[petsc-dev] [GPU] src/ksp/ksp/examples/tutorials/ex9 fails with mpirun -np 2
Matthew Knepley
knepley at gmail.com
Tue Jul 29 10:00:07 CDT 2014
On Tue, Jul 29, 2014 at 9:58 AM, Projet_TRIOU <triou at cea.fr> wrote:
> Hello Karl,
>
> For your interest, I understood why my code crashes on GPU with np CPUs >
> 1.
>
> I am solving Ax=B with KSPSetInitialGuessNonzero set to true so I need
> also to fill x with VecSetValues before each solve.
>
> VecSetValues works on GPU with np=1 but not for np>1. I noticed that
> filling
> x with VecSet worked fine so when I create x, I now initialize also with
> VecSet.
> (I suppose it copy/create something on GPU that VecSetValues doesn't):
>
> Vec x;
> VecCreate(PETSC_COMM_WORLD,&x);
> VecSetSizes(x, nb_rows_, PETSC_DECIDE);
> VecSetType(x, VECMPICUSP);
> VecSet(x,0.0); // Needed on GPU during parallel calculation, else it
> crashes
>
> // Later:
> for (int i=0; i<size; i++)
> {
> VecSetValues(b, 1, &colonne_globale, &secmem(i), INSERT_VALUES);
> VecSetValues(x, 1, &colonne_globale, &solution(i), INSERT_VALUES);
> colonne_globale++;
> }
>
Are you calling VecAssemblyBegin/End() after this? It is required for
VecSetValues().
Matt
> Thanks for your help,
>
> Pierre
>
> Thanks Karl, and sorry for my mistake. Indeed, ex9 runs in // with
> -pc_type none or -pc_type jacobi.
> Good to know I have an example now with VecSetValues I can try to
> replicate in my code.
> I will update the thread as soon as I return to some more tests on it.
>
> Pierre
>
> Hi Pierre,
>
> I could reproduce the problem, but I could also verify that the problem
> you ran into was due to a currently unsupported block-Jacobi
> preconditioner. That is, if you first comment the KSPSolve for the ksp2
> object in ex9, recompile ex9, and then run
>
> $> mpiexec -np 2 ./ex9 -ksp_monitor -mat_type aijcusp -vec_type cusp
> -pc_type none
>
> thinks should work out. This may also be applicable to your case: Give it
> a try with -pc_type none and let us whether the problem with VecSetValues
> remains. (The use of no preconditioner is certainly not great, but at least
> it may give you a first result)
>
> Best regards,
> Karli
>
>
>
> On 03/26/2014 06:38 PM, Projet_TRIOU wrote:
>
> Hello all,
>
> My parallel code is really near to run using GPU device
> thanks to PETSc but I am struggling with the best way
> to fill the PETSc vectors in order in runs on CPU & GPU.
>
> I was using in the past, VecCreateMPIWithArray, to
> create vector but I had trouble with it on GPU.
>
> So I followed the example in the src/ksp/ksp/examples/tutorials/ex2.c
> and create now the vectors like this:
>
> // Build x
> ierr = VecCreate(PETSC_COMM_WORLD,&SecondMembrePetsc_); check(ierr);
> ierr = VecSetSizes(SecondMembrePetsc_, nb_rows, nb_rows_tot);
> check(ierr);
> ierr = VecSetFromOptions(SecondMembrePetsc_); check(ierr);
> // Build b
> ierr = VecDuplicate(SecondMembrePetsc_,&SolutionPetsc_);check(ierr);
>
> And fills it with VecSetValues function. It runs well on CPU and
> GPU but crashed only in parallel on GPU. It I use VecSet instead of
> VecSetValues, it didn't crash (but of course VecSet is not enough
> for me :-)
>
> I tried to find an example to reproduce for you the problem, and I
> think src/ksp/ksp/examples/tutorials/ex9 (it is usingVecSetValues,)
> is a good one.
>
> Or did I miss something (I also try VecPlaceArray/VecRestoreArray
> but without success on GPU) ?
>
> Thanks, and yes you are right, "WARNING: Using GPUs effectively is
> difficult!" :-)
>
> Pierre
>
> sitre.intra.cea.fr:/work/triou/git/petsc-dev/Trio_U/lib/src/LIBPETSC/petsc/linux_opt/src/ksp/ksp/examples/tutorials
>
> > ./ex9 -ksp_monitor
> 0 KSP Residual norm 6.612932697792e+00
> 1 KSP Residual norm 4.261830032389e-01
> 2 KSP Residual norm 2.121746090851e-02
> 3 KSP Residual norm 1.233779841608e-03
> 4 KSP Residual norm 1.265903168531e-05
> 0 KSP Residual norm 1.309416176382e-05
> 0 KSP Residual norm 1.404919664063e-05
>
> sitre.intra.cea.fr:/work/triou/git/petsc-dev/Trio_U/lib/src/LIBPETSC/petsc/linux_opt/src/ksp/ksp/examples/tutorials
>
> > mpiexec -np 2 ./ex9 -ksp_monitor
> 0 KSP Residual norm 2.496821857304e+02
> 1 KSP Residual norm 4.522206074831e+01
> 2 KSP Residual norm 1.959482408314e+01
> 3 KSP Residual norm 7.002013703407e+00
> 4 KSP Residual norm 2.144105201713e+00
> 5 KSP Residual norm 1.780095080270e-01
> 6 KSP Residual norm 5.642702243268e-02
> 7 KSP Residual norm 6.439343992306e-03
> 8 KSP Residual norm 3.012756374415e-04
> Norm of error 0.000249108, Iterations 8
> Norm of error 0.000715584, Iterations 6
> 0 KSP Residual norm 3.422287562824e-04
> Norm of error 0.000249108, Iterations 0
> Norm of error 0.000192805, Iterations 7
> 0 KSP Residual norm 4.140588954098e-04
> Norm of error 0.000249108, Iterations 0
> Norm of error 0.000109507, Iterations 7
>
> sitre.intra.cea.fr:/work/triou/git/petsc-dev/Trio_U/lib/src/LIBPETSC/petsc/linux_opt/src/ksp/ksp/examples/tutorials
>
> > ./ex9 -ksp_monitor -mat_type aijcusp -vec_type cusp
> 0 KSP Residual norm 6.612932697792e+00
> 1 KSP Residual norm 4.261830032389e-01
> 2 KSP Residual norm 2.121746090851e-02
> 3 KSP Residual norm 1.233779841608e-03
> 4 KSP Residual norm 1.265903168531e-05
> 0 KSP Residual norm 1.309416176403e-05
> 0 KSP Residual norm 1.404919664088e-05
>
> sitre.intra.cea.fr:/work/triou/git/petsc-dev/Trio_U/lib/src/LIBPETSC/petsc/linux_opt/src/ksp/ksp/examples/tutorials
>
> > mpiexec -np 2 ./ex9 -ksp_monitor -mat_type aijcusp -vec_type cusp
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [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: configure using --with-debugging=yes, recompile, link,
> and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See
> http://http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-3713-g576f62e
> GIT Date: 2014-03-23 15:59:15 -0500
> [0]PETSC ERROR: ./ex9 on a linux_opt named sitre.intra.cea.fr by triou
> Wed Mar 26 18:32:34 2014
> [0]PETSC ERROR: Configure options
> --prefix=/work/triou/git/petsc-dev/Trio_U/lib/src/LIBPETSC/petsc/linux_opt
> --with-single-library --with-shared-libraries=0 --with-debugging=0
> --with-errorchecking=1 --COPTFLAGS=" -O3 -fPIC " --CXXOPTFLAGS=" -O3
> -fPIC " --FOPTFLAGS=" -O3 -fPIC " --with-fortran=yes --with-clean=1
> --download-scalapack=../scalapack-2.0.2.tgz
> --download-mumps=../MUMPS_4.10.0-p3.tar.gz --download-superlu_dist=yes
> --download-parmetis=../parmetis-4.0.2-p4.tar.gz
> --download-metis=../metis-5.0.2-p3.tar.gz
> --download-ptscotch=../ptscotch.tar.gz
> --download-hypre=../hypre-2.9.1a.tar.gz
> --with-valgrind-include=/work/triou/git/petsc-dev/Trio_U/exec/valgrind/include
>
> --with-blas-lapack-dir=/work/triou/git/petsc-dev/Trio_U/lib/src/LIBLAPACK
> --with-cuda=1
> --with-cuda-dir=/work/triou/git/petsc-dev/Trio_U/exec/cuda5.5
> --with-cusp=1
> --with-cusp-dir=/work/triou/git/petsc-dev/Trio_U/lib/src/LIBPETSC/cusplibrary-0.4.0
>
> --with-thrust=1 --with-cuda-arch=sm_21 --with-ssl=0
> --with-mpi-dir=/work/triou/git/petsc-dev/Trio_U/lib/src/LIBMPI/mpich
> --with-x=1
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
> [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: configure using --with-debugging=yes, recompile, link,
> and run
> [1]PETSC ERROR: application called MPI_Abort(MPI_COMM_WORLD, 59) - process
> 0
> to get more information on the crash.
> [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: Signal received
> [1]PETSC ERROR: See
> http://http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [1]PETSC ERROR: Petsc Development GIT revision: v3.4.4-3713-g576f62e
> GIT Date: 2014-03-23 15:59:15 -0500
> [1]PETSC ERROR: ./ex9 on a linux_opt named sitre.intra.cea.fr by triou
> Wed Mar 26 18:32:34 2014
> [1]PETSC ERROR: Configure options
> --prefix=/work/triou/git/petsc-dev/Trio_U/lib/src/LIBPETSC/petsc/linux_opt
> --with-single-library --with-shared-libraries=0 --with-debugging=0
> --with-errorchecking=1 --COPTFLAGS=" -O3 -fPIC " --CXXOPTFLAGS=" -O3
> -fPIC " --FOPTFLAGS=" -O3 -fPIC " --with-fortran=yes --with-clean=1
> --download-scalapack=../scalapack-2.0.2.tgz
> --download-mumps=../MUMPS_4.10.0-p3.tar.gz --download-superlu_dist=yes
> --download-parmetis=../parmetis-4.0.2-p4.tar.gz
> --download-metis=../metis-5.0.2-p3.tar.gz
> --download-ptscotch=../ptscotch.tar.gz
> --download-hypre=../hypre-2.9.1a.tar.gz
> --with-valgrind-include=/work/triou/git/petsc-dev/Trio_U/exec/valgrind/include
>
> --with-blas-lapack-dir=/work/triou/git/petsc-dev/Trio_U/lib/src/LIBLAPACK
> --with-cuda=1
> --with-cuda-dir=/work/triou/git/petsc-dev/Trio_U/exec/cuda5.5
> --with-cusp=1
> --with-cusp-dir=/work/triou/git/petsc-dev/Trio_U/lib/src/LIBPETSC/cusplibrary-0.4.0
>
> --with-thrust=1 --with-cuda-arch=sm_21 --with-ssl=0
> --with-mpi-dir=/work/triou/git/petsc-dev/Trio_U/lib/src/LIBMPI/mpich
> --with-x=1
> [1]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
>
>
>
> --
> *Trio_U support team*
> Marthe ROUX (01 69 08 00 02) Saclay
> Pierre LEDAC (04 38 78 91 49) Grenoble
>
>
>
>
> --
> *Trio_U support team*
> Marthe ROUX (01 69 08 00 02) Saclay
> Pierre LEDAC (04 38 78 91 49) Grenoble
>
>
>
> --
> *Trio_U support team*
> Marthe ROUX (01 69 08 00 02) Saclay
> Pierre LEDAC (04 38 78 91 49) Grenoble
>
--
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
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