[petsc-users] pets-3.1-p6 with CUDA: Unknown vector type: cuda!

Fri Dec 10 08:11:29 CST 2010

  Just discovered this problem ourselves with 32 bit compiles. You likely need to pass into ./configure the flags --with-cc="gcc -malign-double" --cxx="g++ -malign-double".  Nvcc secretly uses that option of its compiles so we need to use it for all the compilers.

   Barry

On Dec 10, 2010, at 5:33 AM, Jakub Pola wrote:

> After typing --with-cusp=1 and --with-thrust=1 library was compiled
> successfully but when I want to make tests i got following error:
> What could be the reason of that?
> 
> I have GTX 480 with drivers ver. 260
> Ubuntu 10.10 32bit system with 2GB ram.
> Core duo processor 2.2GHz.
> 
> 
> Test.log:
> 
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI
> process
> See http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html
> [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/petsc-as/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] VecCUDACopyFromGPU line 188
> src/vec/vec/impls/seq/seqcuda/veccuda.cu
> [0]PETSC ERROR: [0] VecGetArray line 226
> src/vec/vec/impls/mpi//home/kuba/External/petsc-dev/include/private/vecimpl.h
> [0]PETSC ERROR: [0] VecCreateGhostWithArray line 581
> src/vec/vec/impls/mpi/pbvec.c
> [0]PETSC ERROR: [0] VecCreateGhost line 661
> src/vec/vec/impls/mpi/pbvec.c
> [0]PETSC ERROR: [0] MatFDColoringCreate_SeqAIJ line 21
> src/mat/impls/aij/seq/fdaij.c
> [0]PETSC ERROR: [0] MatFDColoringCreate line 376
> src/mat/matfd/fdmatrix.c
> [0]PETSC ERROR: [0] DMMGSetSNES line 562 src/snes/utils/damgsnes.c
> [0]PETSC ERROR: [0] DMMGSetSNESLocal_Private line 933
> src/snes/utils/damgsnes.c
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision:
> 488e1fcaa13db132861c12416293551e6e00b14e  HG Date: Thu Dec 09 20:23:16
> 2010 +0100
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: ./ex19 on a arch-linu named desktop by kuba Fri Dec 10
> 08:36:02 2010
> [0]PETSC ERROR: Libraries linked
> from /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/lib
> [0]PETSC ERROR: Configure run at Fri Dec 10 08:05:40 2010
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=gfortran
> --download-f-blas-lapack=1 --download-mpich=1 --with-cuda=1
> --with-debug=no --with-cusp=1 --with-thrust=1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [cli_0]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI
> processes
> See http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html
> [0]PETSC ERROR: [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:
> ------------------------------------------------------------------------
> [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/petsc-as/documentation/faq.html#valgrindor
> see
> http://www.mcs.anl.gov/petsc/petsc-as/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
> [1]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
> ------------------------------------
> [1]PETSC ERROR: likely location of problem given in stack below
> [1]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] VecCUDACopyFromGPU line 188
> src/vec/vec/impls/seq/seqcuda/veccuda.cu
> [0]PETSC ERROR: [0] VecGetArray line 226
> src/vec/vec/impls/mpi//home/kuba/External/petsc-dev/include/private/vecimpl.h
> [0]PETSC ERROR: [0] VecCreateGhostWithArray line 581
> src/vec/vec/impls/mpi/pbvec.c
> [0]PETSC ERROR: [0] VecCreateGhost line 661
> src/vec/vec/impls/mpi/pbvec.c
> [0]PETSC ERROR: [0] MatFDColoringCreate_MPIAIJ line 24
> src/mat/impls/aij/mpi/fdmpiaij.c
> [0]PETSC ERROR: [0] MatFDColoringCreate line 376
> src/mat/matfd/fdmatrix.c
> [0]PETSC ERROR: [0] DMMGSetSNES line 562 src/snes/utils/damgsnes.c
> [0]PETSC ERROR: [0] DMMGSetSNESLocal_Private line 933
> src/snes/utils/damgsnes.c
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision:
> 488e1fcaa13db132861c12416293551e6e00b14e  HG Date: Thu Dec 09 20:23:16
> 2010 +0100
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: ./ex19 on a arch-linu named desktop by kuba Fri Dec 10
> 08:36:03 2010
> [0]PETSC ERROR: Libraries linked
> from /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/lib
> [0]PETSC ERROR: Configure run at Fri Dec 10 08:05:40 2010
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=gfortran
> --download-f-blas-lapack=1 --download-mpich=1 --with-cuda=1
> --with-debug=no --with-cusp=1 --with-thrust=1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [1]PETSC ERROR: application called MPI_Abort(MPI_COMM_WORLD, 59) -
> process 0
> [cli_0]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> 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] VecCUDACopyFromGPU line 188
> src/vec/vec/impls/seq/seqcuda/veccuda.cu
> [1]PETSC ERROR: [1] VecGetArray line 226
> src/vec/vec/impls/mpi//home/kuba/External/petsc-dev/include/private/vecimpl.h
> [1]PETSC ERROR: [1] VecCreateGhostWithArray line 581
> src/vec/vec/impls/mpi/pbvec.c
> [1]PETSC ERROR: [1] VecCreateGhost line 661
> src/vec/vec/impls/mpi/pbvec.c
> [1]PETSC ERROR: [1] MatFDColoringCreate_MPIAIJ line 24
> src/mat/impls/aij/mpi/fdmpiaij.c
> [1]PETSC ERROR: [1] MatFDColoringCreate line 376
> src/mat/matfd/fdmatrix.c
> [1]PETSC ERROR: [1] DMMGSetSNES line 562 src/snes/utils/damgsnes.c
> [1]PETSC ERROR: [1] DMMGSetSNESLocal_Private line 933
> src/snes/utils/damgsnes.c
> [1]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [1]PETSC ERROR: Signal received!
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: Petsc Development HG revision:
> 488e1fcaa13db132861c12416293551e6e00b14e  HG Date: Thu Dec 09 20:23:16
> 2010 +0100
> [1]PETSC ERROR: See docs/changes/index.html for recent updates.
> [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [1]PETSC ERROR: See docs/index.html for manual pages.
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: ./ex19 on a arch-linu named desktop by kuba Fri Dec 10
> 08:36:03 2010
> [1]PETSC ERROR: Libraries linked
> from /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/lib
> [1]PETSC ERROR: Configure run at Fri Dec 10 08:05:40 2010
> [1]PETSC ERROR: Configure options --with-cc=gcc --with-fc=gfortran
> --download-f-blas-lapack=1 --download-mpich=1 --with-cuda=1
> --with-debug=no --with-cusp=1 --with-thrust=1
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
> [cli_1]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
> Error running Fortran example src/snes/examples/tutorials/ex5f with 1
> MPI process
> See http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html
> [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/petsc-as/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] VecCUDACopyFromGPU line 188
> src/vec/vec/impls/seq/seqcuda/veccuda.cu
> [0]PETSC ERROR: [0] VecGetArray line 226
> src/vec/vec/interface/ftn-custom//home/kuba/External/petsc-dev/include/private/vecimpl.h
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development HG revision:
> 488e1fcaa13db132861c12416293551e6e00b14e  HG Date: Thu Dec 09 20:23:16
> 2010 +0100
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: ./ex5f on a arch-linu named desktop by kuba Fri Dec 10
> 08:36:09 2010
> [0]PETSC ERROR: Libraries linked
> from /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/lib
> [0]PETSC ERROR: Configure run at Fri Dec 10 08:05:40 2010
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=gfortran
> --download-f-blas-lapack=1 --download-mpich=1 --with-cuda=1
> --with-debug=no --with-cusp=1 --with-thrust=1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [cli_0]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
> Completed test examples
> 
> Dnia 2010-12-10, pią o godzinie 00:38 +0100, Jed Brown pisze:
>> On Fri, Dec 10, 2010 at 00:07, Jakub Pola <jakub.pola at gmail.com>
>> wrote:
>>        I downloaded Petsc 3.1.0 as well as thrust 1.4.0 and cusp
>>        0.2.0
>> 
>> As I said before, you need petsc-dev for this, CUDA support is not in
>> 3.1.
>> 
>> 
>> http://www.mcs.anl.gov/petsc/petsc-as/developers/index.html#Obtaining
> 
> 