[mpich-devel] MPI_Comm_Split/Dup scalability on BGQ and K supercomputers
Sam Williams
swwilliams at lbl.gov
Sat May 24 09:07:09 CDT 2014
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
> _______________________________________________
> To manage subscription options or unsubscribe:
> https://lists.mpich.org/mailman/listinfo/devel
>
> _______________________________________________
> To manage subscription options or unsubscribe:
> https://lists.mpich.org/mailman/listinfo/devel
More information about the devel
mailing list