[petsc-dev] PetscHashIJ scaling problem?

Jed Brown jedbrown at mcs.anl.gov
Sun Nov 10 12:47:03 CST 2013 

Matthew Knepley <knepley at gmail.com> writes:
> Okay, here is the clearly quadratic performance, and its in next. Build
> SNES ex12 and run using
>
> /PETSc3/petsc/petsc-dev/arch-c-opencl-opt-next/lib/ex12-obj/ex12 -run_type
> perf -refinement_limit 0.00000625 -variable_coefficient field
> -petscspace_order 1 -mat_petscspace_order 0 -show_initial 0 -show_solution
> 0 -petscfe_type basic -log_summary -interpolate
>
> -refinement_limit 0.000625     DMPlexInterpolate       4 1.0 1.7443e-02 1.0
> 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 12  0  0  0 24  12  0  0  0 24     0
> -refinement_limit 0.0003125    DMPlexInterpolate       4 1.0 3.3111e-02 1.0
> 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 13  0  0  0 24  13  0  0  0 24     0
> -refinement_limit 0.0000625    DMPlexInterpolate       4 1.0 2.3465e-01 1.0
> 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 21  0  0  0 24  21  0  0  0 24     0
> -refinement_limit 0.00003125   DMPlexInterpolate       4 1.0 7.7508e-01 1.0
> 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 30  0  0  0 24  30  0  0  0 24     0
> -refinement_limit 0.000015625  DMPlexInterpolate       4 1.0 2.7267e+00 1.0
> 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 42  0  0  0 24  42  0  0  0 24     0
> -refinement_limit 0.0000078125 DMPlexInterpolate       4 1.0 1.0175e+01 1.0
> 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 58  0  0  0 24  58  0  0  0 24     0
> -refinement_limit 0.00000625   DMPlexInterpolate       4 1.0 3.8912e+01 1.0
> 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 72  0  0  0 24  72  0  0  0 24     0

Testing in optimized mode, I have

-refinement_limit 0.00001
DMPlexInterpolate       4 1.0 2.1803e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 56  0  0  0 24  56  0  0  0 24     0
DMPlexStratify         9 1.0 2.0112e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 52  0  0  0 24  52  0  0  0 24     0
DMPlexPreallocate       1 1.0 5.3650e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+00 14  0  0  0 12  14  0  0  0 12     0
DMPlexResidualFEM       1 1.0 5.6863e-01 1.0 3.54e+06 1.0 0.0e+00 0.0e+00 0.0e+00 15 54  0  0  0  15 54  0  0  0     6

-refinement_limit 0.000005
DMPlexInterpolate       4 1.0 9.0466e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 72  0  0  0 24  72  0  0  0 24     0
DMPlexStratify         9 1.0 8.6705e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 69  0  0  0 24  69  0  0  0 24     0
DMPlexPreallocate       1 1.0 1.0999e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+00  9  0  0  0 12   9  0  0  0 12     0
DMPlexResidualFEM       1 1.0 1.1739e+00 1.0 7.08e+06 1.0 0.0e+00 0.0e+00 0.0e+00  9 54  0  0  0   9 54  0  0  0     6

-refinement_limit 0.0000025
DMPlexInterpolate       4 1.0 3.9527e+01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 85  0  0  0 24  85  0  0  0 24     0
DMPlexStratify         9 1.0 3.8794e+01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 1.2e+01 83  0  0  0 24  83  0  0  0 24     0
DMPlexPreallocate       1 1.0 2.1816e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+00  5  0  0  0 12   5  0  0  0 12     0
DMPlexResidualFEM       1 1.0 2.4221e+00 1.0 1.42e+07 1.0 0.0e+00 0.0e+00 0.0e+00  5 54  0  0  0   5 54  0  0  0     6

These are coming from DMLabelSetValue(), which is O(N) when the point
does not yet exist.  To insert/modify these entries with storage bounded
by the number of points rather than the number of times you mutate them,
either use a hash (perhaps compressing to sorted array later) or a tree.
(The guy that wrote khash also wrote kbtree, which has the same
interface, though it tends to use more memory and be slower.)

https://github.com/attractivechaos/klib/blob/master/kbtree.h


If you run in a debugger, you'll find that your stack is pretty much always here:

(gdb) bt
#0  0x00007ffff51314be in __memmove_ssse3_back () from /usr/lib/libc.so.6
#1  0x00007ffff751bca4 in PetscMemmove (a=0x26a0030, b=0x26a002c, n=979520) at src/sys/utils/memc.c:94
#2  0x00007ffff78f51b6 in DMLabelSetValue (label=0x4529b0, point=404548, value=<optimized out>) at src/dm/impls/plex/plexlabel.c:279
#3  0x00007ffff78ad27f in DMPlexStratify (dm=0x429350) at src/dm/impls/plex/plex.c:1440
#4  0x00007ffff78e8b63 in DMPlexInterpolateFaces_Internal (cellDepth=<error reading variable: Cannot access memory at address 0x2>, dm=<optimized out>, idm=<optimized out>) at src/dm/impls/plex/plexinterpolate.c:290
#5  DMPlexInterpolate (dm=0x428370, dmInt=0x7fffffffbda0) at src/dm/impls/plex/plexinterpolate.c:331
#6  0x00007ffff78a629a in DMPlexCreateFromCellList (comm=<optimized out>, dim=<optimized out>, numCells=262144, numVertices=131585, numCorners=<optimized out>, interpolate=<optimized out>, cells=<optimized out>, spaceDim=40501292, vertexCoords=0x26ac3a4, dm=0x7fffffffc520) at src/dm/impls/plex/plexcreate.c:945
#7  0x00007ffff78ba14d in DMPlexRefine_Triangle (dm=<optimized out>, maxVolumes=0x42e9f0, dmRefined=0x7fffffffc520) at src/dm/impls/plex/plex.c:3639
#8  0x00007ffff78baae0 in DMRefine_Plex (dm=0x42cb40, comm=40501292, dmRefined=0x7fffffffc520) at src/dm/impls/plex/plex.c:4313
#9  0x00007ffff791d9cc in DMRefine (dm=0x42cb40, comm=40501292, dmf=0x7fffffffc520) at src/dm/interface/dm.c:1498
#10 0x0000000000404c64 in CreateMesh (comm=1140850688, user=0x7fffffffc608, dm=0x7fffffffd740) at /home/jed/petsc/src/snes/examples/tutorials/ex12.c:311
#11 0x0000000000406e60 in main (argc=21, argv=0x7fffffffd858) at /home/jed/petsc/src/snes/examples/tutorials/ex12.c:648




DMPlexStratify also calls ISGetIndices, but forgets ISRestoreIndices.
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