[petsc-users] unable to build petsc with cuda / superlu-dist enabled
byron
lbgpublic at gmail.com
Fri Aug 26 08:47:06 CDT 2022
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>
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> 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 -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 -o
> >
> > CMakeFiles/superlu_dist.dir/superlu_gpu_utils.cu
> >
> >
> >
> >> On Aug 25, 2022, at 9:38 AM, byron <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 I could find, I've attached a copy.
> >>
> >> Thanks
> >>
> >>
> >>
> >> On Thu, Aug 25, 2022 at 1:44 PM Barry Smith <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
> 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> 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 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>
> >
>
>
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