I think its now -dm_refine Matt
On Thu, Mar 30, 2017 at 4:17 PM, Justin Chang <[email protected]> wrote: > 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_libra >> ries_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/s >> leak/petsc-3.7.4/src/dm/impls/da/dareg.c >> [0]PETSC ERROR: #3 DMSetUp() line 744 in /global/cscratch1/sd/swowner/s >> leak/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/s >> leak/petsc-3.7.4/src/dm/interface/dm.c >> [0]PETSC ERROR: #6 PCSetUp_MG() line 616 in /global/cscratch1/sd/swowner/s >> leak/petsc-3.7.4/src/ksp/pc/impls/mg/mg.c >> [0]PETSC ERROR: #7 PCSetUp() line 968 in /global/cscratch1/sd/swowner/s >> leak/petsc-3.7.4/src/ksp/pc/interface/precon.c >> [0]PETSC ERROR: #8 KSPSetUp() line 390 in /global/cscratch1/sd/swowner/s >> leak/petsc-3.7.4/src/ksp/ksp/interface/itfunc.c >> [0]PETSC ERROR: #9 KSPSolve() line 599 in /global/cscratch1/sd/swowner/s >> leak/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/Iceshe >> et/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 >>> >> >> > -- 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
