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Subject: Re: [OMPI users] sge tight intregration leads to bad allocation
From: Ralph Castain (rhc_at_[hidden])
Date: 2012-04-10 11:04:13


On Apr 10, 2012, at 8:55 AM, Eloi Gaudry wrote:

> Hi Ralf,
>
> I haven't tried any of the 1.5 series yet (we have chosen not to use the features releases) but if this is mandatory for you to work on this topic, I will.

Not mandatory, no - however, the 1.4 series has been closed out, so any fix will go into 1.6 (the 1.5 series is about to go "stable").

>
> This might be of interest to Reuti and you : it seems that we cannot reproduce the problem anymore if we don't provide the "-np N" option on the orterun command line. Of course, we need to launch a few other runs to be really sure because the allocation error was not always observable. Actually, I recently understood (from Reuti) that the tight integration mode would supply every necessary bits to the launcher and thus I removed the '-np N' that was around... Could it be that using the '-np N' while using the sge tight integration mode is pathologic ?

No, it should work just fine. Sounds like something weird is going on.

>
> Regards,
> Eloi
>
>
> -----Original Message-----
> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Ralph Castain
> Sent: mardi 10 avril 2012 16:43
> To: Open MPI Users
> Subject: Re: [OMPI users] sge tight intregration leads to bad allocation
>
> Could well be a bug in OMPI - I can take a look, though it may be awhile before I get to it. Have you tried one of the 1.5 series releases?
>
> On Apr 10, 2012, at 3:42 AM, Eloi Gaudry wrote:
>
>> 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".
>>
>>
>>
>>
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