[petsc-users] pets-3.1-p6 with CUDA: Unknown vector type: cuda!
Satish Balay
balay at mcs.anl.gov
Thu Dec 9 17:29:11 CST 2010
Try removing options:
--with-cusp-dir=/usr/local/cuda/include/cusp/ --with-thrust-dir=/usr/local/cuda/include/thrust
[and use --with-cups=1 --with-thrust=1]
As they are in default location - configure picks them automatically. But
since they are incorrectly specified - the 'default cuda path' gets
the configure tests going - but this path causes grief later..
> In file included from /usr/local/cuda/include/cusp/detail/config.h:24,
> from /usr/local/cuda/include/cusp/memory.h:20,
Thats suspporsed to system memory.h - not cups/memory.h
Satish
On Fri, 10 Dec 2010, Jakub Pola wrote:
> Hi again,
>
> I downloaded Petsc 3.1.0 as well as thrust 1.4.0 and cusp 0.2.0
> I have problems with compiling the library. I did following steps:
>
> configured pets:
>
> ./config/configure.py --with-cc=gcc --with-fc=gfortran
> --download-f-blas-lapack=1 --download-mpich=1 --with-cuda=1
> --with-debug=no --with-cusp-dir=/usr/local/cuda/include/cusp/
> --with-thrust-dir=/usr/local/cuda/include/thrust
>
> then make:
> make PETSC_DIR=/home/kuba/External/petsc-dev
> PETSC_ARCH=arch-linux-gnu-c-debug all
>
> here I have problems because compilator says that
> /usr/local/cuda/include/thrust/iterator/iterator_traits.h:34: fatal
> error: iterator: No such file or directory
>
> But actually it is as a symbolic link:
> ls -l /usr/local/cuda/include/
> gives
> lrwxrwxrwx 1 root root 34 2010-12-09 23:44 thrust
> -> /home/kuba/External/thrust/thrust/
>
> and
>
> kuba at desktop:~/External/thrust/thrust/iterator$ ls -l
> razem 96
> -rw-r--r-- 1 kuba kuba 7666 2010-12-09 21:30 constant_iterator.h
> -rw-r--r-- 1 kuba kuba 6959 2010-12-09 21:30 counting_iterator.h
> drwxr-xr-x 3 kuba kuba 4096 2010-12-09 21:30 detail
> -rw-r--r-- 1 kuba kuba 4376 2010-12-09 21:30 iterator_adaptor.h
> -rw-r--r-- 1 kuba kuba 8282 2010-12-09 21:30 iterator_categories.h
> -rw-r--r-- 1 kuba kuba 14279 2010-12-09 21:30 iterator_facade.h
> -rw-r--r-- 1 kuba kuba 2066 2010-12-09 21:30 iterator_traits.h
> -rw-r--r-- 1 kuba kuba 6880 2010-12-09 21:30 permutation_iterator.h
> -rw-r--r-- 1 kuba kuba 7055 2010-12-09 21:30 reverse_iterator.h
> -rw-r--r-- 1 kuba kuba 10089 2010-12-09 21:30 transform_iterator.h
> -rw-r--r-- 1 kuba kuba 7348 2010-12-09 21:30 zip_iterator.h
> kuba at desktop:~/External/thrust/thrust/iterator$
>
>
> Have somebody faced this kind of problem?
>
>
>
>
> Here it is compilation log to first error
>
> kuba at desktop:~/External/petsc-dev$ make
> PETSC_DIR=/home/kuba/External/petsc-dev
> PETSC_ARCH=arch-linux-gnu-c-debug all
> ==========================================
>
> See documentation/faq.html and documentation/bugreporting.html
> for help with installation problems. Please send EVERYTHING
> printed out below when reporting problems
>
> To subscribe to the PETSc announcement list, send mail to
> majordomo at mcs.anl.gov with the message:
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>
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> subscribe petsc-users
>
> ==========================================
> On czw, 9 gru 2010, 23:56:38 CET on desktop
> Machine characteristics: Linux desktop 2.6.35-22-generic #35-Ubuntu SMP
> Sat Oct 16 20:36:48 UTC 2010 i686 GNU/Linux
> -----------------------------------------
> Using PETSc directory: /home/kuba/External/petsc-dev
> Using PETSc arch: arch-linux-gnu-c-debug
> -----------------------------------------
> PETSC_VERSION_RELEASE 0
> PETSC_VERSION_MAJOR 3
> PETSC_VERSION_MINOR 1
> PETSC_VERSION_SUBMINOR 0
> PETSC_VERSION_PATCH 6
> PETSC_VERSION_DATE "Mar, 25, 2010"
> PETSC_VERSION_PATCH_DATE "unknown"
> PETSC_VERSION_HG "unknown"
> PETSC_VERSION_DATE_HG "unknown"
> PETSC_VERSION_(MAJOR,MINOR,SUBMINOR) \
> -----------------------------------------
> Using configure Options: --with-cc=gcc --with-fc=gfortran
> --download-f-blas-lapack=1 --download-mpich=1 --with-cuda=1
> --with-debug=no --with-cusp-dir=/usr/local/cuda/include/cusp/
> --with-thrust-dir=/usr/local/cuda/include/thrust
> Using configuration flags:
> #define INCLUDED_PETSCCONF_H
> #define IS_COLORING_MAX 65535
> #define STDC_HEADERS 1
> #define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT
> #define PETSC_UINTPTR_T uintptr_t
> #define PETSC_HAVE_PTHREAD 1
> #define PETSC_STATIC_INLINE static inline
> #define PETSC_REPLACE_DIR_SEPARATOR '\\'
> #define PETSC_RESTRICT __restrict__
> #define PETSC_HAVE_MPI 1
> #define PETSC_USE_SINGLE_LIBRARY 1
> #define PETSC_USE_SOCKET_VIEWER 1
> #define PETSC_HAVE_THRUST 1
> #define PETSC_LIB_DIR
> "/home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/lib"
> #define PETSC_HAVE_FORTRAN 1
> #define PETSC_HAVE_SOWING 1
> #define PETSC_SLSUFFIX ""
> #define PETSC_FUNCTION_NAME_CXX __func__
> #define PETSC_HAVE_DOUBLE_ALIGN_MALLOC 1
> #define PETSC_UNUSED
> #define PETSC_HAVE_CUDA 1
> #define PETSC_FUNCTION_NAME_C __func__
> #define PETSC_HAVE_C2HTML 1
> #define PETSC_HAVE_VALGRIND 1
> #define PETSC_HAVE_BUILTIN_EXPECT 1
> #define PETSC_DIR_SEPARATOR '/'
> #define PETSC_PATH_SEPARATOR ':'
> #define PETSC_HAVE_X11 1
> #define PETSC_HAVE_CUSP 1
> #define PETSC_Prefetch(a,b,c)
> #define PETSC_HAVE_BLASLAPACK 1
> #define PETSC_HAVE_STRING_H 1
> #define PETSC_HAVE_SYS_TYPES_H 1
> #define PETSC_HAVE_ENDIAN_H 1
> #define PETSC_HAVE_SYS_PROCFS_H 1
> #define PETSC_HAVE_DLFCN_H 1
> #define PETSC_HAVE_STDINT_H 1
> #define PETSC_HAVE_LINUX_KERNEL_H 1
> #define PETSC_HAVE_TIME_H 1
> #define PETSC_HAVE_MATH_H 1
> #define PETSC_HAVE_STDLIB_H 1
> #define PETSC_HAVE_SYS_PARAM_H 1
> #define PETSC_HAVE_SYS_SOCKET_H 1
> #define PETSC_HAVE_UNISTD_H 1
> #define PETSC_HAVE_SYS_WAIT_H 1
> #define PETSC_HAVE_LIMITS_H 1
> #define PETSC_HAVE_SYS_UTSNAME_H 1
> #define PETSC_HAVE_NETINET_IN_H 1
> #define PETSC_HAVE_FENV_H 1
> #define PETSC_HAVE_FLOAT_H 1
> #define PETSC_HAVE_SEARCH_H 1
> #define PETSC_HAVE_SYS_SYSINFO_H 1
> #define PETSC_HAVE_SYS_RESOURCE_H 1
> #define PETSC_HAVE_SYS_TIMES_H 1
> #define PETSC_HAVE_NETDB_H 1
> #define PETSC_HAVE_MALLOC_H 1
> #define PETSC_HAVE_PWD_H 1
> #define PETSC_HAVE_FCNTL_H 1
> #define PETSC_HAVE_STRINGS_H 1
> #define PETSC_HAVE_MEMORY_H 1
> #define PETSC_TIME_WITH_SYS_TIME 1
> #define PETSC_HAVE_SYS_TIME_H 1
> #define PETSC_USING_F90 1
> #define PETSC_HAVE_RTLD_NOW 1
> #define PETSC_HAVE_RTLD_LOCAL 1
> #define PETSC_HAVE_RTLD_LAZY 1
> #define PETSC_C_STATIC_INLINE static inline
> #define PETSC_HAVE_FORTRAN_UNDERSCORE 1
> #define PETSC_HAVE_CXX_NAMESPACE 1
> #define PETSC_HAVE_RTLD_GLOBAL 1
> #define PETSC_C_RESTRICT __restrict__
> #define PETSC_CXX_RESTRICT __restrict__
> #define PETSC_CXX_STATIC_INLINE static inline
> #define PETSC_HAVE_LIBCUBLAS 1
> #define PETSC_HAVE_LIBCUDART 1
> #define PETSC_HAVE_LIBDL 1
> #define PETSC_HAVE_LIBFBLAS 1
> #define PETSC_HAVE_LIBFLAPACK 1
> #define PETSC_HAVE_ERF 1
> #define PETSC_HAVE_LIBCUFFT 1
> #define PETSC_HAVE_LIBRT 1
> #define PETSC_ARCH "arch-linux-gnu-c-debug"
> #define PETSC_VERSION_DATE_HG "Thu Dec 09 20:23:16 2010 +0100"
> #define PETSC_VERSION_BS_HG "47bec558f992b1828a074066eb6df9f5b106a6b6"
> #define PETSC_VERSION_HG "488e1fcaa13db132861c12416293551e6e00b14e"
> #define PETSC_DIR "/home/kuba/External/petsc-dev"
> #define PETSC_VERSION_BS_DATE_HG "Tue Dec 07 14:41:13 2010 -0600"
> #define HAVE_GZIP 1
> #define PETSC_CLANGUAGE_C 1
> #define PETSC_USE_EXTERN_CXX
> #define PETSC_USE_ERRORCHECKING 1
> #define PETSC_MISSING_DREAL 1
> #define PETSC_SIZEOF_MPI_COMM 4
> #define PETSC_BITS_PER_BYTE 8
> #define PETSC_SIZEOF_MPI_FINT 4
> #define PETSC_SIZEOF_VOID_P 4
> #define PETSC_RETSIGTYPE void
> #define PETSC_HAVE_CXX_COMPLEX 1
> #define PETSC_SIZEOF_LONG 4
> #define PETSC_USE_FORTRANKIND 1
> #define PETSC_SIZEOF_SIZE_T 4
> #define PETSC_SIZEOF_CHAR 1
> #define PETSC_SIZEOF_DOUBLE 8
> #define PETSC_SIZEOF_FLOAT 4
> #define PETSC_HAVE_C99_COMPLEX 1
> #define PETSC_SIZEOF_INT 4
> #define PETSC_SIZEOF_LONG_LONG 8
> #define PETSC_SIZEOF_SHORT 2
> #define PETSC_HAVE_STRCASECMP 1
> #define PETSC_HAVE_POPEN 1
> #define PETSC_HAVE_SIGSET 1
> #define PETSC_HAVE_GETWD 1
> #define PETSC_HAVE_VSNPRINTF 1
> #define PETSC_HAVE_TIMES 1
> #define PETSC_HAVE_DLSYM 1
> #define PETSC_HAVE_SNPRINTF 1
> #define PETSC_HAVE_GETPWUID 1
> #define PETSC_HAVE_GETHOSTBYNAME 1
> #define PETSC_HAVE_SLEEP 1
> #define PETSC_HAVE_DLERROR 1
> #define PETSC_HAVE_FORK 1
> #define PETSC_HAVE_RAND 1
> #define PETSC_HAVE_GETTIMEOFDAY 1
> #define PETSC_HAVE_DLCLOSE 1
> #define PETSC_HAVE_UNAME 1
> #define PETSC_HAVE_GETHOSTNAME 1
> #define PETSC_HAVE_MKSTEMP 1
> #define PETSC_HAVE_SIGACTION 1
> #define PETSC_HAVE_DRAND48 1
> #define PETSC_HAVE_NANOSLEEP 1
> #define PETSC_HAVE_VA_COPY 1
> #define PETSC_HAVE_CLOCK 1
> #define PETSC_HAVE_ACCESS 1
> #define PETSC_HAVE_SIGNAL 1
> #define PETSC_HAVE_USLEEP 1
> #define PETSC_HAVE_GETRUSAGE 1
> #define PETSC_HAVE_VFPRINTF 1
> #define PETSC_HAVE_MEMALIGN 1
> #define PETSC_HAVE_GETDOMAINNAME 1
> #define PETSC_HAVE_TIME 1
> #define PETSC_HAVE_LSEEK 1
> #define PETSC_HAVE_SOCKET 1
> #define PETSC_HAVE_SYSINFO 1
> #define PETSC_HAVE_READLINK 1
> #define PETSC_HAVE_REALPATH 1
> #define PETSC_HAVE_DLOPEN 1
> #define PETSC_HAVE_MEMMOVE 1
> #define PETSC_HAVE__GFORTRAN_IARGC 1
> #define PETSC_SIGNAL_CAST
> #define PETSC_HAVE_GETCWD 1
> #define PETSC_HAVE_VPRINTF 1
> #define PETSC_HAVE_BZERO 1
> #define PETSC_HAVE_GETPAGESIZE 1
> #define PETSC_LEVEL1_DCACHE_LINESIZE 64
> #define PETSC_LEVEL1_DCACHE_SIZE 32768
> #define PETSC_LEVEL1_DCACHE_ASSOC 8
> #define PETSC_USE_PROC_FOR_SIZE 1
> #define PETSC_HAVE_DYNAMIC_LIBRARIES 1
> #define PETSC_HAVE_SHARED_LIBRARIES 1
> #define PETSC_MEMALIGN 16
> #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1
> #define PETSC_HAVE_GFORTRAN_IARGC 1
> #define PETSC_HAVE_ISINF 1
> #define PETSC_HAVE_ISNAN 1
> #define PETSC_HAVE_MPI_COMM_C2F 1
> #define PETSC_HAVE_MPI_LONG_DOUBLE 1
> #define PETSC_HAVE_MPI_COMM_F2C 1
> #define PETSC_HAVE_MPI_FINT 1
> #define PETSC_HAVE_MPI_F90MODULE 1
> #define PETSC_HAVE_MPI_FINALIZED 1
> #define PETSC_HAVE_MPI_COMM_SPAWN 1
> #define PETSC_HAVE_MPI_WIN_CREATE 1
> #define PETSC_HAVE_MPIIO 1
> #define PETSC_HAVE_MPI_C_DOUBLE_COMPLEX 1
> #define PETSC_HAVE_MPI_ALLTOALLW 1
> #define PETSC_HAVE_MPI_IN_PLACE 1
> #define PETSC_USE_INFO 1
> #define PETSC_PETSC_USE_BACKWARD_LOOP 1
> #define PETSC_Alignx(a,b)
> #define PETSC_USE_DEBUG 1
> #define PETSC_USE_LOG 1
> #define PETSC_IS_COLOR_VALUE_TYPE short
> #define PETSC_USE_CTABLE 1
> #define PETSC_USE_GDB_DEBUGGER 1
> #define PETSC_CUDA_EXTERN_C_BEGIN extern "C" {
> #define PETSC_CUDA_EXTERN_C_END }
> #define PETSC_HAVE_CUSP_SMOOTHED_AGGREGATION 1
> #define PETSC_BLASLAPACK_UNDERSCORE 1
> -----------------------------------------
> Using C/C++ include paths: -I/home/kuba/External/petsc-dev/include
> -I/home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/include
> -I/usr/local/cuda/include -I/usr/local/cuda/include/cusp/
> -I/usr/local/cuda/include/thrust/
> Using C/C++
> compiler: /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/bin/mpicc
> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3
> Using Fortran include/module paths:
> -I/home/kuba/External/petsc-dev/include
> -I/home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/include
> -I/usr/local/cuda/include -I/usr/local/cuda/include/cusp/
> -I/usr/local/cuda/include/thrust/
> Using Fortran
> compiler: /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/bin/mpif90 -Wall -Wno-unused-variable -g
> -----------------------------------------
> Using C/C++
> linker: /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/bin/mpicc
> Using C/C++ flags: -Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -g3
> Using Fortran
> linker: /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/bin/mpif90
> Using Fortran flags: -Wall -Wno-unused-variable -g
> -----------------------------------------
> Using libraries:
> -L/home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/lib -lpetsc
> -lX11 -Wl,-rpath,/usr/local/cuda/lib -L/usr/local/cuda/lib -lcufft
> -lcublas -lcudart
> -Wl,-rpath,/home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/lib
> -lflapack -lfblas -L/usr/lib/gcc/i686-linux-gnu/4.4.5
> -L/usr/lib/i686-linux-gnu -ldl -lmpich -lopa -lmpl -lrt -lpthread
> -lgcc_s -lmpichf90 -lgfortran -lm -lm -lmpichcxx -lstdc++ -lmpichcxx
> -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s -ldl
> ------------------------------------------
> Using
> mpiexec: /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/bin/mpiexec
> ==========================================
> /bin/rm -f
> -rf /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/lib/libpetsc*.*
> /bin/rm -f
> -f /home/kuba/External/petsc-dev/arch-linux-gnu-c-debug/include/petsc*.mod
> BEGINNING TO COMPILE LIBRARIES IN ALL DIRECTORIES
> =========================================
> libfast in: /home/kuba/External/petsc-dev/src
> libfast in: /home/kuba/External/petsc-dev/src/inline
> libfast in: /home/kuba/External/petsc-dev/src/sys
> libfast in: /home/kuba/External/petsc-dev/src/sys/viewer
> libfast in: /home/kuba/External/petsc-dev/src/sys/viewer/impls
> libfast in: /home/kuba/External/petsc-dev/src/sys/viewer/impls/socket
> In file included from /usr/local/cuda/include/cusp/detail/config.h:24,
> from /usr/local/cuda/include/cusp/memory.h:20,
>
> from /home/kuba/External/petsc-dev/include/petscsys.h:1671,
> from send.c:3:
> /usr/local/cuda/include/thrust/version.h:69: error: expected ‘=’, ‘,’,
> ‘;’, ‘asm’ or ‘__attribute__’ before ‘thrust’
> In file included from /usr/local/cuda/include/cusp/memory.h:22,
>
> from /home/kuba/External/petsc-dev/include/petscsys.h:1671,
> from send.c:3:
> /usr/local/cuda/include/thrust/iterator/iterator_traits.h:34: fatal
> error: iterator: No such file or directory
> compilation terminated.
>
>
>
> Dnia 2010-12-09, czw o godzinie 20:47 +0100, Jed Brown pisze:
> > On Thu, Dec 9, 2010 at 20:44, Jakub Pola <jakub.pola at gmail.com> wrote:
> > Petsc Release Version 3.1.0
> >
> > You need petsc-dev for this.
>
>
>
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