[petsc-users] MatSetValues error with ViennaCL types
Dave May
dave.mayhem23 at gmail.com
Wed Aug 15 23:09:04 CDT 2018
On Thu, 16 Aug 2018 at 04:44, 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,
>
This error has nothing to do with matrix type being used. The size of the
matrix is defined by the particular DM. You should be using DM associated
data/APIs to set values in the matrix.
It's not obvious how the args here
call MatSetValues(A,1,row,sumpos,pos(0:iter-1),vals(0:iter-1),INS
ERT_VALUES,ier
actually relate to the DM. Code snippets aren't helpful in this case to
understand the error.
I suggest you send a complete example illustrating your actual problem.
Thanks,
Dave
>
>
>
>
>
>
>
> 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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