[petsc-users] Failed to compile the PETsc-dev with cuda, mpicc can not recognize c++ key word in thrust and cusp (Lei Shi)
Lei Shi
leishi at ku.edu
Tue Apr 15 03:06:38 CDT 2014
Hi Christophe,
Thanks a lot. I add --with-clanguage=cxx option. It works well now. This
option is not on the manual for the compilation with gpu.
Sincerely Yours,
Lei Shi
---------
On Fri, Apr 11, 2014 at 3:42 AM, Christophe Ortiz <
christophe.ortiz at ciemat.es> wrote:
> 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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