[petsc-users] MatSetValues error with ViennaCL types
Manuel Valera
mvalera-w at sdsu.edu
Wed Aug 29 16:49:13 CDT 2018
Update:
I made it work like you suggested Barry, i had to comment the code line to
set up the pc_type saviennacl, that way i am getting as ksp_view:
KSP Object: 2 MPI processes
type: cg
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-07, absolute=1e-50, divergence=10000.
left preconditioning
using PRECONDITIONED norm type for convergence test
PC Object: 2 MPI processes
type: bjacobi
number of blocks = 2
Local solve is same for all blocks, in the following KSP and PC objects:
KSP Object: (sub_) 1 MPI processes
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000.
left preconditioning
using NONE norm type for convergence test
PC Object: (sub_) 1 MPI processes
type: ilu
out-of-place factorization
0 levels of fill
tolerance for zero pivot 2.22045e-14
matrix ordering: natural
factor fill ratio given 1., needed 1.
Factored matrix follows:
Mat Object: 1 MPI processes
type: seqaij
rows=75, cols=75
package used to perform factorization: petsc
total: nonzeros=927, allocated nonzeros=927
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
Mat Object: 1 MPI processes
type: seqaijviennacl
rows=75, cols=75
total: nonzeros=927, allocated nonzeros=1335
total number of mallocs used during MatSetValues calls =84
not using I-node routines
linear system matrix = precond matrix:
Mat Object: 2 MPI processes
type: mpiaijviennacl
rows=125, cols=125
total: nonzeros=1685, allocated nonzeros=2885
total number of mallocs used during MatSetValues calls =184
has attached near null space
Press_Max: 1.9995807630564922E-004
This is what we want, right?
Still if i try using pc_type saviennacl directly it breaks,
Thanks for your help i'll try my speedup like this,
On Wed, Aug 29, 2018 at 2:21 PM, Manuel Valera <mvalera-w at sdsu.edu> wrote:
> Ok, executing with:
>
> mpirun -n 2 ./gcmLEP.GPU tc=TestCases/LockRelease/LE_6x6x6/
> jid=tiny_cuda_test_n1 -pc_type bjacobi -pc_sub_type saviennacl -ksp_view
>
>
> I get:
>
>
> SETTING GPU TYPES
> Matrix type: mpiaijviennacl
>
> Of sizes: 125 x 125
> Matrix type: mpiaijviennacl
>
> Of sizes: 125 x 125
> [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: v3.9.3-1264-g6fb0cd4 GIT
> Date: 2018-08-29 12:42:36 -0600
> [0]PETSC ERROR: ./gcmLEP.GPU on a cuda-debug named node50 by valera Wed
> Aug 29 14:20:42 2018
> [0]PETSC ERROR: Configure options PETSC_ARCH=cuda-debug --with-cc=mpicc
> --with-cxx=mpic++ --with-fc=mpifort --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 --download-cusp
> [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
> [1]PETSC ERROR: ------------------------------
> ------------------------------------------
> [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [1]PETSC ERROR: likely location of problem given in stack below
> [1]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [1]PETSC ERROR: INSTEAD the line number of the start of the function
> [1]PETSC ERROR: is given.
> [1]PETSC ERROR: [1] PetscTraceBackErrorHandler line 182
> /home/valera/petsc/src/sys/error/errtrace.c
> [1]PETSC ERROR: [1] PetscError line 352 /home/valera/petsc/src/sys/
> error/err.c
> [1]PETSC ERROR: [1] PCSetUp_SAVIENNACL line 45
> /home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu
> [1]PETSC ERROR: [1] PCSetUp line 894 /home/valera/petsc/src/ksp/pc/
> interface/precon.c
> [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: Signal received
> [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [1]PETSC ERROR: Petsc Development GIT revision: v3.9.3-1264-g6fb0cd4 GIT
> Date: 2018-08-29 12:42:36 -0600
> [1]PETSC ERROR: ./gcmLEP.GPU on a cuda-debug named node50 by valera Wed
> Aug 29 14:20:42 2018
> [1]PETSC ERROR: Configure options PETSC_ARCH=cuda-debug --with-cc=mpicc
> --with-cxx=mpic++ --with-fc=mpifort --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 --download-cusp
> [1]PETSC ERROR: #1 User provided function() line 0 in unknown file
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 59.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> [0]PETSC ERROR: ------------------------------
> ------------------------------------------
> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
> batch system) has told this process to end
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/
> documentation/faq.html#valgrind
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [0]PETSC ERROR: INSTEAD the line number of the start of the function
> [0]PETSC ERROR: is given.
> [0]PETSC ERROR: [0] PetscCommDuplicate line 130 /home/valera/petsc/src/sys/
> objects/tagm.c
> [0]PETSC ERROR: [0] PetscHeaderCreate_Private line 41
> /home/valera/petsc/src/sys/objects/inherit.c
> [0]PETSC ERROR: [0] ISCreate line 35 /home/valera/petsc/src/vec/is/
> is/interface/isreg.c
> [0]PETSC ERROR: [0] ISCreateGeneral line 658 /home/valera/petsc/src/vec/is/
> is/impls/general/general.c
> [0]PETSC ERROR: [0] PCSetUp_SAVIENNACL line 45
> /home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu
> [0]PETSC ERROR: [0] PCSetUp line 894 /home/valera/petsc/src/ksp/pc/
> interface/precon.c
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.9.3-1264-g6fb0cd4 GIT
> Date: 2018-08-29 12:42:36 -0600
> [0]PETSC ERROR: ./gcmLEP.GPU on a cuda-debug named node50 by valera Wed
> Aug 29 14:20:42 2018
> [0]PETSC ERROR: Configure options PETSC_ARCH=cuda-debug --with-cc=mpicc
> --with-cxx=mpic++ --with-fc=mpifort --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 --download-cusp
> [0]PETSC ERROR: #3 User provided function() line 0 in unknown file
> [node50:77836] 1 more process has sent help message help-mpi-api.txt /
> mpi-abort
> [node50:77836] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>
>
>
> On Wed, Aug 29, 2018 at 2:02 PM, Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
>
>> Please send complete error message
>>
>>
>> > On Aug 29, 2018, at 3:40 PM, Manuel Valera <mvalera-w at sdsu.edu> wrote:
>> >
>> > Yeah, no sorry, i get the same error with -pc_type bjacobi
>> -sub_pc_type SAVIENNACL : "Currently only handles ViennaCL matrices"
>> >
>> >
>> > Thanks and let me know of any progress on this issue,
>> >
>> >
>> >
>> > On Wed, Aug 29, 2018 at 1:37 PM, Manuel Valera <mvalera-w at sdsu.edu>
>> wrote:
>> > Awesome, thanks!
>> >
>> > On Wed, Aug 29, 2018 at 1:29 PM, Smith, Barry F. <bsmith at mcs.anl.gov>
>> wrote:
>> >
>> >
>> > > On Aug 29, 2018, at 3:26 PM, Manuel Valera <mvalera-w at sdsu.edu>
>> wrote:
>> > >
>> > >
>> > >
>> > > You may need to use just plain PCBJACOBI or PCASM for parallelism
>> and then SAVIENNACL sequentially on each block.
>> > >
>> > >
>> > > Can you elaborate a little in how to do this? do you mean i can only
>> use viennacl in serial at the moment or this is a suggestion of a
>> workaround on how to make it work?
>> >
>> > -pc_type bjacobi -sub_pc_type SAVIENNACL
>> >
>> > This will run in parallel and utilize the GPU for each block of the
>> preconditioner.
>> >
>> > Barry
>> >
>> > >
>> > >
>> > > Thanks,
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > > On Aug 29, 2018, at 1:50 PM, Manuel Valera <mvalera-w at sdsu.edu>
>> wrote:
>> > > >
>> > > > Hi everyone,
>> > > >
>> > > > Thanks for your responses, i understand communicating on this way
>> to this level of technicality can be hard, i still think we can work ways
>> to solve this problem though,
>> > > >
>> > > > I can say the following at this point:
>> > > >
>> > > > • Program works without issues in any other non-gpu
>> preconditioner, just by calling -pc_type ### .
>> > > > • Program works correctly with ViennaCL preconditioners with
>> mpirun -n 1, that is on one processor.
>> > > > • Program breaks with every ViennaCL preconditioner when
>> attempting any more than 1 processors.
>> > > > • I haven't tried other GPU preconditioners because ViennaCL
>> gave the best performance in 1 processor before.
>> > > > • I have made sure the matrix type is mpiaijviennacl as it is
>> printed right before the error log.
>> > > > • I am attaching what i think are the backtrace logs of the
>> run with two cores, as i have limited experience with this kind of
>> debugging, and i cannot make sense of what they say, please let me know if
>> you need me to do something else.
>> > > >
>> > > > Current options i can think of are giving you permission to clone
>> my model repo, or for you to guide me trough the process remotely,
>> > > >
>> > > > Thanks,
>> > > >
>> > > > .-.-.-.-
>> > > >
>> > > >
>> > > > The error i get is still:
>> > > >
>> > > > Matrix type: mpiaijviennacl
>>
>> > > > Of sizes: 125 x 125
>> > > > Matrix type: mpiaijviennacl
>>
>> > > > Of sizes: 125 x 125
>> > > > [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/d
>> ocumentation/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 29 11:43:25 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
>> > > > [1]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> > > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>> Violation, probably memory access out of range
>> > > > [1]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > > > [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> > > > [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>> Mac OS X to find memory corruption errors
>> > > > [1]PETSC ERROR: likely location of problem given in stack below
>> > > > [1]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> > > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> available,
>> > > > [1]PETSC ERROR: INSTEAD the line number of the start of the
>> function
>> > > > [1]PETSC ERROR: is given.
>> > > > [1]PETSC ERROR: [1] PetscTraceBackErrorHandler line 182
>> /home/valera/petsc/src/sys/error/errtrace.c
>> > > > [1]PETSC ERROR: [1] PetscError line 352
>> /home/valera/petsc/src/sys/error/err.c
>> > > > [1]PETSC ERROR: [1] PCSetUp_SAVIENNACL line 45
>> /home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu
>> > > > [1]PETSC ERROR: [1] PCSetUp line 894 /home/valera/petsc/src/ksp/pc/
>> interface/precon.c
>> > > > [1]PETSC ERROR: [1] KSPSetUp line 294 /home/valera/petsc/src/ksp/ksp
>> /interface/itfunc.c
>> > > > [1]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> > > > [1]PETSC ERROR: Signal received
>> > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>> ocumentation/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 29 11:43:25 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 User provided function() line 0 in unknown file
>> > > > ------------------------------------------------------------
>> --------------
>> > > > MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
>> > > > with errorcode 59.
>> > > >
>> > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> > > > You may or may not see output from other processes, depending on
>> > > > exactly when Open MPI kills them.
>> > > > ------------------------------------------------------------
>> --------------
>> > > > [0]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> > > > [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or
>> the batch system) has told this process to end
>> > > > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > > > [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> > > > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>> Mac OS X to find memory corruption errors
>> > > > [0]PETSC ERROR: likely location of problem given in stack below
>> > > > [0]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> > > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> available,
>> > > > [0]PETSC ERROR: INSTEAD the line number of the start of the
>> function
>> > > > [0]PETSC ERROR: is given.
>> > > > [0]PETSC ERROR: [0] MatSetErrorIfFailure line 116
>> /home/valera/petsc/src/mat/utils/gcreate.c
>> > > > [0]PETSC ERROR: [0] PCSetUp line 894 /home/valera/petsc/src/ksp/pc/
>> interface/precon.c
>> > > > [0]PETSC ERROR: [0] PCSetUp_SAVIENNACL line 45
>> /home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu
>> > > > [0]PETSC ERROR: [0] PCSetUp line 894 /home/valera/petsc/src/ksp/pc/
>> interface/precon.c
>> > > > [0]PETSC ERROR: [0] KSPSetUp line 294 /home/valera/petsc/src/ksp/ksp
>> /interface/itfunc.c
>> > > > [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> > > > [0]PETSC ERROR: Signal received
>> > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>> ocumentation/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 29 11:43:25 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: #4 User provided function() line 0 in unknown file
>> > > > [node50:32783] 1 more process has sent help message
>> help-mpi-api.txt / mpi-abort
>> > > > [node50:32783] Set MCA parameter "orte_base_help_aggregate" to 0 to
>> see all help / error messages
>> > > >
>> > > >
>> > > > On Tue, Aug 28, 2018 at 9:34 PM, Karl Rupp <rupp at iue.tuwien.ac.at>
>> wrote:
>> > > > Hi Manuel,
>> > > >
>> > > > as Barry said, it is hard for us to provide any help without having
>> a more complete picture of what is going on.
>> > > >
>> > > > The error you report seems to come from the AMG preconditioner in
>> ViennaCL. This can have many origins. Do other preconditioners run without
>> error? Can you run in a debugger and provide a complete backtrace?
>> > > >
>> > > > Thanks and best regards,
>> > > > Karli
>> > > >
>> > > >
>> > > > On 08/29/2018 01:33 AM, Manuel Valera wrote:
>> > > > Talked too fast,
>> > > >
>> > > > After fixing that problem, i tried more than one mpi processor and
>> got the following:
>> > > >
>> > > > Matrix type: mpiaijviennacl
>> > > > Of sizes: 125 x 125
>> > > > Matrix type: mpiaijviennacl
>> > > > Of sizes: 125 x 125
>> > > > [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/d
>> ocumentation/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
>> Tue Aug 28 16:30:02 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 <
>> http://saviennacl.cu>
>> > > > [0]PETSC ERROR: #2 PCSetUp() line 932 in
>> /home/valera/petsc/src/ksp/pc/interface/precon.c
>> > > > [1]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> > > > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>> Violation, probably memory access out of range
>> > > > [1]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > > > [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> > > > [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>> Mac OS X to find memory corruption errors
>> > > > [1]PETSC ERROR: likely location of problem given in stack below
>> > > > [1]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> > > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> available,
>> > > > [1]PETSC ERROR: INSTEAD the line number of the start of the
>> function
>> > > > [1]PETSC ERROR: is given.
>> > > > [1]PETSC ERROR: [1] PetscTraceBackErrorHandler line 182
>> /home/valera/petsc/src/sys/error/errtrace.c
>> > > > [1]PETSC ERROR: [1] PetscError line 352
>> /home/valera/petsc/src/sys/error/err.c
>> > > > [1]PETSC ERROR: [1] PCSetUp_SAVIENNACL line 45
>> /home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu<
>> http://saviennacl.cu>
>> > > >
>> > > > [1]PETSC ERROR: [1] PCSetUp line 894 /home/valera/petsc/src/ksp/pc/
>> interface/precon.c
>> > > > [1]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> > > > [1]PETSC ERROR: Signal received
>> > > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>> ocumentation/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
>> Tue Aug 28 16:30:02 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 User provided function() line 0 in unknown file
>> > > > ------------------------------------------------------------
>> --------------
>> > > > MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
>> > > > with errorcode 59.
>> > > >
>> > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> > > > You may or may not see output from other processes, depending on
>> > > > exactly when Open MPI kills them.
>> > > > ------------------------------------------------------------
>> --------------
>> > > > [0]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> > > > [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or
>> the batch system) has told this process to end
>> > > > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > > > [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> > > > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
>> Mac OS X to find memory corruption errors
>> > > > [0]PETSC ERROR: likely location of problem given in stack below
>> > > > [0]PETSC ERROR: --------------------- Stack Frames
>> ------------------------------------
>> > > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> available,
>> > > > [0]PETSC ERROR: INSTEAD the line number of the start of the
>> function
>> > > > [0]PETSC ERROR: is given.
>> > > > [0]PETSC ERROR: [0] PetscCommDuplicate line 130
>> /home/valera/petsc/src/sys/objects/tagm.c
>> > > > [0]PETSC ERROR: [0] PetscHeaderCreate_Private line 34
>> /home/valera/petsc/src/sys/objects/inherit.c
>> > > > [0]PETSC ERROR: [0] ISCreate line 35 /home/valera/petsc/src/vec/is/
>> is/interface/isreg.c
>> > > > [0]PETSC ERROR: [0] ISCreateGeneral line 668
>> /home/valera/petsc/src/vec/is/is/impls/general/general.c
>> > > > [0]PETSC ERROR: [0] PCSetUp_SAVIENNACL line 45
>> /home/valera/petsc/src/ksp/pc/impls/saviennaclcuda/saviennacl.cu<
>> http://saviennacl.cu>
>> > > > [0]PETSC ERROR: [0] PCSetUp line 894 /home/valera/petsc/src/ksp/pc/
>> interface/precon.c
>> > > > [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> > > > [0]PETSC ERROR: Signal received
>> > > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/d
>> ocumentation/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
>> Tue Aug 28 16:30:02 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: #3 User provided function() line 0 in unknown file
>> > > > [node50:30582] 1 more process has sent help message
>> help-mpi-api.txt / mpi-abort
>> > > > [node50:30582] Set MCA parameter "orte_base_help_aggregate" to 0 to
>> see all help / error messages
>> > > >
>> > > >
>> > > >
>> > > > It is currently running in 1 mpi processor + GPU but i would like
>> to call at least 16 mpi processors + GPU to do the rest of the data
>> management who is not part of the main laplacian on the mpi and the
>> laplacian solution on the GPU, is this currently possible?
>> > > >
>> > > > Thanks for your help,
>> > > >
>> > > >
>> > > >
>> > > > On Tue, Aug 28, 2018 at 4:21 PM, Manuel Valera <mvalera-w at sdsu.edu
>> <mailto:mvalera-w at sdsu.edu>> wrote:
>> > > >
>> > > > Ok, i found the culprit and we can close this thread,
>> > > >
>> > > > The problem was a missing variable for setting the maximum
>> columns,
>> > > > which i deleted at some point without realizing. The error
>> message
>> > > > was too ambiguous to catch this so i had to compare with a
>> previous
>> > > > working version of the arguments of MatSetValues, it was
>> evident then.
>> > > >
>> > > > Good news is that i can now set the values with the viennacl
>> types too,
>> > > >
>> > > > Thanks for your kind help,
>> > > >
>> > > > Manuel
>> > > >
>> > > > On Tue, Aug 28, 2018 at 11:25 AM, Smith, Barry F.
>> > > > <bsmith at mcs.anl.gov <mailto:bsmith at mcs.anl.gov>> wrote:
>> > > >
>> > > >
>> > > > 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
>> > > > <mvalera-w at sdsu.edu <mailto:mvalera-w at sdsu.edu>> 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.
>> > > > <bsmith at mcs.anl.gov <mailto:bsmith at mcs.anl.gov>> 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
>> > > > <mvalera-w at sdsu.edu <mailto:mvalera-w at sdsu.edu>> 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
>> > > > <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 <mailto: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 <mailto:mvalera-w at sdsu.edu>> wrote:
>> > > > > > >
>> > > > > > > Thanks Matthew and Barry,
>> > > > > > >
>> > > > > > > Now my code looks like:
>> > > > > > >
>> > > > > > > call DMSetMatrixPreallocateOnly(daD
>> ummy,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),IN
>> SERT_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
>> > > > <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 <mailto: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 <mailto: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(daD
>> ummy,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),IN
>> SERT_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
>> > > > <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/savien
>> nacl.cu
>> > > > <http://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 <mailto:knepley at gmail.com>> wrote:
>> > > > > > > > On Wed, Aug 15, 2018 at 5:20 PM Manuel Valera
>> > > > <mvalera-w at sdsu.edu <mailto: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 <mailto:knepley at gmail.com>> wrote:
>> > > > > > > > On Wed, Aug 15, 2018 at 4:53 PM Manuel Valera
>> > > > <mvalera-w at sdsu.edu <mailto: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 <mailto:knepley at gmail.com>> wrote:
>> > > > > > > > On Wed, Aug 15, 2018 at 4:39 PM Manuel Valera
>> > > > <mvalera-w at sdsu.edu <mailto: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
>> > > > <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(daDumm
>> y,Tmpnat,ierr)
>> > > > > > > > call VecGetLocalSize(Tmpnat,locsize,ierr)
>> > > > > > > > call VecDestroy(Tmpnat,ierr)
>> > > > > > > > ! Set matrix
>> > > > > > > > #ifdef GPU
>> > > > > > > > call MatSetType(A,MATAIJVIENNACL,ierr)
>> > > > > > > > call DMSetMatType(daDummy,MATMPIAIJ
>> VIENNACL,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,MATSEQAIJ
>> VIENNACL,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),IN
>> SERT_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/
>> > > > <https://www.cse.buffalo.edu/%7Eknepley/>
>> > > > > > > >
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > --
>> > > > > > > > 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/
>> > > > <https://www.cse.buffalo.edu/%7Eknepley/>
>> > > > > > > >
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > --
>> > > > > > > > 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/
>> > > > <https://www.cse.buffalo.edu/%7Eknepley/>
>> > > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > >
>> > > > > >
>> > > > >
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > <backt-2.log><backt.log>
>> >
>> >
>> >
>>
>>
>
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