[petsc-users] unable to build petsc with cuda / superlu-dist enabled
Barry Smith
bsmith at petsc.dev
Fri Aug 26 12:10:27 CDT 2022
Glad it worked. The plan is the next release will not require these hacks.
> On Aug 26, 2022, at 12:13 PM, byron <lbgpublic at gmail.com> wrote:
>
> It looks like I've (we've) cracked it, at least the petsc stage of what I'm trying to do. To get the configure to work I used the following
>
> python3 ./configure --download-hypre=1 --with-shared-libraries=1 --download-hdf5=1 --download-hdf5-fortran-bindings=0 --with-debugging=no --download-fblaslapack=1 --download-metis=1 --download-ptscotch=1 --download-parmetis=1 --download-superlu_dist=1 --download-mumps=1 --download-strumpack=1 --download-scalapack=1 --download-slepc=1 --with-mpi=1 --with-openmp=1 --with-cxx-dialect=C++11 -with-fortran-bindings=0 --with-sowing=0 --with-64-bit-indices --with-cuda -CUDAOPTFLAGS="" --with-cuda-dialect=cxx11 --prefix=/home/lgoodman/Projects/petscExamples/main-build-CUDAOPTFLAGS-zero-cxx-dialect-unspc-cuda-dial-11/installation
>
> Where -CUDAOPTFLAGS="" was the solutions to getting rid of the duplicate -O3
>
> then I was getting errors about 'redefinition of argument 'std'" so i added
>
> --with-cxx-dialect=C++11
> and
> --with-cuda-dialect=cxx11
>
> and that got rid of those errors. I image there are cleaner / more elegant ways of doing this but I'll settle for this for now.
>
> Thanks a lot for the help guys, much appreciated
>
> Best regards
> Byron
>
> On Fri, Aug 26, 2022 at 4:06 PM Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> wrote:
>
> Yes, PETSc sends down a single -O3 to SuperLU_DIST CMake but internally SuperLU_DIST CMake is adding its own set of nvcc compiler flags to use and these that get added to the one's PETSc passes in (they do not replace them). A little further down in the file it displays a compile line with nvcc that has two sets of -O3 (as well as two sets of other things as well).
>
> I think we changed the main branch PETSc to not pass down the optimization flags to the CMake CUDA to prevent the problem from happening. In other words, we let the package decide its optimization flags instead of trying to tell it what to use.
>
> Barry
>
> The root of the problem is that compiler APIs are a bunch of strings passed on the command line to the compiler without any structure.
>
>
>> On Aug 26, 2022, at 9:47 AM, byron <lbgpublic at gmail.com <mailto:lbgpublic at gmail.com>> wrote:
>>
>> Hi Barry
>>
>> I dont think I see the same thing.
>>
>> When I do a build using the release branch petsc passes the following arguements to superlu_dist (taken from /home/blahblah/Projects/220826-vanilla-petsc-release-branch/petsc/arch-linux-c-opt/externalpackages/git.superlu_dist/superlu_dist.petscconf) which has only one -O3 entry
>>
>> -DCMAKE_INSTALL_PREFIX=/home/blahblah/Projects/220826-vanilla-petsc-release-branch/installation -DCMAKE_INSTALL_NAME_DIR:STRING="/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib" -DCMAKE_INSTALL_LIBDIR:STRING="lib" -DCMAKE_VERBOSE_MAKEFILE=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER="mpicc" -DMPI_C_COMPILER="/usr/bin/mpicc" -DCMAKE_AR=/usr/bin/ar -DCMAKE_RANLIB=/usr/bin/ranlib -DCMAKE_C_FLAGS:STRING="-fPIC -Wno-lto-type-mismatch -fstack-protector -g -O -fopenmp -DDEBUGlevel=0 -DPRNTlevel=0" -DCMAKE_C_FLAGS_DEBUG:STRING="-fPIC -Wno-lto-type-mismatch -fstack-protector -g -O -fopenmp -DDEBUGlevel=0 -DPRNTlevel=0" -DCMAKE_C_FLAGS_RELEASE:STRING="-fPIC -Wno-lto-type-mismatch -fstack-protector -g -O -fopenmp -DDEBUGlevel=0 -DPRNTlevel=0" -DCMAKE_CXX_COMPILER="mpicxx" -DMPI_CXX_COMPILER="/usr/bin/mpicxx" -DCMAKE_CXX_FLAGS:STRING="-Wno-lto-type-mismatch -fstack-protector -g -O -fopenmp -std=c++11 -fPIC -fopenmp -DDEBUGlevel=0 -DPRNTlevel=0" -DCMAKE_CXX_FLAGS_DEBUG:STRING="-Wno-lto-type-mismatch -fstack-protector -g -O -fopenmp -std=c++11 -fPIC -fopenmp -DDEBUGlevel=0 -DPRNTlevel=0" -DCMAKE_CXX_FLAGS_RELEASE:STRING="-Wno-lto-type-mismatch -fstack-protector -g -O -fopenmp -std=c++11 -fPIC -fopenmp -DDEBUGlevel=0 -DPRNTlevel=0" -DCMAKE_Fortran_COMPILER="mpif90" -DMPI_Fortran_COMPILER="/usr/bin/mpif90" -DCMAKE_Fortran_FLAGS:STRING="-fPIC -ffree-line-length-0 -Wno-lto-type-mismatch -g -O -fopenmp" -DCMAKE_Fortran_FLAGS_DEBUG:STRING="-fPIC -ffree-line-length-0 -Wno-lto-type-mismatch -g -O -fopenmp" -DCMAKE_Fortran_FLAGS_RELEASE:STRING="-fPIC -ffree-line-length-0 -Wno-lto-type-mismatch -g -O -fopenmp" -DCMAKE_EXE_LINKER_FLAGS:STRING=" -fopenmp -fopenmp" -DBUILD_SHARED_LIBS:BOOL=ON -DTPL_ENABLE_CUDALIB=TRUE -DTPL_CUDA_LIBRARIES="-lcudart -lcufft -lcublas -lcusparse -lcusolver -lcurand -lcuda" -DCUDA_ARCH_FLAGS="-arch=sm_75" -DCMAKE_CUDA_COMPILER="nvcc" -DCMAKE_CUDA_FLAGS=" -ccbin mpicxx -std=c++14 -Xcompiler -fPIC -O3 -gencode arch=compute_75,code=sm_75 -Wno-deprecated-gpu-targets -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -DDEBUGlevel=0 -DPRNTlevel=0" -DUSE_XSDK_DEFAULTS=YES -DTPL_BLAS_LIBRARIES="-Wl,-rpath,/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -L/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -lflapack -Wl,-rpath,/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -L/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -lfblas -lcudart -lcufft -lcublas -lcusparse -lcusolver -lcurand -lcuda -lm -lstdc++ -ldl -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -lgfortran -lm -lgcc_s -lquadmath -lpthread" -DTPL_LAPACK_LIBRARIES="-Wl,-rpath,/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -L/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -lflapack -Wl,-rpath,/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -L/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -lfblas -lcudart -lcufft -lcublas -lcusparse -lcusolver -lcurand -lcuda -lm -lstdc++ -ldl -Wl,-rpath,/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -lgfortran -lm -lgcc_s -lquadmath -lpthread" -DTPL_PARMETIS_INCLUDE_DIRS="/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/include;/usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/lib" -DTPL_PARMETIS_LIBRARIES="-Wl,-rpath,/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -L/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -lparmetis -Wl,-rpath,/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -L/home/lgoodman/Projects/220826-vanilla-petsc-release-branch/installation/lib -lmetis -lm -lcudart -lcufft -lcublas -lcusparse -lcusolver -lcurand -lcuda" -DXSDK_INDEX_SIZE=64 -DXSDK_ENABLE_Fortran=ON -Denable_tests=0 -Denable_examples=0 -DMPI_C_COMPILE_FLAGS:STRING="" -DMPI_C_INCLUDE_PATH:STRING="" -DMPI_C_HEADER_DIR:STRING="" -DMPI_C_LIBRARIES:STRING=""
>>
>> Or am I looking at the wrong thing?
>>
>> I also tried doing the build downloading petsc from the main branch but that died at the same point and looked to give the same "redefinition of argument 'optimize'" errors
>>
>> Thanks
>> Byron
>>
>>
>>
>> On Thu, Aug 25, 2022 at 4:15 PM Jacob Faibussowitsch <jacob.fai at gmail.com <mailto:jacob.fai at gmail.com>> wrote:
>> > Sadly each one makes different -std=c++11 vs -std=c++14 choices as well.
>>
>> Main should hopefully *also* warn about this, but unless you really really want -std=c++11 or -std=c++14, it is better to leave out this configure flag (--with-cxx-dialect).
>>
>> If --with-cxx-dialect is unspecified (or set to “auto”) configure will pick the most appropriate flag for you, taking your package environment into account when choosing. If you specify the flag configure must assume the user knows something it doesn’t and will blindly take what is given.
>>
>> Best regards,
>>
>> Jacob Faibussowitsch
>> (Jacob Fai - booss - oh - vitch)
>>
>> > On Aug 25, 2022, at 11:05, Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> wrote:
>> >
>> >
>> > Oh yes, my mistake I misinterpreted the error message. It is actually the nvcc compiler complaining about multiple command line arguments related to optimization (which it is really picky about even if the two arguments are identical.) I reformatted some of the configure output to show this
>> >
>> > -ccbin mpicxx -std=c++14 -Xcompiler -fPIC -O3 -gencode arch=compute_75,code=sm_75 -Wno-deprecated-gpu-targets
>> > -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include
>> > -DDEBUGlevel=0 -DPRNTlevel=0
>> >
>> > the next fragment is
>> >
>> > -O3 -DNDEBUG
>> >
>> > --generate-code=arch=compute_75,code=[compute_75,sm_75]
>> >
>> > -Xcompiler=-fPIC -std=c++11 -x cu -rdc=true -c /home/blahblah/Projects/220824-petsc-example-for_forum/petsc/arch-linux-c-opt/externalpackages/git.superlu_dist/SRC/superlu_gpu_utils.cu <http://superlu_gpu_utils.cu/> -o
>> >
>> > Hence the -O3 appears twice, once from the CMAKE argument PETSc passes to superlu_dist
>> >
>> > -DCMAKE_CUDA_FLAGS=" -ccbin mpicxx -std=c++14 -Xcompiler -fPIC -O3 -gencode arch=compute_75,code=sm_75 -Wno-deprecated-gpu-targets -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -DDEBUGlevel=0 -DPRNTlevel=0"
>> >
>> > and then presumably, the superlu_dist cmake process adds its own arguments which overlap.
>> >
>> > If I remember correctly this is fixed in the main branch of PETSc, could you do an identical build with the main branch? If that works we will just need to figure out how to get MOOSE to work with main PETSc branch.
>> >
>> > Barry
>> >
>> > Sadly each one makes different -std=c++11 vs -std=c++14 choices as well.
>> >
>> >
>> > --------------------
>> >
>> > [ 15%] Building CUDA object SRC/CMakeFiles/superlu_dist.dir/superlu_gpu_utils.cu.o
>> > cd /home/blahblah/Projects/220824-petsc-example-for_forum/petsc/arch-linux-c-opt/externalpackages/git.superlu_dist/petsc-build/SRC && /usr/bin/nvcc
>> >
>> > -DSUPERLU_DIST_EXPORTS -Dsuperlu_dist_EXPORTS
>> >
>> > -I/home/blahblah/Projects/220824-petsc-example-for_forum/petsc/arch-linux-c-opt/externalpackages/git.superlu_dist/petsc-build/SRC
>> >
>> > -I/home/blahblah/Projects/220824-petsc-build/installation/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib
>> >
>> > -DUSE_VENDOR_BLAS -ccbin mpicxx -std=c++14 -Xcompiler -fPIC -O3 -gencode arch=compute_75,code=sm_75 -Wno-deprecated-gpu-targets
>> >
>> > -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include
>> >
>> > -DDEBUGlevel=0 -DPRNTlevel=0 -O3 -DNDEBUG
>> >
>> > --generate-code=arch=compute_75,code=[compute_75,sm_75]
>> >
>> > -Xcompiler=-fPIC -std=c++11 -x cu -rdc=true -c /home/blahblah/Projects/220824-petsc-example-for_forum/petsc/arch-linux-c-opt/externalpackages/git.superlu_dist/SRC/superlu_gpu_utils.cu <http://superlu_gpu_utils.cu/> -o
>> >
>> > CMakeFiles/superlu_dist.dir/superlu_gpu_utils.cu <http://superlu_gpu_utils.cu/>
>> >
>> >
>> >
>> >> On Aug 25, 2022, at 9:38 AM, byron <lbgpublic at gmail.com <mailto:lbgpublic at gmail.com>> wrote:
>> >>
>> >> Hi Barry
>> >>
>> >> There doesn't appear to be any reference to 'optimize' in the only copy of superlu_gpu_utils.cu <http://superlu_gpu_utils.cu/> I could find, I've attached a copy.
>> >>
>> >> Thanks
>> >>
>> >>
>> >>
>> >> On Thu, Aug 25, 2022 at 1:44 PM Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> wrote:
>> >>
>> >> nvcc fatal : redefinition of argument 'optimize'
>> >> make[2]: *** [SRC/CMakeFiles/superlu_dist.dir/build.make:499: SRC/CMakeFiles/superlu_dist.dir/superlu_gpu_utils.cu.o] Error 1
>> >> make[2]: *** Waiting for unfinished jobs....
>> >> nvcc fatal : redefinition of argument 'optimize'
>> >> make[2]: *** [SRC/CMakeFiles/superlu_dist-static.dir/build.make:499: SRC/CMakeFiles/superlu_dist-static.dir/superlu_gpu_utils.cu.o] Error 1
>> >> make[2]: *** Waiting for unfinished jobs....
>> >>
>> >> It seems that nvcc is unhappy with something in superlu_gpu_utils.cu <http://superlu_gpu_utils.cu/> Could you check that file for any "redefinition of optimize"? Unfortunately the nvcc compiler isn't kind enough to print the line number of the redefinition or that information is lost somehow in the build process.
>> >>
>> >> Barry
>> >>
>> >>> On Aug 25, 2022, at 6:50 AM, byron <lbgpublic at gmail.com <mailto:lbgpublic at gmail.com>> wrote:
>> >>>
>> >>> Hi All
>> >>>
>> >>> I am having trouble getting petsc to build with cuda / superlu-dist enabled. I have been trying to build it as part of another software tool, moose, hence the choice of options being passed to configure
>> >>>
>> >>> python3 ./configure --download-hypre=1 \
>> >>> --with-shared-libraries=1 \
>> >>> --download-hdf5=1 \
>> >>> --download-hdf5-fortran-bindings=0 \
>> >>> --with-debugging=no \
>> >>> --download-fblaslapack=1 \
>> >>> --download-metis=1 \
>> >>> --download-ptscotch=1 \
>> >>> --download-parmetis=1 \
>> >>> --download-superlu_dist=1 \
>> >>> --download-mumps=1 \
>> >>> --download-strumpack=1 \
>> >>> --download-scalapack=1 \
>> >>> --download-slepc=1 \
>> >>> --with-mpi=1 \
>> >>> --with-openmp=1 \
>> >>> --with-cxx-dialect=C++11 \
>> >>> --with-fortran-bindings=0 \
>> >>> --with-sowing=0 \
>> >>> --with-64-bit-indices \
>> >>> --with-cuda \
>> >>> --prefix=/home/blah/blah
>> >>>
>> >>> it fails with
>> >>>
>> >>> ============================================================================================= Installing PTScotch; this may take several minutes ============================================================================================= ============================================================================================= Trying to download git://https://github.com/xiaoyeli/superlu_dist <https://github.com/xiaoyeli/superlu_dist> for SUPERLU_DIST ============================================================================================= ============================================================================================= Configuring SUPERLU_DIST with cmake; this may take several minutes ============================================================================================= ============================================================================================= Compiling and installing SUPERLU_DIST; this may take several minutes ============================================================================================= *******************************************************************************
>> >>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
>> >>> -------------------------------------------------------------------------------
>> >>> Error running make on SUPERLU_DIST
>> >>> *******************************************************************************
>> >>>
>> >>> I've attached the configure.log.
>> >>>
>> >>> I've tried a few different things but nothing that resulted in a successfull build. The most promising was I tried to build superlu_dist separately with the configure options that petsc passes it and then kept trying the build over and over droping out different configure options until I got it to work. In that case removing a "-std=c++14" entry appeared to fix the problem but then when I made the same change in how petsc builds superlu-dist the make failed on superlu-dist with a different error. I get the feeling I'm dealing with symptoms of the problem rather than the cause.
>> >>>
>> >>> Thanks
>> >>> Byron
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> <configure.log>
>> >>
>> >> <superlu_gpu_utils.cu <http://superlu_gpu_utils.cu/>>
>> >
>>
>
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