[petsc-users] MatSetValues error with ViennaCL types
Manuel Valera
mvalera-w at sdsu.edu
Mon Aug 27 17:51:40 CDT 2018
Hello everyone,
I just had time to work on this again, and checked the code for errors on
the matrix entries, this is the exact code i was using for creating the
matrix without DMSetMatrixPreallocateOnly, using MatMPIAIJSetPreallocation
and it worked that way, but trying this way i get the same 'Column too
large' error using any number at the column position of MatSetValues,
I have set up my code to print the column argument (n) of MatSetValues and
in this case is 7 (lower than 124), it still gives error, even entering a
specific number in the MatSetValues column argument position gives the same
error.
So next i went back to ex.50 here:
http://www.mcs.anl.gov/petsc/petsc-current/src/ts/examples/tutorials/ex50.c.html
and it has a very similar structure except the PetscMalloc1() call, so i
tried adding that and got:
/home/valera/ParGCCOM/Src/DMDALaplacian.f90:114: undefined reference to
`petscmalloc1_'
Any ideas on this behaviour?
Thanks so much,
On Thu, Aug 16, 2018 at 11:20 AM, Smith, Barry F. <bsmith at mcs.anl.gov>
wrote:
>
> Column too large: col 10980 max 124
>
> You need to check the code that is generating the matrix entries. The
> matrix has 124 columns but you are attempting to put a value at column 10980
>
> Barry
>
>
> > On Aug 15, 2018, at 9:44 PM, Manuel Valera <mvalera-w at sdsu.edu> wrote:
> >
> > Thanks Matthew and Barry,
> >
> > Now my code looks like:
> >
> > call DMSetMatrixPreallocateOnly(daDummy,PETSC_TRUE,ierr)
> > call DMSetMatType(daDummy,MATMPIAIJVIENNACL,ierr)
> > call DMSetVecType(daDummy,VECMPIVIENNACL,ierr)
> > call DMCreateMatrix(daDummy,A,ierr)
> > call MatSetFromOptions(A,ierr)
> > call MatSetUp(A,ierr)
> > [...]
> > call MatSetValues(A,1,row,sumpos,
> pos(0:iter-1),vals(0:iter-1),INSERT_VALUES,ierr)
> > [...]
> > call MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY, ierr)
> > call MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY, ierr)
> >
> > And i get a different error, now is:
> >
> > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > [0]PETSC ERROR: Argument out of range
> > [0]PETSC ERROR: Column too large: col 10980 max 124
> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> > [0]PETSC ERROR: Petsc Development GIT revision: v3.9.2-549-g779ab53 GIT
> Date: 2018-05-31 17:31:13 +0300
> > [0]PETSC ERROR: ./gcmLEP.GPU on a cuda-debug named node50 by valera Wed
> Aug 15 19:40:00 2018
> > [0]PETSC ERROR: Configure options PETSC_ARCH=cuda-debug
> --with-mpi-dir=/usr/lib64/openmpi --COPTFLAGS=-O2 --CXXOPTFLAGS=-O2
> --FOPTFLAGS=-O2 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
> --CUDAFLAGS=-arch=sm_60 --with-blaslapack-dir=/usr/lib64
> --download-viennacl
> > [0]PETSC ERROR: #1 MatSetValues_SeqAIJ() line 442 in
> /home/valera/petsc/src/mat/impls/aij/seq/aij.c
> > [0]PETSC ERROR: #2 MatSetValues() line 1339 in
> /home/valera/petsc/src/mat/interface/matrix.c
> >
> >
> > Thanks again,
> >
> >
> >
> >
> >
> >
> >
> >
> > On Wed, Aug 15, 2018 at 7:02 PM, Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
> >
> > Should be
> >
> > call DMSetMatType(daDummy,MATMPIAIJVIENNACL,ierr)
> > call DMSetVecType(daDummy,VECMPIVIENNACL,ierr)
> > call DMCreateMatrix(daDummy,A,ierr)
> >
> > and remove the rest. You need to set the type of Mat you want the DM
> to return BEFORE you create the matrix.
> >
> > Barry
> >
> >
> >
> > > On Aug 15, 2018, at 4:45 PM, Manuel Valera <mvalera-w at sdsu.edu> wrote:
> > >
> > > Ok thanks for clarifying that, i wasn't sure if there were different
> types,
> > >
> > > Here is a stripped down version of my code, it seems like the
> preallocation is working now since the matrix population part is working
> without problem, but here it is for illustration purposes:
> > >
> > > call DMSetMatrixPreallocateOnly(daDummy,PETSC_TRUE,ierr)
> > > call DMCreateMatrix(daDummy,A,ierr)
> > > call MatSetFromOptions(A,ierr)
> > > call DMSetMatType(daDummy,MATMPIAIJVIENNACL,ierr)
> > > call DMSetVecType(daDummy,VECMPIVIENNACL,ierr)
> > > call MatMPIAIJSetPreallocation(A,19,PETSC_NULL_INTEGER,19,
> PETSC_NULL_INTEGER,ierr)
> > > call MatSetUp(A,ierr)
> > > [...]
> > > call MatSetValues(A,1,row,sumpos,
> pos(0:iter-1),vals(0:iter-1),INSERT_VALUES,ierr)
> > > [...]
> > > call MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY, ierr)
> > > call MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY, ierr)
> > >
> > > Adding the first line there did the trick,
> > >
> > > Now the problem seems to be the program is not recognizing the matrix
> as ViennaCL type when i try with more than one processor, i get now:
> > >
> > > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > [0]PETSC ERROR: No support for this operation for this object type
> > > [0]PETSC ERROR: Currently only handles ViennaCL matrices
> > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > [0]PETSC ERROR: Petsc Development GIT revision: v3.9.2-549-g779ab53
> GIT Date: 2018-05-31 17:31:13 +0300
> > > [0]PETSC ERROR: ./gcmLEP.GPU on a cuda-debug named node50 by valera
> Wed Aug 15 14:44:22 2018
> > > [0]PETSC ERROR: Configure options PETSC_ARCH=cuda-debug
> --with-mpi-dir=/usr/lib64/openmpi --COPTFLAGS=-O2 --CXXOPTFLAGS=-O2
> --FOPTFLAGS=-O2 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
> --CUDAFLAGS=-arch=sm_60 --with-blaslapack-dir=/usr/lib64
> --download-viennacl
> > > [0]PETSC ERROR: #1 PCSetUp_SAVIENNACL() line 47 in
> /home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu
> > > [0]PETSC ERROR: #2 PCSetUp() line 932 in /home/valera/petsc/src/ksp/pc/
> interface/precon.c
> > > [0]PETSC ERROR: #3 KSPSetUp() line 381 in /home/valera/petsc/src/ksp/
> ksp/interface/itfunc.c
> > >
> > > When running with:
> > >
> > > mpirun -n 1 ./gcmLEP.GPU tc=TestCases/LockRelease/LE_6x6x6/
> jid=tiny_cuda_test_n2 -ksp_type cg -dm_vec_type viennacl -dm_mat_type
> aijviennacl -pc_type saviennacl -log_view
> > >
> > >
> > > Thanks,
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Wed, Aug 15, 2018 at 2:32 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > > On Wed, Aug 15, 2018 at 5:20 PM Manuel Valera <mvalera-w at sdsu.edu>
> wrote:
> > > It seems to be resumed on: I do not know how to preallocate a DM
> Matrix correctly.
> > >
> > > There is only one matrix type, Mat. There are no separate DM matrices.
> A DM can create a matrix for you
> > > using DMCreateMatrix(), but that is a Mat and it is preallocated
> correctly. I am not sure what you are doing.
> > >
> > > Thanks,
> > >
> > > Matt
> > >
> > > The interesting part is that it only breaks when i need to populate a
> GPU matrix from MPI, so kudos on that, but it seems i need to do better on
> my code to get this setup working,
> > >
> > > Any help would be appreciated,
> > >
> > > Thanks,
> > >
> > >
> > >
> > > On Wed, Aug 15, 2018 at 2:15 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > > On Wed, Aug 15, 2018 at 4:53 PM Manuel Valera <mvalera-w at sdsu.edu>
> wrote:
> > > Thanks Matthew,
> > >
> > > I try to do that when calling:
> > >
> > > call MatMPIAIJSetPreallocation(A,19,PETSC_NULL_INTEGER,19,
> PETSC_NULL_INTEGER,ierr)
> > >
> > > But i am not aware on how to do this for the DM if it needs something
> more specific/different,
> > >
> > > The error says that your preallocation is wrong for the values you are
> putting in. The DM does not control either,
> > > so I do not understand your email.
> > >
> > > Thanks,
> > >
> > > Matt
> > >
> > > Thanks,
> > >
> > > On Wed, Aug 15, 2018 at 1:51 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > > On Wed, Aug 15, 2018 at 4:39 PM Manuel Valera <mvalera-w at sdsu.edu>
> wrote:
> > > Hello PETSc devs,
> > >
> > > I am running into an error when trying to use the MATMPIAIJVIENNACL
> Matrix type in MPI calls, the same code runs for MATSEQAIJVIENNACL type in
> one processor. The error happens when calling MatSetValues for this
> specific configuration. It does not occur when using MPI DMMatrix types
> only.
> > >
> > > The DM properly preallocates the matrix. I am assuming you do not here.
> > >
> > > Matt
> > >
> > > Any help will be appreciated,
> > >
> > > Thanks,
> > >
> > >
> > >
> > > My program call:
> > >
> > > mpirun -n 2 ./gcmLEP.GPU tc=TestCases/LockRelease/LE_6x6x6/
> jid=tiny_cuda_test_n2 -ksp_type cg -dm_vec_type viennacl -dm_mat_type
> aijviennacl -pc_type saviennacl -log_view
> > >
> > >
> > > The error (repeats after each MatSetValues call):
> > >
> > > [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > > [1]PETSC ERROR: Argument out of range
> > > [1]PETSC ERROR: Inserting a new nonzero at global row/column (75, 50)
> into matrix
> > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/
> documentation/faq.html for trouble shooting.
> > > [1]PETSC ERROR: Petsc Development GIT revision: v3.9.2-549-g779ab53
> GIT Date: 2018-05-31 17:31:13 +0300
> > > [1]PETSC ERROR: ./gcmLEP.GPU on a cuda-debug named node50 by valera
> Wed Aug 15 13:10:44 2018
> > > [1]PETSC ERROR: Configure options PETSC_ARCH=cuda-debug
> --with-mpi-dir=/usr/lib64/openmpi --COPTFLAGS=-O2 --CXXOPTFLAGS=-O2
> --FOPTFLAGS=-O2 --with-shared-libraries=1 --with-debugging=1 --with-cuda=1
> --CUDAFLAGS=-arch=sm_60 --with-blaslapack-dir=/usr/lib64
> --download-viennacl
> > > [1]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 608 in
> /home/valera/petsc/src/mat/impls/aij/mpi/mpiaij.c
> > > [1]PETSC ERROR: #2 MatSetValues() line 1339 in
> /home/valera/petsc/src/mat/interface/matrix.c
> > >
> > >
> > > My Code structure:
> > >
> > > call DMCreateMatrix(daDummy,A,ierr)
> > > call MatSetFromOptions(A,ierr)
> > > call MPI_Comm_size(PETSC_COMM_WORLD, numprocs, ierr)
> > > if (numprocs > 1) then ! set matrix type parallel
> > > ! Get local size
> > > call DMDACreateNaturalVector(daDummy,Tmpnat,ierr)
> > > call VecGetLocalSize(Tmpnat,locsize,ierr)
> > > call VecDestroy(Tmpnat,ierr)
> > > ! Set matrix
> > > #ifdef GPU
> > > call MatSetType(A,MATAIJVIENNACL,ierr)
> > > call DMSetMatType(daDummy,MATMPIAIJVIENNACL,ierr)
> > > call DMSetVecType(daDummy,VECMPIVIENNACL,ierr)
> > > print*,'SETTING GPU TYPES'
> > > #else
> > > call DMSetMatType(daDummy,MATMPIAIJ,ierr)
> > > call DMSetMatType(daDummy,VECMPI,ierr)
> > > call MatSetType(A,MATMPIAIJ,ierr)!
> > > #endif
> > > call MatMPIAIJSetPreallocation(A,19,PETSC_NULL_INTEGER,19,
> PETSC_NULL_INTEGER,ierr)
> > > else ! set matrix type sequential
> > > #ifdef GPU
> > > call DMSetMatType(daDummy,MATSEQAIJVIENNACL,ierr)
> > > call DMSetVecType(daDummy,VECSEQVIENNACL,ierr)
> > > call MatSetType(A,MATSEQAIJVIENNACL,ierr)
> > > print*,'SETTING GPU TYPES'
> > > #else
> > > call DMSetMatType(daDummy,MATSEQAIJ,ierr)
> > > call DMSetMatType(daDummy,VECSEQ,ierr)
> > > call MatSetType(A,MATSEQAIJ,ierr)
> > > #endif
> > > call MatSetUp(A,ierr)
> > > call getCenterInfo(daGrid,xstart,ystart,zstart,xend,yend,zend)
> > >
> > > do k=zstart,zend-1
> > > do j=ystart,yend-1
> > > do i=xstart,xend-1
> > > [..]
> > > call MatSetValues(A,1,row,sumpos,
> pos(0:iter-1),vals(0:iter-1),INSERT_VALUES,ierr)
> > > [..]
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > 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/
> > >
> > >
> > >
> > > --
> > > 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/
> > >
> > >
> > >
> > > --
> > > 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/
> > >
> >
> >
>
>
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