> clang: error: unsupported option '-fopenmp' If you need openmp build on OSX - perhaps its best to install with brew/gcc - that actually accepts -fopenmp option?
Or - install all externalpackages - that don't need openmp without openmp? step-1 ./configure --download-hdf5 PETSC_ARCH=arch-prebuid --prefix=$HOME/packages step-2 ./configure --with-hdf5-dir=$HOME/packages --with-openmp=1 Satish On Mon, 13 Apr 2020, Mark Adams wrote: > Ah, you have zlib=1. Now hdf5 fails. > > On Mon, Apr 13, 2020 at 1:19 PM Satish Balay <ba...@mcs.anl.gov> wrote: > > > And here is a p4est build. > > > > Satish > > -------- > > > > balay@kpro petsc % ./configure --with-mpi-dir=$HOME/soft/mpich-3.3.2 > > --with-zlib=1 --download-p4est > > > > =============================================================================== > > Configuring PETSc to compile on your system > > > > > > =============================================================================== > > =============================================================================== > > > > ***** WARNING: You have an older version of Gnu make, it will > > work, > > but may not support all the parallel testing > > options. You can install the > > latest Gnu make with your > > package manager, such as brew or macports, or use > > the > > --download-make option to get the latest Gnu make ***** > > > > > > > > =============================================================================== > > > > ====== > > ========================================================================= > > > > Trying to download git:// > > https://bitbucket.org/petsc/pkg-sowing.git for SOWING > > > > =============================================================================== > > > > > > > > =============================================================================== > > > > Running configure on SOWING; this may take several minutes > > > > > > =============================================================================== > > > > =========== > > ==================================================================== > > > > Running make on SOWING; this may take several minutes > > > > > > > > =============================================================================== > > > > > > > > =============================================================================== > > > > Running make install on SOWING; this may take several minutes > > > > > > > > =============================================================================== > > > > ================ > > =============================================================== > > > > Trying to download git://https://github.com/tisaac/p4est for P4EST > > > > > > =============================================================================== > > > > > > > > =============================================================================== > > > > Trying to bootstrap p4est using autotools; this may take > > several minutes > > > > =============================================================================== > > > > ===================== > > ========================================================== > > > > Running configure on P4EST; this may take several minutes > > > > > > > > =============================================================================== > > > > > > > > =============================================================================== > > > > Running make on P4EST; this may take several minutes > > > > > > =============================================================================== > > > > ========================== > > ===================================================== > > > > Running make install on P4EST; this may take several minutes > > > > > > =============================================================================== > > > > Compilers: > > > > > > C Compiler: /Users/balay/soft/mpich-3.3.2/bin/mpicc -Wall > > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 > > Version: Apple clang version 11.0.0 (clang-1100.0.33.8) > > C++ Compiler: /Users/balay/soft/mpich-3.3.2/bin/mpicxx -Wall > > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fno-stack-check -fvisibility=hidden -g > > Version: Apple clang version 11.0.0 (clang-1100.0.33.8) > > Fortran Compiler: /Users/balay/soft/mpich-3.3.2/bin/mpif90 -Wall > > -ffree-line-length-0 -Wno-unused-dummy-argument -g > > Version: GNU Fortran (Homebrew GCC 9.3.0) 9.3.0 > > Linkers: > > Shared linker: /Users/balay/soft/mpich-3.3.2/bin/mpicc -dynamiclib > > -single_module -undefined dynamic_lookup -multiply_defined suppress -Wall > > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 > > Dynamic linker: /Users/balay/soft/mpich-3.3.2/bin/mpicc -dynamiclib > > -single_module -undefined dynamic_lookup -multiply_defined suppress -Wall > > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 > > Libraries linked against: -lc++ -ldl > > make: > > Version: 3.81 > > /usr/bin/make > > BlasLapack: > > Library: -llapack -lblas > > Unknown if this uses OpenMP (try export OMP_NUM_THREADS=<1-4> > > yourprogram -log_view) > > uses 4 byte integers > > MPI: > > Version: 3 > > Includes: -I/Users/balay/soft/mpich-3.3.2/include > > Mpiexec: /Users/balay/soft/mpich-3.3.2/bin/mpiexec > > MPICH_NUMVERSION: 30302300 > > pthread: > > X: > > Includes: -I/opt/X11/include > > Library: -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -lX11 > > zlib: > > Library: -lz > > cmake: > > Version: 3.16.5 > > /usr/local/bin/cmake > > regex: > > p4est: > > Includes: -I/Users/balay/petsc/arch-darwin-c-debug/include > > Library: -Wl,-rpath,/Users/balay/petsc/arch-darwin-c-debug/lib > > -L/Users/balay/petsc/arch-darwin-c-debug/lib -lp4est -lsc > > sowing: > > Version: 1.1.25 > > /Users/balay/petsc/arch-darwin-c-debug/bin/bfort > > Language used to compile PETSc: C > > PETSc: > > PETSC_ARCH: arch-darwin-c-debug > > PETSC_DIR: /Users/balay/petsc > > Scalar type: real > > Precision: double > > Integer size: 4 bytes > > shared libraries: enabled > > Memory alignment from malloc(): 16 bytes > > > > xxx=========================================================================xxx > > Configure stage complete. Now build PETSc libraries with: > > make PETSC_DIR=/Users/balay/petsc PETSC_ARCH=arch-darwin-c-debug all > > > > xxx=========================================================================xxx > > balay@kpro petsc % > > > > > > On Mon, 13 Apr 2020, Satish Balay via petsc-users wrote: > > > > > you haven't sent any logs for this issue.. > > > [../arch-macosx-gnu-O-omp.py script or configure.log with the failure] > > > > > > Satish > > > > > > ------- > > > ipro:petsc balay$ ./configure --with-fortran-bindings=0 --with-mpi=0 > > --with-zlib=1 > > > > > =============================================================================== > > > Configuring PETSc to compile on your system > > > > > > > =============================================================================== > > > > > =============================================================================== > > > > ***** WARNING: You have an older version of Gnu make, it will > > work, > > but may not support all the parallel testing > > options. You can install the > > latest Gnu make with your > > package manager, such as brew or macports, or use > > the > > --download-make option to get the latest Gnu make ***** > > > > > > > > =============================================================================== > > > > Comp > > il > > > ers: > > > > > > > C Compiler: gcc -Wall -Wwrite-strings -Wno-strict-aliasing > > -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments > > -fvisibility=hidden -g3 > > > Version: Apple clang version 11.0.3 (clang-1103.0.32.29) > > > C++ Compiler: g++ -Wall -Wwrite-strings -Wno-strict-aliasing > > -Wno-unknown-pragmas -fstack-protector -fno-stack-check -fvisibility=hidden > > -g -std=c++14 > > > Version: Apple clang version 11.0.3 (clang-1103.0.32.29) > > > Fortran Compiler: gfortran -Wall -ffree-line-length-0 > > -Wno-unused-dummy-argument -g > > > Version: GNU Fortran (Homebrew GCC 9.3.0) 9.3.0 > > > Linkers: > > > Shared linker: gcc -dynamiclib -single_module -undefined > > dynamic_lookup -multiply_defined suppress -Wall -Wwrite-strings > > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 > > > Dynamic linker: gcc -dynamiclib -single_module -undefined > > dynamic_lookup -multiply_defined suppress -Wall -Wwrite-strings > > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 > > > Libraries linked against: -lc++ -ldl > > > make: > > > Version: 3.81 > > > /usr/bin/make > > > BlasLapack: > > > Library: -llapack -lblas > > > Unknown if this uses OpenMP (try export OMP_NUM_THREADS=<1-4> > > yourprogram -log_view) > > > uses 4 byte integers > > > pthread: > > > zlib: > > > Library: -lz > > > cmake: > > > Version: 3.16.5 > > > /usr/local/bin/cmake > > > X: > > > Includes: -I/opt/X11/include > > > Library: -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -lX11 > > > regex: > > > Language used to compile PETSc: C > > > PETSc: > > > PETSC_ARCH: arch-darwin-c-debug > > > PETSC_DIR: /Users/balay/petsc > > > Scalar type: real > > > Precision: double > > > Integer size: 4 bytes > > > shared libraries: enabled > > > Memory alignment from malloc(): 16 bytes > > > > > xxx=========================================================================xxx > > > Configure stage complete. Now build PETSc libraries with: > > > make PETSC_DIR=/Users/balay/petsc PETSC_ARCH=arch-darwin-c-debug all > > > > > xxx=========================================================================xxx > > > ipro:petsc balay$ > > > > > > > > > > > > > > > > On Mon, 13 Apr 2020, Mark Adams wrote: > > > > > > > On Mon, Apr 13, 2020 at 12:48 PM Satish Balay <ba...@mcs.anl.gov> > > wrote: > > > > > > > > > This is very funky > > > > > > > > > > >>> > > > > > Configure Options: --configModules=PETSc.Configure > > > > > --optionsModule=config.compilerOptions > > > > > --with-mpi-dir=/usr/local/Cellar/mpich/3.3.2 COPTFLAGS="-O2 -g > > > > > -Xpreprocessor -fopenmp -I"$(brew --prefix libomp)/include" -L"$(brew > > > > > --prefix libomp)/lib -lomp"" CXXOPTFLAGS="-O2 -g -Xpreprocessor > > -fopenmp > > > > > -I"$(brew --prefix libomp)/include" -L"$(brew --prefix libomp)/lib > > -lomp"" > > > > > FOPTFLAGS="-O2 -g -Xpreprocessor -fopenmp -I"$(brew --prefix > > > > > libomp)/include" -L"$(brew --prefix libomp)/lib -lomp"" > > > > > --download-parmetis=1 --download-metis=1 --download-hypre=1 > > > > > --download-triangle=1 --download-p4est=1 --download-zlib --with-x=0 > > > > > --download-ctetgen --with-debugging=0 --download-hdf5=1 > > > > > PETSC_ARCH=arch-macosx-gnu-O-omp --with-openmp=1 --with-log=0 > > > > > --with-threadsafety --download-chaco > > > > > <<< > > > > > > > > > > -I"$(brew --prefix libomp)/include" type options to configure > > doesn't make > > > > > sense. You are using bash syntax here - and expecting configure to > > resolve > > > > > it. Its best for your bash shell to evaluate this before passing > > this info > > > > > to configure > > > > > > > > > > Also --download-zlib isn't needed on OSX > > > > > > > > > > > > > Hum, I get: > > > > > > > > 12:52 mark/feature-xgc-interface-rebase *= ~/Codes/petsc$ > > > > ../arch-macosx-gnu-O-omp.py > > > > > > =============================================================================== > > > > Configuring PETSc to compile on your system > > > > > > > > > > =============================================================================== > > > > TESTING: configureExternalPackagesDir from > > > > config.framework(config/BuildSystem/config/framework.py:911) > > > > > > > > > > > > > > ******************************************************************************* > > > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > > for > > > > details): > > > > > > ------------------------------------------------------------------------------- > > > > Package p4est requested but dependency zlib not requested. Perhaps you > > want > > > > --download-zlib > > > > > > ******************************************************************************* > > > > > > > > > > > > > > > > > > > > > > Satish > > > > > > > > > > > > > > > On Mon, 13 Apr 2020, Mark Adams wrote: > > > > > > > > > > > Now that I look at it, I see: > > > > > > > > > > > > CFLAGS="-fstack-protector -fno-stack-check -Qunused-arguments -O2 > > -g > > > > > > -Xpreprocessor -fopenmp -I"$(brew --prefix libomp)/include" > > -L"$(brew > > > > > > --prefix libomp)/lib -lomp"" > > > > > > prefix="/Users/markadams/Codes/petsc/arch-macosx-gnu-O-omp" > > > > > > > > > > > > Note the two ". That does not look right. I use > > > > > > > > > > > > 'COPTFLAGS=-O2 -g -Xpreprocessor -fopenmp -I"$(brew --prefix > > > > > > libomp)/include" -L"$(brew --prefix libomp)/lib -lomp" ', > > > > > > > > > > > > I know how to do stuff like: > > > > > > > > > > > > '--with-blaslapack-lib=-L' + os.environ['OLCF_NETLIB_LAPACK_ROOT'] > > + > > > > > > '/lib64 -lblas -llapack' > > > > > > > > > > > > Is there like and os.exec that I could use like this for my FLAGS? > > > > > > > > > > > > > > > > > > > > > > > > On Mon, Apr 13, 2020 at 11:46 AM Matthew Knepley < > > knep...@gmail.com> > > > > > wrote: > > > > > > > > > > > > > On Mon, Apr 13, 2020 at 11:34 AM Mark Adams <mfad...@lbl.gov> > > wrote: > > > > > > > > > > > > > >> I get this error configuring zlib, osx, with OpenMP. > > > > > > >> Any ideas? > > > > > > >> > > > > > > > > > > > > > > This failed without output > > > > > > > > > > > > > > Executing: cd > > > > > > > > > > > > > > /Users/markadams/Codes/petsc/arch-macosx-gnu-O-omp/externalpackages/zlib-1.2.11 > > > > > > > && CC="/usr/local/Cellar/mpich/3.3.2/bin/mpicc" > > > > > CFLAGS="-fstack-protector > > > > > > > -fno-stack-check -Qunused-arguments -O2 -g -Xpreprocessor > > -fopenmp > > > > > > > -I"$(brew --prefix libomp)/include" -L"$(brew --prefix > > libomp)/lib > > > > > -lomp"" > > > > > > > prefix="/Users/markadams/Codes/petsc/arch-macosx-gnu-O-omp" > > > > > ./configure && > > > > > > > /usr/bin/make -j7 -l12.0 && /usr/bin/make install > > > > > > > > > > > > > > So execute each step in turn and see what fails. > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > Matt > > > > > > > > > > > > > > > > > > > > >> Thanks, > > > > > > >> Mark > > > > > > >> > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > What most experimenters take for granted before they begin their > > > > > > > experiments is infinitely more interesting than any results to > > which > > > > > their > > > > > > > experiments lead. > > > > > > > -- Norbert Wiener > > > > > > > > > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > > <http://www.cse.buffalo.edu/~knepley/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
