[petsc-users] 'Inserting a new nonzero' issue on a reassembled matrix in parallel
Matthew Knepley
knepley at gmail.com
Thu Oct 24 05:15:20 CDT 2019
On Thu, Oct 24, 2019 at 6:09 AM Thibaut Appel <t.appel17 at imperial.ac.uk>
wrote:
> Hi Matthew,
>
> Thanks for having a look, your example runs just like mine in Fortran.
>
> In serial, the value (0.0,0.0) was inserted whereas it shouldn't have.
>
I do not see that in serial.
> In parallel, you'll see that an error "Inserting a new nonzero at global
> row/column" is triggered.
>
Yes, I see the error running in parallel. Will check Barry's fix.
Thanks,
Matt
> In both cases, MatSetValues tries to insert a zero value whereas
> IGNORE_ZERO_ENTRIES was set. That's what Barry is looking into, if I'm not
> mistaken.
>
>
> Thibaut
>
>
> On 24/10/2019 02:31, Matthew Knepley wrote:
>
> On Tue, Oct 22, 2019 at 1:37 PM Thibaut Appel <t.appel17 at imperial.ac.uk>
> wrote:
>
>> Hi both,
>>
>> Please find attached a tiny example (in Fortran, sorry Matthew) that - I
>> think - reproduces the problem we mentioned.
>>
>> Let me know.
>>
> Okay, I converted to C so I could understand, and it runs fine for me:
>
> master *:~/Downloads/tmp$ PETSC_ARCH=arch-master-complex-debug make main
>
> /PETSc3/petsc/bin/mpicc -o main.o -c -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
> -Qunused-arguments -fvisibility=hidden -g3 -I/PETSc3/petsc/petsc-dev/include
> -I/PETSc3/petsc/petsc-dev/arch-master-complex-debug/include
> -I/PETSc3/petsc/include -I/opt/X11/include `pwd`/main.c
>
> /PETSc3/petsc/bin/mpicc -Wl,-multiply_defined,suppress
> -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs
> -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
> -Qunused-arguments -fvisibility=hidden -g3 -o main main.o
> -Wl,-rpath,/PETSc3/petsc/petsc-dev/arch-master-complex-debug/lib
> -L/PETSc3/petsc/petsc-dev/arch-master-complex-debug/lib
> -Wl,-rpath,/PETSc3/petsc/petsc-dev/arch-master-complex-debug/lib
> -L/PETSc3/petsc/petsc-dev/arch-master-complex-debug/lib
> -Wl,-rpath,/PETSc3/petsc/lib -L/PETSc3/petsc/lib -Wl,-rpath,/opt/X11/lib
> -L/opt/X11/lib
> -Wl,-rpath,/usr/local/lib/gcc/x86_64-apple-darwin10.4.0/4.6.0
> -L/usr/local/lib/gcc/x86_64-apple-darwin10.4.0/4.6.0
> -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lpetsc -lfftw3_mpi -lfftw3
> -llapack -lblas -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lchaco
> -lparmetis -lmetis -ltriangle -lz -lX11 -lctetgen -lstdc++ -ldl -lmpichf90
> -lpmpich -lmpich -lopa -lmpl -lpthread -lgfortran -lgcc_s.10.5 -lstdc++ -ldl
>
> master *:~/Downloads/tmp$ ./main
>
> After first assembly:
>
> Mat Object: 1 MPI processes
>
> type: seqaij
>
> row 0: (0, 1. + 1. i)
>
> row 1: (1, 1. + 1. i)
>
> row 2: (2, 1. + 1. i)
>
> row 3: (3, 1. + 1. i)
>
> row 4: (4, 1. + 1. i)
>
> row 5: (5, 1. + 1. i)
>
> row 6: (6, 1. + 1. i)
>
> row 7: (7, 1. + 1. i)
>
> row 8: (8, 1. + 1. i)
>
> row 9: (9, 1. + 1. i)
>
> After second assembly:
>
> Mat Object: 1 MPI processes
>
> type: seqaij
>
> row 0: (0, 1. + 1. i)
>
> row 1: (1, 1. + 1. i)
>
> row 2: (2, 1. + 1. i)
>
> row 3: (3, 1. + 1. i)
>
> row 4: (4, 1. + 1. i)
>
> row 5: (5, 1. + 1. i)
>
> row 6: (6, 1. + 1. i)
>
> row 7: (7, 1. + 1. i)
>
> row 8: (8, 1. + 1. i)
>
> row 9: (9, 1. + 1. i)
> row 0 col: 9 val: 0. + 0. i
>
> I attach my code. So then I ran your Fortran:
>
> /PETSc3/petsc/bin/mpif90 -c -Wall -ffree-line-length-0
> -Wno-unused-dummy-argument -Wno-unused-variable -g -I/PETSc3/petsc/petsc-dev/include
> -I/PETSc3/petsc/petsc-dev/arch-master-complex-debug/include
> -I/PETSc3/petsc/include -I/opt/X11/include -o main2.o main2.F90
>
> /PETSc3/petsc/bin/mpif90 -Wl,-multiply_defined,suppress
> -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs
> -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall
> -ffree-line-length-0 -Wno-unused-dummy-argument -Wno-unused-variable -g -o
> main2 main2.o
> -Wl,-rpath,/PETSc3/petsc/petsc-dev/arch-master-complex-debug/lib
> -L/PETSc3/petsc/petsc-dev/arch-master-complex-debug/lib
> -Wl,-rpath,/PETSc3/petsc/petsc-dev/arch-master-complex-debug/lib
> -L/PETSc3/petsc/petsc-dev/arch-master-complex-debug/lib
> -Wl,-rpath,/PETSc3/petsc/lib -L/PETSc3/petsc/lib -Wl,-rpath,/opt/X11/lib
> -L/opt/X11/lib
> -Wl,-rpath,/usr/local/lib/gcc/x86_64-apple-darwin10.4.0/4.6.0
> -L/usr/local/lib/gcc/x86_64-apple-darwin10.4.0/4.6.0
> -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lpetsc -lfftw3_mpi -lfftw3
> -llapack -lblas -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lchaco
> -lparmetis -lmetis -ltriangle -lz -lX11 -lctetgen -lstdc++ -ldl -lmpichf90
> -lpmpich -lmpich -lopa -lmpl -lpthread -lgfortran -lgcc_s.10.5 -lstdc++ -ldl
>
> master *:~/Downloads/tmp$ ./main2
>
> After first assembly:
>
> Mat Object: 1 MPI processes
>
> type: seqaij
>
> row 0: (0, 1.)
>
> row 1: (1, 1.)
>
> row 2: (2, 1.)
>
> row 3: (3, 1.)
>
> row 4: (4, 1.)
>
> row 5: (5, 1.)
>
> row 6: (6, 1.)
>
> row 7: (7, 1.)
>
> row 8: (8, 1.)
>
> row 9: (9, 1.)
>
> After second assembly:
>
> Mat Object: 1 MPI processes
>
> type: seqaij
>
> row 0: (0, 1.)
>
> row 1: (1, 1.)
>
> row 2: (2, 1.)
>
> row 3: (3, 1.)
>
> row 4: (4, 1.)
>
> row 5: (5, 1.)
>
> row 6: (6, 1.)
>
> row 7: (7, 1.)
>
> row 8: (8, 1.)
>
> row 9: (9, 1.)
>
> row: 0 col: 9 val: 0.000000000000000000E+00 0.000000000000000000E+00
>
> I am not seeing an error. Am I not running it correctly?
>
> Thanks,
>
> MAtt
>
>> Thibaut
>>
>>
>> On 22/10/2019 17:48, Matthew Knepley wrote:
>>
>> On Tue, Oct 22, 2019 at 12:43 PM Thibaut Appel via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>>
>>> Hi Hong,
>>>
>>> Thank you for having a look, I copied/pasted your code snippet into
>>> ex28.c and the error indeed appears if you change that col[0]. That's
>>> because you did not allow a new non-zero location in the matrix with the
>>> option MAT_NEW_NONZERO_LOCATION_ERR.
>>>
>>> I spent the day debugging the code and already checked my calls to
>>> MatSetValues:
>>>
>>> For all MatSetValues calls corresponding to the row/col location in the
>>> error messages in the subsequent assembly, the numerical value associated
>>> with that row/col was exactly (0.0,0.0) (complex arithmetic) so it
>>> shouldn't be inserted w.r.t. the option MAT_IGNORE_ZERO_ENTRIES. It seems
>>> MatSetValues still did it anyway.
>>>
>> Okay, lets solve this problem first. You say that
>>
>> - You called MatSetOption(A, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE)
>> - You called MatSetValues(A, ,,,, ADD_VALUES, ..., val) and val had a
>> complex 0 in it
>> - PETSc tried to insert the complex 0
>>
>> This should be really easy to test in a tiny example. Do you mind making
>> it? If its broken, I will fix it.
>>
>> Thanks,
>>
>> Matt
>>
>>> I was able to solve the problem by adding
>>> MatSetOption(L,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE) after my first
>>> assembly. However I don't know why it fixed it as the manual seems to say
>>> this is just for efficiency purposes
>>>
>>> It "should be specified after the first matrix has been fully assembled.
>>> This option ensures that certain data structures and communication
>>> information will be reused (instead of regenerated during successive steps,
>>> thereby increasing efficiency"
>>>
>>> So I'm still puzzled by why I got that error in the first place. Unless
>>> "regenerated" implies resetting some attributes of the preallocated
>>> non-zero structure / first assembly?
>>>
>>>
>>> Thibaut
>>>
>>>
>>> On 22/10/2019 17:06, Zhang, Hong wrote:
>>>
>>> Thibaut:
>>> Check your code on MatSetValues(), likely you set a value "to a new
>>> nonzero at global row/column (200, 160) into matrix" L.
>>> I tested petsc/src/mat/examples/tests/ex28.c by adding
>>> @@ -95,6 +95,26 @@ int main(int argc,char **args)
>>> /* Compute numeric factors using same F, then solve */
>>> for (k = 0; k < num_numfac; k++) {
>>> /* Get numeric factor of A[k] */
>>> + if (k==0) {
>>> + ierr = MatZeroEntries(A[0]);CHKERRQ(ierr);
>>> + for (i=rstart; i<rend; i++) {
>>> + col[0] = i-1; col[1] = i; col[2] = i+1;
>>> + if (i == 0) {
>>> + ierr =
>>> MatSetValues(A[k],1,&i,2,col+1,value+1,INSERT_VALUES);CHKERRQ(ierr);
>>> + } else if (i == N-1) {
>>> + ierr =
>>> MatSetValues(A[k],1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
>>> + } else {
>>> + ierr =
>>> MatSetValues(A[k],1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
>>> + }
>>> + }
>>> + if (!rank) {
>>> + i = N - 1; col[0] = N - 1;
>>> + ierr =
>>> MatSetValues(A[k],1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
>>> + }
>>> + ierr = MatAssemblyBegin(A[k],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>> + ierr = MatAssemblyEnd(A[k],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>> + }
>>> +
>>>
>>> It works in both sequential and parallel. If I set col[0] = 0, then I
>>> get the same error as yours.
>>> Hong
>>>
>>>> Dear PETSc developers,
>>>>
>>>> I'm extending a validated matrix preallocation/assembly part of my code
>>>> to solve multiple linear systems with MUMPS at each iteration of a main
>>>> loop, following the example src/mat/examples/tests/ex28.c that Hong Zhang
>>>> added a few weeks ago. The difference is that I'm using just 1 matrix to
>>>> solve different systems.
>>>>
>>>> I'm trying to investigate a nasty bug arising when I try to assemble
>>>> "for a second time" that MPIAIJ matrix. The issue arises only in parallel,
>>>> serial works fine.
>>>>
>>>> Creating 1 MPIAIJ matrix, preallocating it "perfectly" with the case
>>>> where I have the fewest zero entries in the non-zero structure, before
>>>> getting its symbolic factorization.
>>>>
>>>> Further in the main loop, I'm solely changing its entries *retaining
>>>> the non-zero structure*.
>>>>
>>>> Here is the simplified Fortran code I'm using:
>>>>
>>>> ! Fill (M,N) case to ensure all non-zero entries are preallocated
>>>> CALL set_equations(M,N)
>>>>
>>>> CALL alloc_matrix(L)
>>>> ! --> Call MatSeqAIJSetPreallocation/MatMPIAIJSetPreallocation
>>>> ! --> Sets MAT_IGNORE_ZERO_ENTRIES, MAT_NEW_NONZERO_ALLOCATION_ERR,
>>>> MAT_NO_OFF_PROC_ENTRIES to true
>>>>
>>>> CALL assemble_matrix(L)
>>>> ! --> Calls MatSetValues with ADD_VALUES
>>>> ! --> Call MatAssemblyBegin/MatAssemblyEnd
>>>>
>>>> ! Tell PETSc that new non-zero insertions in matrix are forbidden
>>>> CALL MatSetOption(L,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE,ierr)
>>>>
>>>> CALL set_mumps_parameters()
>>>>
>>>> ! Get symbolic LU factorization using MUMPS
>>>> CALL MatGetFactor(L,MATSOLVERMUMPS,MAT_FACTOR_LU,F,ierr)
>>>> CALL MatGetOrdering(L,MATORDERINGNATURAL,rperm,cperm,ierr)
>>>> CALL MatLUFactorSymbolic(F,L,rperm,cperm,info,ierr)
>>>>
>>>> CALL initialize_right_hand_sides()
>>>>
>>>> ! Zero matrix entries
>>>> CALL MatZeroEntries(L,ierr)
>>>>
>>>> ! Main loop
>>>> DO itr=1, maxitr
>>>>
>>>> DO m = 1, M
>>>> DO n = 1, N
>>>>
>>>> CALL set_equations(m,n)
>>>> CALL assemble_matrix(L) ! ERROR HERE when m=1, n=1, CRASH IN
>>>> MatSetValues call
>>>>
>>>> ! Solving the linear system associated with (m,n)
>>>> CALL MatLUFactorNumeric(F,L,info,ierr)
>>>> CALL MatSolve(F,v_rhs(m,n),v_sol(m,n),ierr)
>>>>
>>>> ! Process v_rhs's from v_sol's for next iteration
>>>>
>>>> CALL MatZeroEntries(L,ierr)
>>>>
>>>> END DO
>>>> END DO
>>>>
>>>> END DO
>>>>
>>>>
>>>> Testing on a small case, the error I get is
>>>> [1]PETSC ERROR: --------------------- Error Message
>>>> --------------------------------------------------------------
>>>> [1]PETSC ERROR: Argument out of range
>>>> [1]PETSC ERROR: Inserting a new nonzero at global row/column (200, 160)
>>>> into matrix
>>>> [1]PETSC ERROR: See
>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>>> shooting.
>>>> [1]PETSC ERROR: Petsc Release Version 3.12.0, unknown
>>>> [1]PETSC ERROR: Configure options --PETSC_ARCH=cplx_gcc_debug
>>>> --with-scalar-type=complex --with-precision=double --with-debugging=1
>>>> --with-valgrind=1 --with-debugger=gdb --with-fortran-kernels=1
>>>> --download-mpich --download-fblaslapack --download-scalapack
>>>> --download-metis --download-parmetis --download-ptscotch --download-mumps
>>>> --download-slepc --COPTFLAGS="-O0 -g" --CXXOPTFLAGS="-O0 -g"
>>>> --FOPTFLAGS="-O0 -g -fbacktrace"
>>>> [1]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 634 in
>>>> /home/thibaut/Packages/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>>> [1]PETSC ERROR: #2 MatSetValues() line 1375 in
>>>> /home/thibaut/Packages/petsc/src/mat/interface/matrix.c
>>>> [1]PETSC ERROR: #3 User provided function() line 0 in User file
>>>> application called MPI_Abort(MPI_COMM_SELF, 63) - process 0
>>>>
>>>>
>>>>
>>>> which I don't understand. That element was not in the non-zero
>>>> structure and wasn't preallocated. I printed the value to be inserted at
>>>> this location (200,160) and it is exactly
>>>> (0.0000000000000000,0.0000000000000000) so this entry should not be
>>>> inserted due to MAT_IGNORE_ZERO_ENTRIES, however it seems it is. I'm using
>>>> ADD_VALUES in MatSetValues but it is the only call where (200,160) is
>>>> inserted.
>>>>
>>>>
>>>> - I zero the matrix entries with MatZeroEntries which retains the
>>>> non-zero structure (checked when I print the matrix) but tried to comment
>>>> the corresponding calls.
>>>>
>>>> - I tried to set MAT_NEW_NONZERO_LOCATION_ERR AND
>>>> MAT_NEW_NONZERO_ALLOCATION_ERR to PETSC_FALSE without effect.
>>>>
>>>>
>>>> Perhaps there's something fundamentally wrong in my approach, in any
>>>> case would you have any suggestions to identify the exact problem?
>>>>
>>>> Using PETSc 3.12.0. Thanks for your support,
>>>>
>>>>
>>>> Thibaut
>>>>
>>>
>>
>> --
>> 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.cse.buffalo.edu/~knepley/>
>>
>>
>
> --
> 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.cse.buffalo.edu/~knepley/>
>
>
--
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.cse.buffalo.edu/~knepley/>
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