1) PetscMalloc() is never valid or needed in Fortran
2) there is no reason to use DMSetMatrixPreallocateOnly() just use
DMCreateMatrix() assuming that using a DM (DMDA, DMPLEX, etc) is suitable for
your problem.
At this end we are totally guessing at what you are doing and so have
little help we can provide. A simple, nonworking code that tries to do what
you would need would help us a great deal in understanding that you are trying
to do.
Barry
> On Aug 28, 2018, at 1:18 PM, Manuel Valera <[email protected]> wrote:
>
> Matthew, PetscMalloc gives the same error,
>
> Barry, it would be very hard for me to get the code to a minimum working
> example, i guess all i need to understand is how to setup a DM matrix with
> DMSetMatrixPreallocateOnly() instead of MatMPIAIJSetPreallocation() as we
> were doing before, is there a simple example who does this in Fortran?
>
> Is the PetscMalloc call needed? is 'call PetscMalloc(1,row,ierr)' a valid,
> compilable call to PetscMalloc? what other reason may there be for this error
> to happen ?
>
> Just remembering, that trying to setup the matrix with the
> MatAIJSetPreallocation() brings up an error to acknowledge the viennacl
> datatypes and that's why i'm trying to make this change on your
> recommendation,
>
> Thanks for your help,
>
>
>
>
>
> On Mon, Aug 27, 2018 at 7:35 PM, Smith, Barry F. <[email protected]> wrote:
>
> Send your code in a way we can compile and run it; it must be some simple
> issue that is hard to communicate in email.
>
> Barry
>
>
> > On Aug 27, 2018, at 5:51 PM, Manuel Valera <[email protected]> wrote:
> >
> > 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. <[email protected]>
> > 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 <[email protected]> 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. <[email protected]>
> > > 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 <[email protected]> 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 <[email protected]>
> > > > wrote:
> > > > On Wed, Aug 15, 2018 at 5:20 PM Manuel Valera <[email protected]>
> > > > 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 <[email protected]>
> > > > wrote:
> > > > On Wed, Aug 15, 2018 at 4:53 PM Manuel Valera <[email protected]>
> > > > 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 <[email protected]>
> > > > wrote:
> > > > On Wed, Aug 15, 2018 at 4:39 PM Manuel Valera <[email protected]>
> > > > 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/
> > > >
> > >
> > >
> >
> >
>
>
