[petsc-users] error with xlib
Satish Balay
balay at mcs.anl.gov
Wed Apr 15 17:37:04 CDT 2020
> 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 <balay at mcs.anl.gov> wrote:
>
> > And here is a p4est build.
> >
> > Satish
> > --------
> >
> > balay at 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 at 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 <balay at 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 <
> > knepley at gmail.com>
> > > > > wrote:
> > > > > >
> > > > > > > On Mon, Apr 13, 2020 at 11:34 AM Mark Adams <mfadams at 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/>
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> >
>
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