[petsc-users] Correlation between da_refine and pg_mg_levels

Matthew Knepley knepley at gmail.com
Thu Mar 30 16:21:20 CDT 2017 

I think its now -dm_refine

   Matt

On Thu, Mar 30, 2017 at 4:17 PM, Justin Chang <jychang48 at gmail.com> 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 <jychang48 at gmail.com> 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 petsc-maint at mcs.anl.gov----------
>> 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 <knepley at gmail.com>
>> wrote:
>>
>>> On Thu, Mar 30, 2017 at 3:38 PM, Justin Chang <jychang48 at gmail.com>
>>> 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 <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Thu, Mar 30, 2017 at 3:04 PM, Justin Chang <jychang48 at gmail.com>
>>>>> 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 <bsmith at mcs.anl.gov>
>>>>>> 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 <jychang48 at gmail.com>
>>>>>>> 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
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