[petsc-users] MatSetValues error with ViennaCL types
Manuel Valera
mvalera-w at sdsu.edu
Thu Aug 30 09:51:57 CDT 2018
I thought newer NVIDIA cards had integrated circuits, not using PCI
anymore, still the same case?
How would the GPU clusters work, then? Let's say i have a cluster of GPUs
communicated by an MPI node, would PETSc work on this configuration at some
point? This would be my next step if I could make the MPI matrices work
with GPU, we have such a cluster on campus.
Are you familiar with the Magma library? It was recommended recently to
tackle this problem,
I am most interested in your insight,
Thanks,
On Thu, Aug 30, 2018, 3:10 AM Matthew Knepley <knepley at gmail.com> wrote:
> On Wed, Aug 29, 2018 at 6:21 PM Manuel Valera <mvalera-w at sdsu.edu> wrote:
>
>> I understand that Matthew, thanks,
>>
>> I am trying to see if i get any speedup in this configuration, otherwise
>> i will be waiting for the MPIAIJ support on PETSc,
>>
>> Is there any other gpu preconditioner that works on parallel matrices
>> directly?
>>
>
> Not that I know of . Such a hypothetical preconditioner would need to pass
> information back and forth, across the PCI bus, and
> then through MPI (even if you imagine direct GPU-GPU communication, it
> still hits the PCI bus). This channel has small bandwidth,
> but even more limiting is the high latency. Its unclear what kind of
> algorithm would do well in this situation.
>
> Thanks,
>
> Matt
>
>
>> Thanks again,
>>
>>
>>
>> On Wed, Aug 29, 2018 at 3:05 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Wed, Aug 29, 2018 at 5:49 PM Manuel Valera <mvalera-w at sdsu.edu>
>>> wrote:
>>>
>>>> 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,
>>>>
>>>
>>> You are missing the point of the error message.
>>>
>>> We do not support SAVIENNACL on parallel matrices (MPIAIJ). We do
>>> support it
>>> on serial matrices (SEQAIJ). When you are setting in directly, you are
>>> applying it
>>> to a parallel matrix. If you use Block-Jacobi, you are applying it to
>>> each submatrix,
>>> and those submatrices are all serial.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> 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/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 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/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: [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/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 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/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] 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/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 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/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 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/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<
>>>>>> 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/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 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/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 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/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 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(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
>>>>>> > > > <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(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
>>>>>> > > > <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
>>>>>> > > > <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(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/
>>>>>> > > > <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>
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>> --
>>> 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/>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180830/dbf7b502/attachment-0001.html>
More information about the petsc-users
mailing list