On Wed, Apr 25, 2018 at 12:40 PM, Danyang Su <[email protected]> wrote:
> Hi Matthew, > > In the worst case, every node/cell may have different label. > > Do not use Label for this. Its not an appropriate thing. If every cell is different, just use the cell number. Labels are for mapping a relatively small number of keys (like material IDs) to sets of points (cells, vertices, etc.) Its not a great data structure for a permutation. However, I still do not believe these numbers. The old code does a string comparison every time. I will setup a test. Matt > Below is one of the worst scenario with 102299 nodes and 102299 different > labels for test. I found the time cost increase during the loop. The first > 9300 loop takes least time (<0.5) while the last 9300 loops takes much more > time (>7.7), as shown below. If I use larger mesh with >1 million nodes, it > runs very very slowly in this part. The PETSc is configured with > optimization on. > > Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran > --download-mpich --download-scalapack --download-parmetis --download-metis > --download-ptscotch --download-fblaslapack --download-hypre > --download-superlu_dist --download-hdf5=yes --download-ctetgen > --with-debugging=0 COPTFLAGS="-O3 -march=native -mtune=native" > CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3 -march=native > -mtune=native" > > istart iend progress CPU_Time time cost - old (sec) time cost - new (sec) > 0 9299 0 1524670045.51166 > > 9300 18599 0.100010753 1524670045.99605 0.4843890667 0.497246027 > 18600 27899 0.200010747 1524670047.32635 1.330302 1.3820912838 > 27900 37199 0.300010741 1524670049.3066 1.9802515507 2.2439446449 > 37200 46499 0.400010765 1524670052.1594 2.852804184 3.0739262104 > 46500 55799 0.500010729 1524670055.90961 3.7502081394 3.9270553589 > 55800 65099 0.600010753 1524670060.47654 4.5669286251 4.7571902275 > 65100 74399 0.700010777 1524670066.0941 5.6175630093 5.7428796291 > 74400 83699 0.800010741 1524670072.53886 6.44475317 6.5761549473 > 83700 92998 0.900010765 1524670079.99072 7.4518604279 7.4606924057 > 92999 102298 1 1524670087.71066 7.7199423313 8.2424075603 > > old code > > do ipoint = 0, istart-1 > !c output time cost, use 1 processor to test > if (b_enable_output .and. rank == 0) then > if (mod(ipoint,iprogress) == 0 .or. ipoint == istart-1) then > !write(*,'(f3.1,1x)',advance="no") (ipoint+1.0)/istart > write(*,*) ipoint, (ipoint+1.0)/istart,"time",MPI_Wtime() > end if > end if > > call DMSetLabelValue(dmda_flow%da,"cid_lg2g",ipoint, & > ipoint+1,ierr) > CHKERRQ(ierr) > end do > > > new code > > call DMCreateLabel(dmda_flow%da,'cid_lg2g',ierr) > CHKERRQ(ierr) > > call DMGetLabel(dmda_flow%da,'cid_lg2g',label, ierr) > CHKERRQ(ierr) > > do ipoint = 0, istart-1 > !c output time cost, use 1 processor to test > if (b_enable_output .and. rank == 0) then > if (mod(ipoint,iprogress) == 0 .or. ipoint == istart-1) then > !write(*,'(f3.1,1x)',advance="no") (ipoint+1.0)/istart > write(*,*) ipoint, (ipoint+1.0)/istart,"time",MPI_Wtime() > end if > end if > > call DMLabelSetValue(label,ipoint,ipoint+1,ierr) > CHKERRQ(ierr) > end do > > Thanks, > > Danyang > > On 2018-04-25 03:16 AM, Matthew Knepley wrote: > > On Tue, Apr 24, 2018 at 11:57 PM, Danyang Su <[email protected]> wrote: > >> Hi All, >> >> I use DMPlex in unstructured grid code and recently found DMSetLabelValue >> takes a lot of time for large problem, e.g., num. of cells > 1 million. In >> my code, I use >> > > I read your code wrong. For large loop, you should not use the convenience > function. You should use > > >> DMPlexCreateFromCellList () > > > DMGetLabel(dm, name, &label) > > >> > > >> Loop over all cells/nodes{ >> >> DMSetLabelValue >> > > Replace this by DMLabelSetValue(label, point, val) > > >> } >> >> DMPlexDistribute >> >> The code works fine except DMSetLabelValue takes a lot of time for large >> problem. I use DMSetLabelValue to set material id for all the nodes or >> cells so that each subdomain has a copy of material id. Is there any other >> functions that can be used more efficient, e.g. set labels by array, not 1 >> by 1? >> > > That should take much less time. > > Thanks, > > Matt > > >> Thanks, >> >> Danyang >> >> > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/%7Emk51/> > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
