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Date view	Thread view	Subject view	Author view

Subject: Re: [OMPI users] sge tight intregration leads to bad allocation
From: Eloi Gaudry (eloi.gaudry_at_[hidden])
Date: 2012-04-06 06:17:58

Next message: Mathieu westphal: "Re: [OMPI users] "Partial" Reduce and overlapping communicator"
Previous message: Anton Morgan: "Re: [OMPI users] Myid changes to 0 after using a mpi_recv"
In reply to: Reuti: "Re: [OMPI users] sge tight intregration leads to bad allocation"
Next in thread: Reuti: "Re: [OMPI users] sge tight intregration leads to bad allocation"
Reply: Reuti: "Re: [OMPI users] sge tight intregration leads to bad allocation"

> - Can you please post while it's running the relevant lines from:
> ps -e f --cols=500
> (f w/o -) from both machines.
> It's allocated between the nodes more like in a round-robin fashion.
> [eg: ] I'll try to do this tomorrow, as soon as some slots become free. Thanks for your feedback Reuti, I appreciate.

Â
hi reuti, here is the information related to another run that is failing in the same way:

Â
qstat -g t:

------------
---------------------------------------------------------------------------------
smp4.q_at_barney.fftÂ Â Â Â Â Â Â Â Â Â Â Â Â BIPÂ Â 0/3/4Â Â Â Â Â Â Â Â Â 3.37Â Â Â Â lx-amd64
Â hc:mem_available=1.715G
Â hc:proc_available=1
Â Â 1416 0.60500 semi_green jjÂ Â Â Â Â Â Â Â Â Â rÂ Â Â Â 04/06/2012 11:57:34 SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
---------------------------------------------------------------------------------
smp4.q_at_carl.fftÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â BIPÂ Â 0/3/4Â Â Â Â Â Â Â Â Â 3.44Â Â Â Â lx-amd64
Â hc:mem_available=1.715G
Â hc:proc_available=1
Â Â 1416 0.60500 semi_green jjÂ Â Â Â Â Â Â Â Â Â rÂ Â Â Â 04/06/2012 11:57:34 SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
---------------------------------------------------------------------------------
smp8.q_at_charlie.fftÂ Â Â Â Â Â Â Â Â Â Â Â BIPÂ Â 0/6/8Â Â Â Â Â Â Â Â Â 3.46Â Â Â Â lx-amd64
Â hc:mem_available=4.018G
Â hc:proc_available=2
Â Â 1416 0.60500 semi_green jjÂ Â Â Â Â Â Â Â Â Â rÂ Â Â Â 04/06/2012 11:57:34 MASTER
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE
Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â SLAVE

Â
barney: ps -e f --cols=500:

-----------------------------------

Â 2048 ?Â Â Â Â Â Â Â SlÂ Â Â Â 3:33 /opt/sge/bin/lx-amd64/sge_execd
27502 ?Â Â Â Â Â Â Â SlÂ Â Â Â 0:00Â \_ sge_shepherd-1416 -bg
27503 ?Â Â Â Â Â Â Â SsÂ Â Â Â 0:00Â Â Â Â Â \_ /opt/sge/utilbin/lx-amd64/qrsh_starter /opt/sge/default/spool/barney/active_jobs/1416.1/1.barney
27510 ?Â Â Â Â Â Â Â SÂ Â Â Â Â 0:00Â Â Â Â Â Â Â Â Â \_ bash -cÂ PATH=/opt/openmpi-1.4.4/bin:$PATH ; export PATH ; LD_LIBRARY_PATH=/opt/openmpi-1.4.4/lib:$LD_LIBRARY_PATH ; export LD_LIBRARY_PATH ;Â /opt/openmpi-1.4.4/bin/orted -mca ess e
nv -mca orte_ess_jobid 3800367104 -mca orte_ess_vpid 1 -mca orte_ess_num_procs 3 --hnp-uri "3800367104.0;tcp://192.168.0.20:57233" --mca pls_gridengine_verbose 1 --mca ras_gridengine_show_jobid 1 --mca ras_gridengine_verbose 1
27511 ?Â Â Â Â Â Â Â SÂ Â Â Â Â 0:00Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/openmpi-1.4.4/bin/orted -mca ess env -mca orte_ess_jobid 3800367104 -mca orte_ess_vpid 1 -mca orte_ess_num_procs 3 --hnp-uri 3800367104.0;tcp://192.168.0.20:57233 --mca pls_gridengine_verbose 1 --mca ras_gridengine_show_jobid 1 --mca ras_gridengine_verbose 1
27512 ?Â Â Â Â Â Â Â RlÂ Â Â 12:54Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
27513 ?Â Â Â Â Â Â Â RlÂ Â Â 12:54Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
Â
carl: ps -e f --cols=500:

-------------------------------

Â 1928 ?Â Â Â Â Â Â Â SlÂ Â Â Â 3:10 /opt/sge/bin/lx-amd64/sge_execd
29022 ?Â Â Â Â Â Â Â SlÂ Â Â Â 0:00Â \_ sge_shepherd-1416 -bg
29023 ?Â Â Â Â Â Â Â SsÂ Â Â Â 0:00Â Â Â Â Â \_ /opt/sge/utilbin/lx-amd64/qrsh_starter /opt/sge/default/spool/carl/active_jobs/1416.1/1.carl
29030 ?Â Â Â Â Â Â Â SÂ Â Â Â Â 0:00Â Â Â Â Â Â Â Â Â \_ bash -cÂ PATH=/opt/openmpi-1.4.4/bin:$PATH ; export PATH ; LD_LIBRARY_PATH=/opt/openmpi-1.4.4/lib:$LD_LIBRARY_PATH ; export LD_LIBRARY_PATH ;Â /opt/openmpi-1.4.4/bin/orted -mca ess e
nv -mca orte_ess_jobid 3800367104 -mca orte_ess_vpid 2 -mca orte_ess_num_procs 3 --hnp-uri "3800367104.0;tcp://192.168.0.20:57233" --mca pls_gridengine_verbose 1 --mca ras_gridengine_show_jobid 1 --mca ras_gridengine_verbose 1
29031 ?Â Â Â Â Â Â Â SÂ Â Â Â Â 0:00Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/openmpi-1.4.4/bin/orted -mca ess env -mca orte_ess_jobid 3800367104 -mca orte_ess_vpid 2 -mca orte_ess_num_procs 3 --hnp-uri 3800367104.0;tcp://192.168.0.20:57233 --mca pls_gridengine_verbose 1 --mca ras_gridengine_show_jobid 1 --mca ras_gridengine_verbose 1
29032 ?Â Â Â Â Â Â Â RlÂ Â Â 13:49Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
29033 ?Â Â Â Â Â Â Â RlÂ Â Â 13:50Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
29034 ?Â Â Â Â Â Â Â RlÂ Â Â 13:49Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
29035 ?Â Â Â Â Â Â Â RlÂ Â Â 13:49Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
Â
Â
charlie: ps -e f --cols=500:

-----------------------------------

Â 1591 ?Â Â Â Â Â Â Â SlÂ Â Â Â 3:13 /opt/sge/bin/lx-amd64/sge_execd
Â 8793 ?Â Â Â Â Â Â Â SÂ Â Â Â Â 0:00Â \_ sge_shepherd-1416 -bg
Â 8795 ?Â Â Â Â Â Â Â SsÂ Â Â Â 0:00Â Â Â Â Â \_ -bash /opt/sge/default/spool/charlie/job_scripts/1416
Â 8800 ?Â Â Â Â Â Â Â SÂ Â Â Â Â 0:00Â Â Â Â Â Â Â Â Â \_ /opt/openmpi-1.4.4/bin/orterun --mca pls_gridengine_verbose 1 --mca ras_gridengine_show_jobid 1 --mca ras_gridengine_verbose 1 --bynode -report-bindings -display-map -display-devel-map -display-allocation -display-devel-allocation -np 12 -x ACTRAN_LICENSE -x ACTRAN_PRODUCTLINE -x LD_LIBRARY_PATH -x PATH -x ACTRAN_DEBUG /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parall
Â 8801 ?Â Â Â Â Â Â Â SlÂ Â Â Â 0:00Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/sge/bin/lx-amd64/qrsh -inherit -nostdin -V barney.fftÂ PATH=/opt/openmpi-1.4.4/bin:$PATH ; export PATH ; LD_LIBRARY_PATH=/opt/openmpi-1.4.4/lib:$LD_LIBRARY_PATH ; export LD_LIBRARY_PATH ;Â /opt/openmpi-1.4.4/bin/orted -mca ess env -mca orte_ess_jobid 3800367104 -mca orte_ess_vpid 1 -mca orte_ess_num_procs 3 --hnp-uri "3800367104.0;tcp://192.168.0.20:57233" --mca pls_gridengine_verbose 1 --mca ras_gridengine_show_jobid 1 --mca ras_gridengine_verbose
Â 8802 ?Â Â Â Â Â Â Â SlÂ Â Â Â 0:00Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/sge/bin/lx-amd64/qrsh -inherit -nostdin -V carl.fftÂ PATH=/opt/openmpi-1.4.4/bin:$PATH ; export PATH ; LD_LIBRARY_PATH=/opt/openmpi-1.4.4/lib:$LD_LIBRARY_PATH ; export LD_LIBRARY_PATH ;Â /opt/openmpi-1.4.4/bin/orted -mca ess env -mca orte_ess_jobid 3800367104 -mca orte_ess_vpid 2 -mca orte_ess_num_procs 3 --hnp-uri "3800367104.0;tcp://192.168.0.20:57233" --mca pls_gridengine_verbose 1 --mca ras_gridengine_show_jobid 1 --mca ras_gridengine_verbose 1
Â 8807 ?Â Â Â Â Â Â Â RlÂ Â Â 14:23Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
Â 8808 ?Â Â Â Â Â Â Â RlÂ Â Â 14:23Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
Â 8809 ?Â Â Â Â Â Â Â RlÂ Â Â 14:23Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat
Â 8810 ?Â Â Â Â Â Â Â RlÂ Â Â 14:23Â Â Â Â Â Â Â Â Â Â Â Â Â \_ /opt/fft/actran_product/Actran_13.0.b.57333/bin/actranpy_mp --apl=/opt/fft/actran_product/Actran_13.0.b.57333 -e radiation -m 10000 --parallel=frequency --scratch=/scratch/cluster/1416 --inputfile=/home/jj/Projects/Toyota/REFERENCE_JPC/semi_green_PML_06/semi_green_coarse.edat

Â
oretrun information:

--------------------------

[charlie:08800] ras:gridengine: JOB_ID: 1416
[charlie:08800] ras:gridengine: PE_HOSTFILE: /opt/sge/default/spool/charlie/active_jobs/1416.1/pe_hostfile
[charlie:08800] ras:gridengine: charlie.fft: PE_HOSTFILE shows slots=6
[charlie:08800] ras:gridengine: barney.fft: PE_HOSTFILE shows slots=3
[charlie:08800] ras:gridengine: carl.fft: PE_HOSTFILE shows slots=3

======================Â Â ALLOCATED NODESÂ Â ======================

Â Data for node: Name: charlieÂ Â Launch id: -1 Arch: ffc91200Â State: 2
Â Num boards: 1 Num sockets/board: 2Â Num cores/socket: 4
Â Daemon: [[57989,0],0] Daemon launched: True
Â Num slots: 6Â Slots in use: 0
Â Num slots allocated: 6Â Max slots: 0
Â Username on node: NULL
Â Num procs: 0Â Next node_rank: 0
Â Data for node: Name: barney.fftÂ Â Â Launch id: -1 Arch: 0 State: 2
Â Num boards: 1 Num sockets/board: 2Â Num cores/socket: 4
Â Daemon: Not defined Daemon launched: False
Â Num slots: 3Â Slots in use: 0
Â Num slots allocated: 3Â Max slots: 0
Â Username on node: NULL
Â Num procs: 0Â Next node_rank: 0
Â Data for node: Name: carl.fftÂ Â Â Launch id: -1 Arch: 0 State: 2
Â Num boards: 1 Num sockets/board: 2Â Num cores/socket: 4
Â Daemon: Not defined Daemon launched: False
Â Num slots: 3Â Slots in use: 0
Â Num slots allocated: 3Â Max slots: 0
Â Username on node: NULL
Â Num procs: 0Â Next node_rank: 0

=================================================================

Â Map generated by mapping policy: 0200
Â Npernode: 0 Oversubscribe allowed: TRUE CPU Lists: FALSE
Â Num new daemons: 2Â New daemon starting vpid 1
Â Num nodes: 3

Â Data for node: Name: charlieÂ Â Launch id: -1 Arch: ffc91200Â State: 2
Â Num boards: 1 Num sockets/board: 2Â Num cores/socket: 4
Â Daemon: [[57989,0],0] Daemon launched: True
Â Num slots: 6Â Slots in use: 4
Â Num slots allocated: 6Â Max slots: 0
Â Username on node: NULL
Â Num procs: 4Â Next node_rank: 4
Â Data for proc: [[57989,1],0]
Â Â Â Pid: 0Â Local rank: 0 Node rank: 0
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],3]
Â Â Â Pid: 0Â Local rank: 1 Node rank: 1
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],6]
Â Â Â Pid: 0Â Local rank: 2 Node rank: 2
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],9]
Â Â Â Pid: 0Â Local rank: 3 Node rank: 3
Â Â Â State: 0Â App_context: 0Â Slot list: NULL

Â Data for node: Name: barney.fftÂ Â Â Launch id: -1 Arch: 0 State: 2
Â Num boards: 1 Num sockets/board: 2Â Num cores/socket: 4
Â Daemon: [[57989,0],1] Daemon launched: False
Â Num slots: 3Â Slots in use: 4
Â Num slots allocated: 3Â Max slots: 0
Â Username on node: NULL
Â Num procs: 4Â Next node_rank: 4
Â Data for proc: [[57989,1],1]
Â Â Â Pid: 0Â Local rank: 0 Node rank: 0
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],4]
Â Â Â Pid: 0Â Local rank: 1 Node rank: 1
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],7]
Â Â Â Pid: 0Â Local rank: 2 Node rank: 2
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],10]
Â Â Â Pid: 0Â Local rank: 3 Node rank: 3
Â Â Â State: 0Â App_context: 0Â Slot list: NULL

Â Data for node: Name: carl.fftÂ Â Â Launch id: -1 Arch: 0 State: 2
Â Num boards: 1 Num sockets/board: 2Â Num cores/socket: 4
Â Daemon: [[57989,0],2] Daemon launched: False
Â Num slots: 3Â Slots in use: 4
Â Num slots allocated: 3Â Max slots: 0
Â Username on node: NULL
Â Num procs: 4Â Next node_rank: 4
Â Data for proc: [[57989,1],2]
Â Â Â Pid: 0Â Local rank: 0 Node rank: 0
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],5]
Â Â Â Pid: 0Â Local rank: 1 Node rank: 1
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],8]
Â Â Â Pid: 0Â Local rank: 2 Node rank: 2
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â Data for proc: [[57989,1],11]
Â Â Â Pid: 0Â Local rank: 3 Node rank: 3
Â Â Â State: 0Â App_context: 0Â Slot list: NULL
Â
Â

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