slots allocated: 2 Max slots: 0 > Username on node: NULL > Num procs: 0 Next node_rank: 0 > Data for node: Name: barney.fft Launch id: -1 Arch: 0 State: 2 > Num boards: 1 Num sockets/board: 2 Num cores/socket: 4 > Daemon: Not defined Daemon launched: False > Num slots: 1 Slots in use: 0 > Num slots allocated: 1 Max slots: 0 > Username on node: NULL > Num procs: 0 Next node_rank: 0 > Data for node: Name: carl.fft Launch id: -1 Arch: 0 State: 2 > Num boards: 1 Num sockets/board: 2 Num cores/socket: 4 > Daemon: Not defined Daemon launched: False > Num slots: 1 Slots in use: 0 > Num slots allocated: 1 Max slots: 0 > Username on node: NULL > Num procs: 0 Next node_rank: 0 > > ================================================================= > > Map generated by mapping policy: 0200 > Npernode: 0 Oversubscribe allowed: TRUE CPU Lists: FALSE > Num new daemons: 2 New daemon starting vpid 1 > Num nodes: 3 > > Data for node: Name: charlie Launch id: -1 Arch: ffc91200 State: 2 > Num boards: 1 Num sockets/board: 2 Num cores/socket: 4 > Daemon: [[54347,0],0] Daemon launched: True > Num slots: 2 Slots in use: 2 > Num slots allocated: 2 Max slots: 0 > Username on node: NULL > Num procs: 2 Next node_rank: 2 > Data for proc: [[54347,1],0] > Pid: 0 Local rank: 0 Node rank: 0 > State: 0 App_context: 0 Slot list: NULL > Data for proc: [[54347,1],3] > Pid: 0 Local rank: 1 Node rank: 1 > State: 0 App_context: 0 Slot list: NULL > Data for node: Name: barney.fft Launch id: -1 Arch: 0 State: 2 > Num boards: 1 Num sockets/board: 2 Num cores/socket: 4 > Daemon: [[54347,0],1] Daemon launched: False > Num slots: 1 Slots in use: 1 > Num slots allocated: 1 Max slots: 0 > Username on node: NULL > Num procs: 1 Next node_rank: 1 > Data for proc: [[54347,1],1] > Pid: 0 Local rank: 0 Node rank: 0 > State: 0 App_context: 0 Slot list: NULL > > Data for node: Name: carl.fft Launch id: -1 Arch: 0 State: 2 > Num boards: 1 Num sockets/board: 2 Num cores/socket: 4 > Daemon: [[54347,0],2] Daemon launched: False > Num slots: 1 Slots in use: 1 > Num slots allocated: 1 Max slots: 0 > Username on node: NULL > Num procs: 1 Next node_rank: 1 > Data for proc: [[54347,1],2] > Pid: 0 Local rank: 0 Node rank: 0 > State: 0 App_context: 0 Slot list: NULL > > Regards, > Eloi > > > > -----Original Message----- > From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On > Behalf Of Reuti > Sent: mardi 3 avril 2012 16:24 > To: Open MPI Users > Subject: Re: [OMPI users] sge tight intregration leads to bad allocation > > Hi, > > Am 03.04.2012 um 16:12 schrieb Eloi Gaudry: > >> Thanks for your feedback. >> No, this is the other way around, the "reserved" slots on all nodes are ok >> but the "used" slots are different. >> >> Basically, I'm using SGE to schedule and book resources for a distributed >> job. When the job is finally launched, it uses a different allocation than >> the one that was reported by pls_gridengine_info. >> >> pls_grid_engine_info report states that 3 nodes were booked: barney (1 >> slot), carl (1 slot) and charlie (2 slots). This booking was done by sge >> depending on the memory requirements of the job (among others). >> >> When orterun starts the jobs (i.e. when Sge finally start the scheduled >> job), it uses 3 nodes but the first one (barney: 2 slots instead of 1) is >> oversubscribed and the last one (carl: 1 slot instead of 2) is underused. > > you configured Open MPI to support SGE tight integration and used a PE for > submitting the job? Can you please post the defintion of the PE. > > What was the allocation you saw in SGE's `qstat -g t ` for the job? > > -- Reuti > > >> If you need further information, please let me know. >> >> Eloi >> >> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On >> Behalf Of Ralph Castain >> Sent: mardi 3 avril 2012 15:58 >> To: Open MPI Users >> Subject: Re: [OMPI users] sge tight intregration leads to bad allocation >> >> I'm afraid there isn't enough info here to help. Are you saying you only >> allocated one slot/node, so the two slots on charlie is in error? >> >> Sent from my iPad >> >> On Apr 3, 2012, at 6:23 AM, "Eloi Gaudry" <eloi.gau...@fft.be> wrote: >> >> Hi, >> >> I've observed a strange behavior during rank allocation on a distributed run >> schedule and submitted using Sge (Son of Grid Egine 8.0.0d) and >> OpenMPI-1.4.4. >> Briefly, there is a one-slot difference between allocated rank/slot for Sge >> and OpenMPI. The issue here is that one node becomes oversubscribed at >> runtime. >> >> Here is the output of the allocation done for gridengine: >> >> ====================== ALLOCATED NODES ====================== >> >> Data for node: Name: barney Launch id: -1 Arch: >> ffc91200 State: 2 >> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2 >> Daemon: [[22904,0],0] Daemon launched: True >> Num slots: 1 Slots in use: 0 >> Num slots allocated: 1 Max slots: 0 >> Username on node: NULL >> Num procs: 0 Next node_rank: 0 >> Data for node: Name: carl.fft Launch id: -1 Arch: 0 >> State: 2 >> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2 >> Daemon: Not defined Daemon launched: False >> Num slots: 1 Slots in use: 0 >> Num slots allocated: 1 Max slots: 0 >> Username on node: NULL >> Num procs: 0 Next node_rank: 0 >> Data for node: Name: charlie.fft Launch id: -1 >> Arch: 0 State: 2 >> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2 >> Daemon: Not defined Daemon launched: False >> Num slots: 2 Slots in use: 0 >> Num slots allocated: 2 Max slots: 0 >> Username on node: NULL >> Num procs: 0 Next node_rank: 0 >> >> >> And here is the allocation finally used: >> ================================================================= >> >> Map generated by mapping policy: 0200 >> Npernode: 0 Oversubscribe allowed: TRUE CPU Lists: FALSE >> Num new daemons: 2 New daemon starting vpid 1 >> Num nodes: 3 >> >> Data for node: Name: barney Launch id: -1 Arch: >> ffc91200 State: 2 >> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2 >> Daemon: [[22904,0],0] Daemon launched: True >> Num slots: 1 Slots in use: 2 >> Num slots allocated: 1 Max slots: 0 >> Username on node: NULL >> Num procs: 2 Next node_rank: 2 >> Data for proc: [[22904,1],0] >> Pid: 0 Local rank: 0 Node rank: 0 >> State: 0 App_context: 0 >> Slot list: NULL >> Data for proc: [[22904,1],3] >> Pid: 0 Local rank: 1 Node rank: 1 >> State: 0 App_context: 0 >> Slot list: NULL >> >> Data for node: Name: carl.fft Launch id: -1 Arch: 0 >> State: 2 >> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2 >> Daemon: [[22904,0],1] Daemon launched: False >> Num slots: 1 Slots in use: 1 >> Num slots allocated: 1 Max slots: 0 >> Username on node: NULL >> Num procs: 1 Next node_rank: 1 >> Data for proc: [[22904,1],1] >> Pid: 0 Local rank: 0 Node rank: 0 >> State: 0 App_context: 0 >> Slot list: NULL >> >> Data for node: Name: charlie.fft Launch id: -1 >> Arch: 0 State: 2 >> Num boards: 1 Num sockets/board: 2 Num cores/socket: 2 >> Daemon: [[22904,0],2] Daemon launched: False >> Num slots: 2 Slots in use: 1 >> Num slots allocated: 2 Max slots: 0 >> Username on node: NULL >> Num procs: 1 Next node_rank: 1 >> Data for proc: [[22904,1],2] >> Pid: 0 Local rank: 0 Node rank: 0 >> State: 0 App_context: 0 >> Slot list: NULL >> >> Has anyone already encounter the same behavior ? >> Is there a simple fix than not using the tight integration mode between Sge >> and OpenMPI ? >> >> Eloi >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
