[petsc-users] Failed to compile the PETsc-dev with cuda, mpicc can not recognize c++ key word in thrust and cusp (Lei Shi)
Christophe Ortiz
christophe.ortiz at ciemat.es
Fri Apr 11 03:42:27 CDT 2014
Hi,
Maybe I'm wrong but I think the following options are missing if you want
to use C++:
--with-cxx=(g++ or icc....) --with-clanguage=cxx
Christophe
>
> Message: 2
> Date: Fri, 11 Apr 2014 03:26:09 -0500
> From: Lei Shi <stoneszone at gmail.com>
> To: petsc-users at mcs.anl.gov
> Subject: [petsc-users] Failed to compile the PETsc-dev with cuda,
> mpicc can not recognize c++ key word in thrust and cusp
> Message-ID:
> <CAEV8=
> V9JJr+8Np5JaOKqgrkS12KJ6TaO3V4wM9YPo-NG29EU-A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi guys,
>
> I tried to compile petsc-dev with cuda5, but failed. I think the problem
> is the PETsc-dev with cuda, mpicc can not recognize c++ key word in thrust
> and cusp. Please help me out. here is my option file
>
> configure_options = [
>
>
> '--with-shared-libraries=0',
>
>
> '--with-mpi-dir=/media/public/MPICH3/mpich-install/',
>
>
> '--with-cuda=1',
>
>
> '--with-cuda-dir=/usr/local/cuda',
>
>
> '--with-cudac=/usr/local/cuda/bin/nvcc',
>
>
> '--with-cuda-arch=sm_20',
>
>
> '--with-cusp-dir=/usr/local/cuda/include/cusp',
>
>
> '--with-thrust=1',
>
>
> '--with-cusp=1',
>
>
> '--with-debugging=0',
>
>
> '--with-precision=double',
>
>
> 'COPTFLAGS=-O3',
>
>
> 'CXXOPTFLAGS=-O3',
>
>
> 'FOPTFLAGS=-O3',
>
>
> ]
>
> and the error i got
>
> -------------------------------------------------------------------------------------------
>
> ===============================================================================
>
>
> Configuring PETSc to compile on your system
>
>
>
> ===============================================================================
>
>
> TESTING: alternateConfigureLibrary from
> PETSc.packages.petsc4py(config/PETSc/packages/petsc4py.py:65)
> \
> Compilers:
>
>
> C Compiler: /media/public/MPICH3/mpich-install/bin/mpicc -Wall
> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O3
>
> CUDA Compiler: /usr/local/cuda/bin/nvcc -O -arch=sm_20
>
>
> C++ Compiler: /media/public/MPICH3/mpich-install/bin/mpicxx -Wall
> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O3
>
> Linkers:
>
>
> Static linker: /usr/bin/ar cr
>
>
> Dynamic linker: /usr/bin/ar
>
>
> make:
>
>
> MPI:
>
>
> Includes: -I/media/public/MPICH3/mpich-install/include
>
>
> BLAS/LAPACK: -llapack -lblas
>
>
> X:
>
>
> Library: -lX11
>
>
> pthread:
>
>
> Library: -lpthread
>
>
> valgrind:
>
>
> cuda:
>
>
> Includes: -I/usr/local/cuda/include
>
>
> Library: -Wl,-rpath,/usr/local/cuda/lib64 -L/usr/local/cuda/lib64
> -lcufft -lcublas -lcudart -lcusparse
>
> Arch: -arch=sm_20
>
>
> cusp:
>
>
> Includes: -I/usr/local/cuda/include/cusp/
> -I/usr/local/cuda/include/cusp/include
>
> thrust:
>
>
> sowing:
>
>
> c2html:
>
>
> PETSc:
>
>
> PETSC_ARCH: arch-cuda5-cg-opt
>
>
> PETSC_DIR: /home/leishi/work/development/3rd_party/petsc/petsc
>
>
> Clanguage: C
>
>
> Memory alignment: 16
>
>
> Scalar type: real
>
>
> Precision: double
>
>
> shared libraries: disabled
>
>
>
> xxx=========================================================================xxx
>
>
> Configure stage complete. Now build PETSc libraries with (gnumake build):
>
>
> make PETSC_DIR=/home/leishi/work/development/3rd_party/petsc/petsc
> PETSC_ARCH=arch-cuda5-cg-opt all
>
>
> xxx=========================================================================xxx
>
>
> Using C/C++ compile: /media/public/MPICH3/mpich-install/bin/mpicc -c -Wall
> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O3
> -I/home/leishi/work/development/3rd_party/pet\
> sc/petsc/include
>
> -I/home/leishi/work/development/3rd_party/petsc/petsc/arch-cuda5-cg-opt/include
> -I/usr/local/cuda/include -I/usr/local/cuda/include/cusp/
> -I/usr/local/cuda/include/cus\
> p/include -I/media/public/MPICH3/mpich-install/include
>
>
> mpicc -show: gcc -I/media/public/MPICH3/mpich-install/include
> -L/media/public/MPICH3/mpich-install/lib -lmpich -lopa -lmpl -lrt -lpthread
>
> Using CUDA compile: /usr/local/cuda/bin/nvcc -O -arch=sm_20 -c
> --compiler-options=-Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -O3 -I/home/leishi/work/development/3\
> rd_party/petsc/petsc/include
>
> -I/home/leishi/work/development/3rd_party/petsc/petsc/arch-cuda5-cg-opt/include
> -I/usr/local/cuda/include -I/usr/local/cuda/include/cusp/
> -I/usr/local/cuda\
> /include/cusp/include -I/media/public/MPICH3/mpich-install/include
>
>
> -----------------------------------------
>
>
> Using C/C++ linker: /media/public/MPICH3/mpich-install/bin/mpicc
>
>
> Using C/C++ flags: -Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -O3
>
> -----------------------------------------
>
>
> Using libraries:
> -L/home/leishi/work/development/3rd_party/petsc/petsc/arch-cuda5-cg-opt/lib
> -lpetsc -llapack -lblas -lX11 -lpthread -Wl,-rpath,/usr/local/cuda/lib64
> -L/usr/local/cuda\
> /lib64 -lcufft -lcublas -lcudart -lcusparse -lm
> -L/media/public/MPICH3/mpich-install/lib
> -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/x86_64-linux-gnu
> -L/lib/x86_64-linux-gnu -L/usr/\
> lib/gcc/x86_64-linux-gnu/4.8 -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl
> -lrt -lpthread -lgcc_s -ldl
>
> ------------------------------------------
>
>
> Using mpiexec: /media/public/MPICH3/mpich-install/bin/mpiexec
>
>
> ==========================================
>
>
> Building PETSc using GNU Make with 18 build threads
>
>
> ==========================================
>
>
> make[2]: Entering directory
> `/home/leishi/work/development/3rd_party/petsc/petsc'
>
>
> Use "/usr/bin/make V=1" to see the verbose compile lines.
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/arch.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/fhost.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/fuser.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/memc.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/mpiu.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/psleep.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/sortd.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/sorti.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/str.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/sortip.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/pbarrier.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/pdisplay.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/ctable.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/psplit.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/select.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/mpimesg.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/sseenabled.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/utils/mpitr.o
>
>
>
> In file included from /usr/local/cuda/include/cusp/detail/config.h:24:0,
>
>
> from /usr/local/cuda/include/cusp/complex.h:63,
>
>
> from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petscmath.h:145,
>
>
> from
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petscsys.h:366,
>
>
> from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petsc-private/petscimpl.h:8,
>
> from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/src/sys/objects/options.c:14:
>
>
> /usr/local/cuda/include/thrust/version.h:69:1: error: unknown type name
> ?namespace?
>
> /usr/local/cuda/include/thrust/version.h:70:1: error: expected ?=?, ?,?,
> ?;?, ?asm? or ?__attribute__? before ?{? token
>
> In file included from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petscmath.h:145:0,
>
>
> from
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petscsys.h:366,
>
>
> from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petsc-private/petscimpl.h:8,
>
> from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/src/sys/objects/options.c:14:
>
>
> /usr/local/cuda/include/cusp/complex.h:70:19: fatal error: complex: No such
> file or directory
>
> compilation terminated.
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/objects/state.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/objects/aoptions.o
>
>
> CC arch-cuda5-cg-opt/obj/src/sys/objects/subcomm.o
>
>
> In file included from /usr/local/cuda/include/cusp/detail/config.h:24:0,
>
>
> from /usr/local/cuda/include/cusp/complex.h:63,
>
>
> from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petscmath.h:145,
>
>
> from
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petscsys.h:366,
>
>
> from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/src/sys/objects/init.c:10:
>
>
> /usr/local/cuda/include/thrust/version.h:69:1: error:* unknown type name
> ?namespace? *
>
> /usr/local/cuda/include/thrust/version.h:70:1: error: expected ?=?, ?,?,
> ?;?, ?asm? or ?__attribute__? before ?{? token
>
> In file included from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petscmath.h:145:0,
>
>
> from
> /home/leishi/work/development/3rd_party/petsc/petsc/include/petscsys.h:366,
>
>
> from
>
> /home/leishi/work/development/3rd_party/petsc/petsc/src/sys/objects/init.c:10:
>
>
> /usr/local/cuda/include/cusp/complex.h:70:19: fatal error: complex: No such
> file or directory
>
>
>
> make: *** [all] Error 1
>
> Sincerely Yours,
>
> Lei Shi
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