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Subject: Re: [OMPI users] sge tight intregration leads to bad allocation
From: Eloi Gaudry (eloi.gaudry_at_[hidden])
Date: 2012-04-10 05:42:20


Thx. This is the allocation which is also confirmed by the Open MPI output.
[eg: ] exactly, but not the one used afterwards by openmpi

- The application was compiled with the same version of Open MPI?
[eg: ] yes, version 1.4.4 for all

- Does the application start something on its own besides the tasks granted by mpiexec/orterun?
[eg: ] no

You want 12 ranks in total, and to barney.fft and carl.fft there are also "-mca orte_ess_num_procs 3 " given in to the qrsh_starter. In total I count only 10 ranks in this example given - 4+4+2 - do you observe the same?
[eg: ] i don't know why the -mca orte_ess_num_procs 3 is added here...
In the "Map generated by mapping policy" output in my last email, I see that 4 processes were started on each node (barney, carl and charlie), but yes, in the ps -elf output, two of them are missing for one node (barney)... sorry about that, a bad copy/paste. Here is the actual output for this node:
2048 ? Sl 3:33 /opt/sge/bin/lx-amd64/sge_execd
27502 ? Sl 0:00 \_ sge_shepherd-1416 -bg
27503 ? Ss 0:00 \_ /opt/sge/utilbin/lx-amd64/qrsh_starter /opt/sge/default/spool/barney/active_jobs/1416.1/1.barney
27510 ? S 0:00 \_ bash -c 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 ; /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
27511 ? S 0:00 \_ /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 ? Rl 12:54 \_ /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 ? Rl 12:54 \_ /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
27514 ? Rl 12:54 \_ /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
27515 ? Rl 12:53 \_ /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

It looks like Open MPI is doing the right thing, but the applications decided to start in a different allocation.
[eg: ] if the "Map generated by mapping policy" is different than the sge allocation, then openmpi is not doing the right thing, don't you think ?

Does the application use OpenMP in addition or other kinds of threads? The suffix "_mp" in the name "actranpy_mp" makes me suspicious about it.
[eg: ] no, the suffix _mp stands for "parallel".