Also, this was the output before the error message: Level 0 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 5 x 5 x 3 (75), size (m) 2000. x 2000. x 500. Level -1 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 2 x 2 x 2 (8), size (m) 5000. x 5000. x 1000. Level -2 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 1 x 1 x 1 (1), size (m) 10000. x 10000. x inf.
Which tells me '-da_refine 4' is not registering On Thu, Mar 30, 2017 at 4:15 PM, Justin Chang <[email protected]> wrote: > Okay I'll give it a shot. > > Somewhat unrelated, but I tried running this on Cori's Haswell node > (loaded the module 'petsc/3.7.4-64'). But I get these errors: > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Argument out of range > [0]PETSC ERROR: Partition in y direction is too fine! 0 1 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.7.4, Oct, 02, 2016 > [0]PETSC ERROR: /global/u1/j/jychang/Icesheet/./ex48 on a > arch-cori-opt64-INTEL-3.7.4-64 named nid00020 by jychang Thu Mar 30 > 14:04:35 2017 > [0]PETSC ERROR: Configure options --known-sizeof-void-p=8 > --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 > --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-size_t=8 > --known-mpi-int64_t=1 --known-has-attribute-aligned=1 > --prefix=/global/common/cori/software/petsc/3.7.4-64/hsw/intel > PETSC_ARCH=arch-cori-opt64-INTEL-3.7.4-64 --COPTFLAGS="-mkl -O2 -no-ipo > -g -axMIC-AVX512,CORE-AVX2,AVX" --CXXOPTFLAGS="-mkl -O2 -no-ipo -g > -axMIC-AVX512,CORE-AVX2,AVX" --FOPTFLAGS="-mkl -O2 -no-ipo -g > -axMIC-AVX512,CORE-AVX2,AVX" --with-hdf5-dir=/opt/cray/pe/ > hdf5-parallel/1.8.16/INTEL/15.0 --with-hwloc-dir=/global/ > common/cori/software/hwloc/1.11.4/hsw --with-scalapack-include=/opt/ > intel/compilers_and_libraries_2017.1.132/linux/mkl/include > --with-scalapack-lib= --LIBS="-mkl -L/global/common/cori/ > software/petsc/3.7.4-64/hsw/intel/lib -I/global/common/cori/ > software/petsc/3.7.4-64/hsw/intel/include > -L/global/common/cori/software/xz/5.2.2/hsw/lib > -I/global/common/cori/software/xz/5.2.2/hsw/include -L/global/common/cori/ > software/zlib/1.2.8/hsw/intel/lib -I/global/common/cori/ > software/zlib/1.2.8/hsw/intel/include > -L/global/common/cori/software/libxml2/2.9.4/hsw/lib > -I/global/common/cori/software/libxml2/2.9.4/hsw/include > -L/global/common/cori/software/numactl/2.0.11/hsw/lib > -I/global/common/cori/software/numactl/2.0.11/hsw/include > -L/global/common/cori/software/hwloc/1.11.4/hsw/lib -I/global/common/cori/ > software/hwloc/1.11.4/hsw/include -L/global/common/cori/ > software/openssl/1.1.0a/hsw/lib -I/global/common/cori/ > software/openssl/1.1.0a/hsw/include -L/global/common/cori/ > software/subversion/1.9.4/hsw/lib -I/global/common/cori/ > software/subversion/1.9.4/hsw/include -lhwloc -lpciaccess -lxml2 -lz > -llzma -Wl,--start-group /opt/intel/compilers_and_ > libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a > /opt/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_core.a > /opt/intel/compilers_and_libraries_2017.1.132/linux/ > mkl/lib/intel64/libmkl_intel_thread.a /opt/intel/compilers_and_ > libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a > -Wl,--end-group -lstdc++" --download-parmetis --download-metis --with-ssl=0 > --with-batch --known-mpi-shared-libraries=0 --with-clib-autodetect=0 > --with-cxxlib-autodetect=0 --with-debugging=0 > --with-fortranlib-autodetect=0 --with-mpiexec=srun > --with-shared-libraries=0 --with-x=0 --known-mpi-int64-t=0 > --known-bits-per-byte=8 --known-sdot-returns-double=0 > --known-snrm2-returns-double=0 --known-level1-dcache-assoc=0 > --known-level1-dcache-linesize=32 --known-level1-dcache-size=32768 > --known-memcmp-ok=1 --known-mpi-c-double-complex=1 > --known-mpi-long-double=1 --known-sizeof-MPI_Comm=4 > --known-sizeof-MPI_Fint=4 --known-sizeof-char=1 --known-sizeof-double=8 > CC=cc MPICC=cc CXX=CC MPICXX=CC FC=ftn F77=ftn F90=ftn MPIF90=ftn > MPIF77=ftn CFLAGS=-axMIC-AVX512,CORE-AVX2,AVX > CXXFLAGS=-axMIC-AVX512,CORE-AVX2,AVX > FFLAGS=-axMIC-AVX512,CORE-AVX2,AVX CC=cc MPICC=cc CXX=CC MPICXX=CC FC=ftn > F77=ftn F90=ftn MPIF90=ftn MPIF77=ftn CFLAGS=-fPIC FFLAGS=-fPIC > LDFLAGS=-fPIE --download-hypre --with-64-bit-indices > [0]PETSC ERROR: #1 DMSetUp_DA_3D() line 298 in > /global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/dm/impls/da/da3.c > [0]PETSC ERROR: #2 DMSetUp_DA() line 27 in /global/cscratch1/sd/swowner/ > sleak/petsc-3.7.4/src/dm/impls/da/dareg.c > [0]PETSC ERROR: #3 DMSetUp() line 744 in /global/cscratch1/sd/swowner/ > sleak/petsc-3.7.4/src/dm/interface/dm.c > [0]PETSC ERROR: #4 DMCoarsen_DA() line 1196 in > /global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/dm/impls/da/da.c > [0]PETSC ERROR: #5 DMCoarsen() line 2371 in /global/cscratch1/sd/swowner/ > sleak/petsc-3.7.4/src/dm/interface/dm.c > [0]PETSC ERROR: #6 PCSetUp_MG() line 616 in /global/cscratch1/sd/swowner/ > sleak/petsc-3.7.4/src/ksp/pc/impls/mg/mg.c > [0]PETSC ERROR: #7 PCSetUp() line 968 in /global/cscratch1/sd/swowner/ > sleak/petsc-3.7.4/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: #8 KSPSetUp() line 390 in /global/cscratch1/sd/swowner/ > sleak/petsc-3.7.4/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #9 KSPSolve() line 599 in /global/cscratch1/sd/swowner/ > sleak/petsc-3.7.4/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #10 SNESSolve_NEWTONLS() line 230 in > /global/cscratch1/sd/swowner/sleak/petsc-3.7.4/src/snes/impls/ls/ls.c > [0]PETSC ERROR: #11 SNESSolve() line 4005 in /global/cscratch1/sd/swowner/ > sleak/petsc-3.7.4/src/snes/interface/snes.c > [0]PETSC ERROR: #12 main() line 1548 in /global/homes/j/jychang/ > Icesheet/ex48.c > [0]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -da_refine 4 > [0]PETSC ERROR: -ksp_rtol 1e-7 > [0]PETSC ERROR: -M 5 > [0]PETSC ERROR: -N 5 > [0]PETSC ERROR: -P 3 > [0]PETSC ERROR: -pc_mg_levels 5 > [0]PETSC ERROR: -pc_type mg > [0]PETSC ERROR: -thi_mat_type baij > [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to [email protected] > Rank 0 [Thu Mar 30 14:04:35 2017] [c0-0c0s5n0] application called > MPI_Abort(MPI_COMM_WORLD, 63) - process 0 > srun: error: nid00020: task 0: Aborted > srun: Terminating job step 4363145.1z > > it seems to me the PETSc from this module is not registering the > '-da_refine' entry. This is strange because I have no issue with this on > the latest petsc-dev version, anyone know about this error and/or why it > happens? > > On Thu, Mar 30, 2017 at 3:39 PM, Matthew Knepley <[email protected]> > wrote: > >> On Thu, Mar 30, 2017 at 3:38 PM, Justin Chang <[email protected]> >> wrote: >> >>> Okay, got it. What are the options for setting GAMG as the coarse solver? >>> >> >> -mg_coarse_pc_type gamg I think >> >> >>> On Thu, Mar 30, 2017 at 3:37 PM, Matthew Knepley <[email protected]> >>> wrote: >>> >>>> On Thu, Mar 30, 2017 at 3:04 PM, Justin Chang <[email protected]> >>>> wrote: >>>> >>>>> Yeah based on my experiments it seems setting pc_mg_levels to >>>>> $DAREFINE + 1 has decent performance. >>>>> >>>>> 1) is there ever a case where you'd want $MGLEVELS <= $DAREFINE? In >>>>> some of the PETSc tutorial slides (e.g., http://www.mcs.anl.gov/ >>>>> petsc/documentation/tutorials/TutorialCEMRACS2016.pdf on slide >>>>> 203/227) they say to use $MGLEVELS = 4 and $DAREFINE = 5, but when I ran >>>>> this, it was almost twice as slow as if $MGLEVELS >= $DAREFINE >>>>> >>>> >>>> Depending on how big the initial grid is, you may want this. There is a >>>> balance between coarse grid and fine grid work. >>>> >>>> >>>>> 2) So I understand that one cannot refine further than one grid point >>>>> in each direction, but is there any benefit to having $MGLEVELS > >>>>> $DAREFINE >>>>> by a lot? >>>>> >>>> >>>> Again, it depends on the size of the initial grid. >>>> >>>> On really large problems, you want to use GAMG as the coarse solver, >>>> which will move the problem onto a smaller number of nodes >>>> so that you can coarsen further. >>>> >>>> Matt >>>> >>>> >>>>> Thanks, >>>>> Justin >>>>> >>>>> On Thu, Mar 30, 2017 at 2:35 PM, Barry Smith <[email protected]> >>>>> wrote: >>>>> >>>>>> >>>>>> -da_refine $DAREFINE determines how large the final problem will >>>>>> be. >>>>>> >>>>>> By default if you don't supply pc_mg_levels then it uses $DAREFINE >>>>>> + 1 as the number of levels of MG to use; for example -da_refine 1 would >>>>>> result in 2 levels of multigrid. >>>>>> >>>>>> >>>>>> > On Mar 30, 2017, at 2:17 PM, Justin Chang <[email protected]> >>>>>> wrote: >>>>>> > >>>>>> > Hi all, >>>>>> > >>>>>> > Just a general conceptual question: say I am tinkering around with >>>>>> SNES ex48.c and am running the program with these options: >>>>>> > >>>>>> > mpirun -n $NPROCS -pc_type mg -M $XSEED -N $YSEED -P $ZSEED >>>>>> -thi_mat_type baij -da_refine $DAREFINE -pc_mg_levels $MGLEVELS >>>>>> > >>>>>> > I am not too familiar with mg, but it seems to me there is a very >>>>>> strong correlation between $MGLEVELS and $DAREFINE as well as perhaps >>>>>> even >>>>>> the initial coarse grid size (provided by $X/YZSEED). >>>>>> > >>>>>> > Is there a rule of thumb on how these parameters should be? I am >>>>>> guessing it probably is also hardware/architectural dependent? >>>>>> > >>>>>> > Thanks, >>>>>> > Justin >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> 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 >>>> >>> >>> >> >> >> -- >> 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 >> > >
