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 <[email protected]> wrote: > Awesome, thanks! > > On Wed, Aug 29, 2018 at 1:29 PM, Smith, Barry F. <[email protected]> > wrote: > >> >> >> > On Aug 29, 2018, at 3:26 PM, Manuel Valera <[email protected]> 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 <[email protected]> >> 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/err >> or/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 <[email protected]> >> 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/err >> or/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 <[email protected] >> <mailto:[email protected]>> 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. >> > > <[email protected] <mailto:[email protected]>> 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 >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > >> > > > Matthew, PetscMalloc gives the same error, >> > > > >> > > > Barry, it would be very hard for me to get the code to a >> > > minimum working example, i guess all i need to understand is >> how >> > > to setup a DM matrix with DMSetMatrixPreallocateOnly() instead >> > > of MatMPIAIJSetPreallocation() as we were doing before, is >> there >> > > a simple example who does this in Fortran? >> > > > >> > > > Is the PetscMalloc call needed? is 'call >> > > PetscMalloc(1,row,ierr)' a valid, compilable call to >> > > PetscMalloc? what other reason may there be for this error to >> > > happen ? >> > > > >> > > > Just remembering, that trying to setup the matrix with the >> > > MatAIJSetPreallocation() brings up an error to acknowledge the >> > > viennacl datatypes and that's why i'm trying to make this >> change >> > > on your recommendation, >> > > > >> > > > Thanks for your help, >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > On Mon, Aug 27, 2018 at 7:35 PM, Smith, Barry F. >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > >> > > > Send your code in a way we can compile and run it; it >> must >> > > be some simple issue that is hard to communicate in email. >> > > > >> > > > Barry >> > > > >> > > > >> > > > > On Aug 27, 2018, at 5:51 PM, Manuel Valera >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > >> > > > > Hello everyone, >> > > > > >> > > > > I just had time to work on this again, and checked the >> code >> > > for errors on the matrix entries, this is the exact code i was >> > > using for creating the matrix without >> > > DMSetMatrixPreallocateOnly, using MatMPIAIJSetPreallocation >> and >> > > it worked that way, but trying this way i get the same 'Column >> > > too large' error using any number at the column position of >> > > MatSetValues, >> > > > > >> > > > > I have set up my code to print the column argument (n) of >> > > MatSetValues and in this case is 7 (lower than 124), it still >> > > gives error, even entering a specific number in the >> MatSetValues >> > > column argument position gives the same error. >> > > > > >> > > > > So next i went back to ex.50 here: >> > > http://www.mcs.anl.gov/petsc/petsc-current/src/ts/examples/ >> tutorials/ex50.c.html >> > > <http://www.mcs.anl.gov/petsc/petsc-current/src/ts/ >> examples/tutorials/ex50.c.html> >> > > and it has a very similar structure except the PetscMalloc1() >> > > call, so i tried adding that and got: >> > > > > >> > > > > /home/valera/ParGCCOM/Src/DMDALaplacian.f90:114: >> undefined >> > > reference to `petscmalloc1_' >> > > > > >> > > > > Any ideas on this behaviour? >> > > > > >> > > > > Thanks so much, >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > On Thu, Aug 16, 2018 at 11:20 AM, Smith, Barry F. >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > >> > > > > Column too large: col 10980 max 124 >> > > > > >> > > > > You need to check the code that is generating the >> matrix >> > > entries. The matrix has 124 columns but you are attempting to >> > > put a value at column 10980 >> > > > > >> > > > > Barry >> > > > > >> > > > > >> > > > > > On Aug 15, 2018, at 9:44 PM, Manuel Valera >> > > <[email protected] <mailto:[email protected]>> 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. >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > > >> > > > > > Should be >> > > > > > >> > > > > > call DMSetMatType(daDummy,MATMPIAIJVIENNACL,ierr) >> > > > > > call DMSetVecType(daDummy,VECMPIVIENNACL,ierr) >> > > > > > call DMCreateMatrix(daDummy,A,ierr) >> > > > > > >> > > > > > and remove the rest. You need to set the type of Mat >> > > you want the DM to return BEFORE you create the matrix. >> > > > > > >> > > > > > Barry >> > > > > > >> > > > > > >> > > > > > >> > > > > > > On Aug 15, 2018, at 4:45 PM, Manuel Valera >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > >> > > > > > > Ok thanks for clarifying that, i wasn't sure if there >> > > were different types, >> > > > > > > >> > > > > > > Here is a stripped down version of my code, it seems >> > > like the preallocation is working now since the matrix >> > > population part is working without problem, but here it is for >> > > illustration purposes: >> > > > > > > >> > > > > > > call DMSetMatrixPreallocateOnly(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 >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > On Wed, Aug 15, 2018 at 5:20 PM Manuel Valera >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > It seems to be resumed on: I do not know how to >> > > preallocate a DM Matrix correctly. >> > > > > > > >> > > > > > > There is only one matrix type, Mat. There are no >> > > separate DM matrices. A DM can create a matrix for you >> > > > > > > using DMCreateMatrix(), but that is a Mat and it is >> > > preallocated correctly. I am not sure what you are doing. >> > > > > > > >> > > > > > > Thanks, >> > > > > > > >> > > > > > > Matt >> > > > > > > >> > > > > > > The interesting part is that it only breaks when i >> need >> > > to populate a GPU matrix from MPI, so kudos on that, but it >> > > seems i need to do better on my code to get this setup >> working, >> > > > > > > >> > > > > > > Any help would be appreciated, >> > > > > > > >> > > > > > > Thanks, >> > > > > > > >> > > > > > > >> > > > > > > >> > > > > > > On Wed, Aug 15, 2018 at 2:15 PM, Matthew Knepley >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > On Wed, Aug 15, 2018 at 4:53 PM Manuel Valera >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > Thanks Matthew, >> > > > > > > >> > > > > > > I try to do that when calling: >> > > > > > > >> > > > > > > call >> > > MatMPIAIJSetPreallocation(A,19,PETSC_NULL_INTEGER,19,PETSC_ >> NULL_INTEGER,ierr) >> > > > > > > >> > > > > > > But i am not aware on how to do this for the DM if it >> > > needs something more specific/different, >> > > > > > > >> > > > > > > The error says that your preallocation is wrong for >> the >> > > values you are putting in. The DM does not control either, >> > > > > > > so I do not understand your email. >> > > > > > > >> > > > > > > Thanks, >> > > > > > > >> > > > > > > Matt >> > > > > > > >> > > > > > > Thanks, >> > > > > > > >> > > > > > > On Wed, Aug 15, 2018 at 1:51 PM, Matthew Knepley >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > On Wed, Aug 15, 2018 at 4:39 PM Manuel Valera >> > > <[email protected] <mailto:[email protected]>> wrote: >> > > > > > > Hello PETSc devs, >> > > > > > > >> > > > > > > I am running into an error when trying to use the >> > > MATMPIAIJVIENNACL Matrix type in MPI calls, the same code runs >> > > for MATSEQAIJVIENNACL type in one processor. The error happens >> > > when calling MatSetValues for this specific configuration. It >> > > does not occur when using MPI DMMatrix types only. >> > > > > > > >> > > > > > > The DM properly preallocates the matrix. I am >> assuming >> > > you do not here. >> > > > > > > >> > > > > > > Matt >> > > > > > > >> > > > > > > Any help will be appreciated, >> > > > > > > >> > > > > > > Thanks, >> > > > > > > >> > > > > > > >> > > > > > > >> > > > > > > My program call: >> > > > > > > >> > > > > > > mpirun -n 2 ./gcmLEP.GPU >> > > tc=TestCases/LockRelease/LE_6x6x6/ jid=tiny_cuda_test_n2 >> > > -ksp_type cg -dm_vec_type viennacl -dm_mat_type aijviennacl >> > > -pc_type saviennacl -log_view >> > > > > > > >> > > > > > > >> > > > > > > The error (repeats after each MatSetValues call): >> > > > > > > >> > > > > > > [1]PETSC ERROR: --------------------- Error Message >> > > ----------------------------------------------------------- >> --- >> > > > > > > [1]PETSC ERROR: Argument out of range >> > > > > > > [1]PETSC ERROR: Inserting a new nonzero at global >> > > row/column (75, 50) into matrix >> > > > > > > [1]PETSC ERROR: See >> > > http://www.mcs.anl.gov/petsc/documentation/faq.html >> > > <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> >> >> >
