[mpich-devel] MPI_Comm_Split/Dup scalability on BGQ and K supercomputers

Sat May 24 09:17:04 CDT 2014

to be clear, I ran these experiments in late February (<27th).

On May 24, 2014, at 7:07 AM, Sam Williams <SWWilliams at lbl.gov> wrote:

> I saw the problem on Mira and K but not Edison.  I don't know if that is due to scale or implementation.
> 
> On Mira, I was running jobs with a 10min wallclock limit.  I scaled to 46656 processes with 64 threads per process (c1, OMP_NUM_THREADS=64) and all jobs completed successfully.  However, I was only looking at MGSolve times and not MGBuild times.  I then decided to explore 8 threads per process (c8, OMP_NUM_THREADS=8) and started at the high concurrency.  The jobs timed out while still in MGBuild after 10mins with 373248 processes as well as with a 20min timeout.  At that point I added the USE_SUBCOMM option to enable/disable the use of comm_split.  I haven't tried scaling with the sub communicator on Mira since then.
> 
> 
> On May 24, 2014, at 6:39 AM, Junchao Zhang <jczhang at mcs.anl.gov> wrote:
> 
>> Hi, Sam,
>>  Could you give me the exact number of MPI ranks for your results on Mira? 
>>  I run hpgmg on Edison with export OMP_NUM_THREADS=1, aprun -n 64000 -ss -cc numa_node ./hpgmg-fv 6 1. The total time in MGBuild is about 0.005 seconds. I was wondering how many cores I need to apply to reproduce the problem.
>>  Thanks.
>> 
>> 
>> --Junchao Zhang
>> 
>> 
>> On Sat, May 17, 2014 at 9:06 AM, Sam Williams <swwilliams at lbl.gov> wrote:
>> I've been conducting scaling experiments on the Mira (Blue Gene/Q) and K (Sparc) supercomputers.  I've noticed that the time required for MPI_Comm_split and MPI_Comm_dup can grow quickly with scale (~P^2).  As such, its performance eventually becomes a bottleneck.  That is, although the benefit of using a subcommunicator is huge (multigrid solves are weak-scalable), the penalty of creating one (multigrid build time) is also huge.
>> 
>> For example, when scaling from 1 to 46K nodes (= cubes of integers) on Mira, the time (in seconds) required to build a MG solver (including a subcommunicator) scales as
>> 222335.output:   Total time in MGBuild      0.056704
>> 222336.output:   Total time in MGBuild      0.060834
>> 222348.output:   Total time in MGBuild      0.064782
>> 222349.output:   Total time in MGBuild      0.090229
>> 222350.output:   Total time in MGBuild      0.075280
>> 222351.output:   Total time in MGBuild      0.091852
>> 222352.output:   Total time in MGBuild      0.137299
>> 222411.output:   Total time in MGBuild      0.301552
>> 222413.output:   Total time in MGBuild      0.606444
>> 222415.output:   Total time in MGBuild      0.745272
>> 222417.output:   Total time in MGBuild      0.779757
>> 222418.output:   Total time in MGBuild      4.671838
>> 222419.output:   Total time in MGBuild     15.123162
>> 222420.output:   Total time in MGBuild     33.875626
>> 222421.output:   Total time in MGBuild     49.494547
>> 222422.output:   Total time in MGBuild    151.329026
>> 
>> If I disable the call to MPI_Comm_Split, my time scales as
>> 224982.output:   Total time in MGBuild      0.050143
>> 224983.output:   Total time in MGBuild      0.052607
>> 224988.output:   Total time in MGBuild      0.050697
>> 224989.output:   Total time in MGBuild      0.078343
>> 224990.output:   Total time in MGBuild      0.054634
>> 224991.output:   Total time in MGBuild      0.052158
>> 224992.output:   Total time in MGBuild      0.060286
>> 225008.output:   Total time in MGBuild      0.062925
>> 225009.output:   Total time in MGBuild      0.097357
>> 225010.output:   Total time in MGBuild      0.061807
>> 225011.output:   Total time in MGBuild      0.076617
>> 225012.output:   Total time in MGBuild      0.099683
>> 225013.output:   Total time in MGBuild      0.125580
>> 225014.output:   Total time in MGBuild      0.190711
>> 225016.output:   Total time in MGBuild      0.218329
>> 225017.output:   Total time in MGBuild      0.282081
>> 
>> Although I didn't directly measure it, this suggests the time for MPI_Comm_Split is growing roughly quadratically with process concurrency.
>> 
>> 
>> 
>> 
>> I see the same effect on the K machine (8...64K nodes) where the code uses comm_split/dup in conjunction:
>> run00008_7_1.sh.o2412931:   Total time in MGBuild      0.026458 seconds
>> run00064_7_1.sh.o2415876:   Total time in MGBuild      0.039121 seconds
>> run00512_7_1.sh.o2415877:   Total time in MGBuild      0.086800 seconds
>> run01000_7_1.sh.o2414496:   Total time in MGBuild      0.129764 seconds
>> run01728_7_1.sh.o2415878:   Total time in MGBuild      0.224576 seconds
>> run04096_7_1.sh.o2415880:   Total time in MGBuild      0.738979 seconds
>> run08000_7_1.sh.o2414504:   Total time in MGBuild      2.123800 seconds
>> run13824_7_1.sh.o2415881:   Total time in MGBuild      6.276573 seconds
>> run21952_7_1.sh.o2415882:   Total time in MGBuild     13.634200 seconds
>> run32768_7_1.sh.o2415884:   Total time in MGBuild     36.508670 seconds
>> run46656_7_1.sh.o2415874:   Total time in MGBuild     58.668228 seconds
>> run64000_7_1.sh.o2415875:   Total time in MGBuild    117.322217 seconds
>> 
>> 
>> A glance at the implementation on Mira (I don't know if the implementation on K is stock) suggests it should be using qsort to sort based on keys.  Unfortunately, qsort is not performance robust like heap/merge sort.  If one were to be productive and call comm_split like...
>> MPI_Comm_split(...,mycolor,myrank,...)
>> then one runs the risk that the keys are presorted.  This hits the worst case computational complexity for qsort... O(P^2).  Demanding programmers avoid sending sorted keys seems unreasonable.
>> 
>> 
>> I should note, I see a similar lack of scaling with MPI_Comm_dup on the K machine.  Unfortunately, my BGQ data used an earlier version of the code that did not use comm_dup.  As such, I can’t definitively say that it is a problem on that machine as well.
>> 
>> Thus, I'm asking for scalable implementations of comm_split/dup using merge/heap sort whose worst case complexity is still PlogP to be prioritized in the next update.
>> 
>> 
>> thanks
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