[petsc-users] error with xlib
Mark Adams
mfadams at lbl.gov
Mon Apr 13 14:02:47 CDT 2020
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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